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\"doc\"","evidence_level":"declared","evidence":"dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl#METADATA/Requires-Dist"},{"from_id":"wheel:staged-wheel/dnatco/bin/fr3d:scipy:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl","to_id":"external:staged-wheel/dnatco/bin/fr3d:sphinx:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl%23wheel-metadata/sphinx","edge_type":"requires","scope":"external","marker":"sphinx<=7.3.7,>=5.0.0; extra == \"doc\"","evidence_level":"declared","evidence":"dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl#METADATA/Requires-Dist"},{"from_id":"wheel:staged-wheel/dnatco/bin/fr3d:scipy:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl","to_id":"external:staged-wheel/dnatco/bin/fr3d:threadpoolctl:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl%23wheel-metadata/threadpoolctl","edge_type":"requires","scope":"external","marker":"threadpoolctl; extra == \"test\"","evidence_level":"declared","evidence":"dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl#METADATA/Requires-Dist"},{"from_id":"wheel:staged-wheel/dnatco/bin/fr3d:scipy:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl","to_id":"external:staged-wheel/dnatco/bin/fr3d:types-psutil:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl%23wheel-metadata/types-psutil","edge_type":"requires","scope":"external","marker":"types-psutil; extra == \"dev\"","evidence_level":"declared","evidence":"dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl#METADATA/Requires-Dist"},{"from_id":"wheel:staged-wheel/dnatco/bin/fr3d:scipy:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl","to_id":"external:staged-wheel/dnatco/bin/fr3d:typing-extensions:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl%23wheel-metadata/typing-extensions","edge_type":"requires","scope":"external","marker":"typing_extensions; extra == \"dev\"","evidence_level":"declared","evidence":"dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl#METADATA/Requires-Dist"},{"from_id":"wheel:staged-wheel/dnatco/bin/fr3d:scipy:dnatco/bin/fr3d/pyodide/scipy-1.14.1-cp313-cp313-pyemscripten_2025_0_wasm32.whl","to_id":"wheel:staged-wheel/dnatco/bin/fr3d:numpy:dnatco/bin/fr3d/pyodide/numpy-2.2.5-cp313-cp313-pyemscripten_2025_0_wasm32.whl","edge_type":"requires","scope":"external","marker":"numpy","evidence_level":"declared","evidence":"dnatco/bin/fr3d/pyodide/pyodide-lock.json#packages/scipy/depends"}],"checks":[{"component_id":"component:core:arcimboldo aleph","env":"core","topic":"runtime","status":"verified","detail":"unitCellTools fits sklearn KernelDensity; ALEPH frobenius constructs AgglomerativeClustering. SciPy kmeans also exists outside framework-target imports. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/arcimboldo/unitCellTools.py:14,713,761; lib/python3.11/site-packages/arcimboldo/ALEPH/aleph/core/ALEPH.py:101,6934; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:buccaneer nn","env":"core","topic":"external","status":"unresolved","detail":"Inspected native symbols establish the local mechanism; complete external/transitive dependency requirements and any training framework installation are unverified.","evidence":"bin/cbuccaneerNN: symbol SelectNN::predict @0x437e80; nnmodel::nnmodel @0x45e040; k2c_recurrent_layers::k2c_lstm @0x4d5a70"},{"component_id":"component:core:buccaneer nn","env":"core","topic":"models","status":"unresolved","detail":"The named CSV and matching nnselect array labels ship; exact loader/path resolution and numerical equivalence to the compiled model remain unverified.","evidence":"bin/cbuccaneerNN: string /buccaneer_nn_weights.csv @0xe65d9; examples/unix/runnable/cbuccaneerNN.exam:12-22; lib/data/buccaneer_nn_weights.csv:1-3,36,1061,525350,787495,788008,919081,984618,984875,1017644,1034029,1034158,1042351,1046448,1048497,1077170"},{"component_id":"component:core:buccaneer nn","env":"core","topic":"provenance","status":"unresolved","detail":"The primary paper describes Keras 2.3.1 training and Keras2c conversion to C++; exact shipped weights, conversion versions and build receipt remain unknown.","evidence":"bin/cbuccaneerNN: symbol SelectNN::predict @0x437e80; nnmodel::nnmodel @0x45e040; k2c_recurrent_layers::k2c_lstm @0x4d5a70; https://journals.iucr.org/d/issues/2023/04/00/di5061/ sections 2.3.2-2.4; DOI 10.1107/S205979832300181X"},{"component_id":"component:core:buccaneer nn","env":"core","topic":"runtime","status":"verified","detail":"The nn-select example and native SelectNN/nnmodel/k2c LSTM symbols establish a shipped native NN path; runtime operation and dependency resolution were not tested.","evidence":"bin/cbuccaneerNN: symbol SelectNN::predict @0x437e80; nnmodel::nnmodel @0x45e040; k2c_recurrent_layers::k2c_lstm @0x4d5a70; examples/unix/runnable/cbuccaneerNN.exam:12-22"},{"component_id":"component:core:ccp4 cloud structure prediction","env":"core","topic":"runtime","status":"verified","detail":"Shipped CCP4-facing programs outside site-packages launch configured AlphaFold/ColabFold/OpenFold backend scripts or gapTrick via apptainer. These are separate source consumers from ABCFold. Backend frameworks, containers, models, GPU capability and successful operation are not established by shipped launcher source. Source location is in the base bundle; actual launcher/backend interpreter is unresolved.","evidence":"share/jscofe/pycofe/tasks/structureprediction.py:209,253,462,468,481,484,519; share/jscofe/pycofe/tasks/gaptrick.py:165,197,217,220,221,238"},{"component_id":"component:core:ccp4fitligand","env":"core","topic":"runtime","status":"verified","detail":"Outside site-packages: main program imports lf_fitligand, which imports lf_energy and lf_zscore; energy module imports torch and uses LBFGS/Adam/SGD with backward for coordinate optimisation. This does not prove a trained neural model. lf_blobs fits MiniBatchKMeans; lf_zscore applies PolynomialFeatures to shipped scoring coefficients. Source is shipped, but core torch installation and successful launcher/runtime are unresolved. Source location is in the base bundle; actual launcher/backend interpreter is unresolved.","evidence":"share/jscofe/pycofe/apps/ccp4fitligand/ccp4.fitligand.py:27; share/jscofe/pycofe/apps/ccp4fitligand/lf_fitligand.py:28,29; share/jscofe/pycofe/apps/ccp4fitligand/lf_energy.py:949,958,969,971,1080,1093; share/jscofe/pycofe/apps/ccp4fitligand/lf_blobs.py:22,278,279; share/jscofe/pycofe/apps/ccp4fitligand/lf_zscore.py:9,1266,1267"},{"component_id":"component:core:cctbx kramers kronig","env":"core","topic":"runtime","status":"verified","detail":"Production-path library code uses torch FFT and differentiable interpolation; optimise script has run_example_opt and SGD. This is additional PyTorch consumer code, not proof of a trained ML component or installed core torch. cctbx/run_tests explicitly guards torch tests. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/cctbx/dispersion/kramers_kronig/kramers_kronig.py:6,29,42; lib/python3.11/site-packages/cctbx/dispersion/kramers_kronig/kramers_kronig_helper.py:8,33; lib/python3.11/site-packages/cctbx/dispersion/kramers_kronig/kramers_kronig_optimize.py:6,130; lib/python3.11/site-packages/cctbx/run_tests.py:164"},{"component_id":"component:core:coot chemical feature clustering","env":"core","topic":"runtime","status":"verified","detail":"Multiple methods fit sklearn GaussianMixture; this is scientific application support, not sklearn internals. UI/default reach not established. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/coot/coot_chemical_feature_clusters.py:26,105,128,292,665; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:crank2 map segmentation","env":"core","topic":"runtime","status":"unresolved","detail":"dm and dmfull describe map_segmentation as deep learning and dmfull references GetProcess/AddProcess segmentmap. Expected processes/segmentmap.py is not present at the investigated path. Do not count as shipped working inference without tracing the missing implementation.","evidence":"lib/python3.11/site-packages/ccp4i2/pipelines/crank2/crank2/processes/dm.py; map_segmentation/segmentmap references; lib/python3.11/site-packages/ccp4i2/pipelines/crank2/crank2/processes/dmfull.py; map_segmentation/segmentmap references"},{"component_id":"component:core:fmslib","env":"core","topic":"external","status":"verified","detail":"torch is an external conditional fallback, with training/conversion engines recorded as external provenance only; these source imports establish neither installed packages nor successful operation.","evidence":"lib/python3.11/site-packages/fmslib/nn_predict.py:23-34; lib/python3.11/site-packages/fmslib/nn_train.py:11-15,69-143; lib/python3.11/site-packages/fmslib/export2onnx.py:25-33,42-58,83; lib/python3.11/site-packages/fmslib/import2tf.py:14-22,46-48,77-102"},{"component_id":"component:core:fmslib","env":"core","topic":"models","status":"unresolved","detail":"Native emmodel/xraymodel symbols suggest embedded models; exact arrays and equivalence to .dat checkpoints are unverified. Fallback selects EM/XRAY checkpoints; xtst_100.dat loader remains unresolved.","evidence":"lib/python3.11/site-packages/fmslib/nn_predict.py:13-36,57-79,115-125; lib/python3.11/site-packages/fmslib/fms_nnmodel.so: symbols predict @0x1b99; emmodel @0x1d71; xraymodel @0x2249; k2c_dense @0x4685; lib/python3.11/site-packages/fmslib/nn_predict.py:57-75; lib/python3.11/site-packages/fmslib/data/xtst_100.dat: strings dense1.weight @0xb0; FloatStorage @0xf9"},{"component_id":"component:core:fmslib","env":"core","topic":"provenance","status":"unresolved","detail":"Shipped scripts train PyTorch state dictionaries, export ONNX, convert to Keras and print keras2c commands. Exact generated source, conversion versions and .so build receipt are unknown.","evidence":"lib/python3.11/site-packages/fmslib/nn_train.py:11-15,69-143; lib/python3.11/site-packages/fmslib/export2onnx.py:25-33,42-58,83; lib/python3.11/site-packages/fmslib/import2tf.py:14-22,46-48,77-102"},{"component_id":"component:core:fmslib","env":"core","topic":"runtime","status":"verified","detail":"nn_predict tries ctypes.CDLL first and calls native predict with an EM/XRAY flag; only initial CDLL failure imports torch. Native exports ship; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/fmslib/nn_predict.py:13-36,57-79,115-125; lib/python3.11/site-packages/fmslib/fms_nnmodel.so: symbols predict @0x1b99; emmodel @0x1d71; xraymodel @0x2249; k2c_dense @0x4685"},{"component_id":"component:core:libtbx covariance helpers","env":"core","topic":"runtime","status":"verified","detail":"Functions fit sklearn EmpiricalCovariance / MinCovDet. Library presence and tests are proven; independent CCP4 command reach is unresolved. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/libtbx/math_utils.py:280,283,285; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:mrparse","env":"core","topic":"runtime","status":"verified","detail":"--do_classify path constructs MrClassifier: CCPred launches configurable DeepCoil executable via run_cmd; TMPred launches [deeptmhmm_exe, run, DTU/DeepTMHMM, --fasta, seqin] via pyjob.cexec; JPred supplies online secondary-structure prediction (backend ML identity not independently established here). Separate mr_esmatlas.make_esm_prediction POSTs a sequence to ESM Atlas foldSequence and is called by its __main__ helper. Ordinary MrParse database search retrieves predicted structures and is not itself inference. No external executable/service availability, framework versions, or default successful operation established. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/mrparse/mr_analyse.py:15,100,101; lib/python3.11/site-packages/mrparse/mr_classify.py:10,11,12,70,71,81,82,91,92; lib/python3.11/site-packages/mrparse/mr_deepcoil.py:26,64,75,78; lib/python3.11/site-packages/mrparse/mr_deeptmhmm.py:7,63,64,65; lib/python3.11/site-packages/mrparse/mr_args.py:27,39,41; lib/python3.11/site-packages/mrparse/mr_esmatlas.py:207,238,239,289; lib/python3.11/site-packages/mrparse/mr_jpred.py:128,129"},{"component_id":"component:core:phasertng matthews ml","env":"core","topic":"external","status":"unresolved","detail":"The inspected glue imports NumPy and calls Phasertng native APIs; it does not import TensorFlow. Complete external/transitive runtime closure remains unverified.","evidence":"lib/python3.11/site-packages/phasertng/tensorflow/setup_mle_matthews.py:1-2,12-25,27-39; lib/python3.11/lib-dynload/phasertng_ext.so: symbols phasertng::Phasertng::mle_matthews_load_weights @0x7bbba0; mle_matthews_inference @0x7bf1f0; mle_matthews_predict_probabilities @0x7bede0"},{"component_id":"component:core:phasertng matthews ml","env":"core","topic":"models","status":"verified","detail":"Ten shipped .bin files match architecture filenames and native filename strings; sizes fit shape products times four. Encoding and exact numerical equivalence remain unknown.","evidence":"lib/python3.11/lib-dynload/phasertng_ext.so: weight filename strings @0xe14403-0xe144c7; lib/python3.11/site-packages/phasertng/tensorflow/mle_export/architecture.json:3-74,106-177,209-280,330-379,402-451"},{"component_id":"component:core:phasertng matthews ml","env":"core","topic":"provenance","status":"unresolved","detail":"Keras layer metadata ships, but training framework/version, dataset, exporter and exact build receipt are unknown; the tensorflow directory/comment does not establish that runtime.","evidence":"lib/python3.11/site-packages/phasertng/tensorflow/setup_mle_matthews.py:1-2,12-25,27-39; lib/python3.11/site-packages/phasertng/tensorflow/mle_export/architecture.json:3-74,106-177,209-280,330-379,402-451"},{"component_id":"component:core:phasertng matthews ml","env":"core","topic":"runtime","status":"verified","detail":"MLEMatthews passes package weights to the native API, then supplies 13 image paths to predict_probabilities; matching Phasertng exports ship. Runtime operation was not tested.","evidence":"lib/python3.11/site-packages/phasertng/tensorflow/setup_mle_matthews.py:1-2,12-25,27-39; lib/python3.11/lib-dynload/phasertng_ext.so: symbols phasertng::Phasertng::mle_matthews_load_weights @0x7bbba0; mle_matthews_inference @0x7bf1f0; mle_matthews_predict_probabilities @0x7bede0"},{"component_id":"component:core:rdkit contributed np scorer","env":"core","topic":"models","status":"verified","detail":"Shipped NP score table has a static default loader and fragment-scoring routine. This is not asserted to be a neural network; application-level use, training provenance and successful deserialization remain unverified.","evidence":"share/RDKit/Contrib/NP_Score/npscorer.py:27-33,36-74"},{"component_id":"component:core:slicendice","env":"core","topic":"models","status":"verified","detail":"Dice EM additionally ships a fitted StandardScaler and SGDClassifier pair. Static loader source transforms scores, calls decision_function and expit, then thresholds the result. Headers were inspected without deserialization; runtime compatibility and scientific output were not tested.","evidence":"lib/python3.11/site-packages/slicendice/slice/clustering_tasks.py:15,73,89,95,111; lib/python3.11/site-packages/slicendice/slice/cluster.py:10,15,16,18; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:slicendice","env":"core","topic":"provenance","status":"unresolved","detail":"The shipped classifier/scaler hashes are pinned; training data, training framework version and fitting receipt have not been established.","evidence":"lib/python3.11/site-packages/slicendice/slice/clustering_tasks.py:15,73,89,95,111; lib/python3.11/site-packages/slicendice/slice/cluster.py:10,15,16,18; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:slicendice","env":"core","topic":"runtime","status":"verified","detail":"The default Birch path fits scikit-learn; alternate clustering algorithms can be selected. Runtime operation is untested.","evidence":"lib/python3.11/site-packages/slicendice/slice/clustering_tasks.py:15,73,89,95,111; lib/python3.11/site-packages/slicendice/slice/cluster.py:10,15,16,18; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:struvolpy","env":"core","topic":"runtime","status":"verified","detail":"Structure builds sklearn BallTree; counts as framework dependency, not necessarily learned inference. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/struvolpy/Structure.py:397,408; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"component:core:xfel","env":"core","topic":"runtime","status":"verified","detail":"Reflection filter fits IsolationForest; panel_fitting fits robust/empirical covariance. aux_cosym DBSCAN is a plotting/diagnostic method, not independently proven production ML. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/xfel/merging/application/filter/reflection_filter.py:438,443,451; lib/python3.11/site-packages/xfel/metrology/panel_fitting.py:8,35,37; lib/python3.11/site-packages/xfel/merging/application/modify/aux_cosym.py:90,91; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:checkmysequence","env":"core","topic":"runtime","status":"verified","detail":"Constructs fmslib.sequence_utils.model2sequence; shares FMSLib neural engine, not separate weights proven here. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/checkmysequence/__main__.py:46,242; lib/python3.11/site-packages/fmslib/sequence_utils.py:34,90,487; lib/python3.11/site-packages/checkmysequence-1.5.2-py3.11.egg-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:core:conkit","env":"core","topic":"models","status":"verified","detail":"ConKit ships trained_classifier.joblib and standard_scaler.joblib; loader passes them to joblib.load and ModelValidation transforms features and calls predict_proba. Exact estimator/training lineage and runtime compatibility were not established.","evidence":"lib/python3.11/site-packages/conkit/misc/__init__.py:36,40-41,50-57; lib/python3.11/site-packages/conkit/plot/modelvalidation.py:51,142,314-315"},{"component_id":"pydist:core:conkit","env":"core","topic":"runtime","status":"verified","detail":"get_contact_density imports sklearn.neighbors and fits KernelDensity; positive classical-ML relationship. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/conkit/core/contactmap.py:621,633; lib/python3.11/site-packages/conkit-0.13.2-py3.11.egg-info/top_level.txt; distribution/package ownership; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:dials","env":"core","topic":"runtime","status":"verified","detail":"Correlation analysis fits OPTICS and optimises using Optuna; cosym uses nearest neighbours and PCA. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/dials/algorithms/correlation/analysis.py:11,14,15,424,425; lib/python3.11/site-packages/dials/algorithms/symmetry/cosym/__init__.py:16,482,561,575; lib/python3.11/site-packages/dials-3.30.dist-info/top_level.txt; distribution/package ownership; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:doublehelix","env":"core","topic":"models","status":"unresolved","detail":"Shipped native .so is hash-pinned and predictor calls predict with EM/DNA flags. Exact embedded arrays, fallback checkpoint availability and equivalence were not established; no model deserialization or execution.","evidence":"lib/python3.11/site-packages/doubleHelix/__main__.py:493,573; lib/python3.11/site-packages/doubleHelixLib/sequence_utils.py:25,139,258; lib/python3.11/site-packages/doubleHelixLib/nn4na_predict.py:27,74,77,80,92,96; lib/python3.11/site-packages/doubleHelixLib/nn4na_utils.py:176,200,287,352; lib/python3.11/site-packages/doubleHelixLib/doublehelix_nnmodel.so; SHA-256 pinned shipped binary; lib/python3.11/site-packages/doubleHelix-5.6.3-py3.11.egg-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:core:doublehelix","env":"core","topic":"provenance","status":"unresolved","detail":"Training and conversion source workflows are present; exact training/export/build lineage for the shipped native .so is unverified.","evidence":"lib/python3.11/site-packages/doubleHelix/__main__.py:493,573; lib/python3.11/site-packages/doubleHelixLib/sequence_utils.py:25,139,258; lib/python3.11/site-packages/doubleHelixLib/nn4na_predict.py:27,74,77,80,92,96; lib/python3.11/site-packages/doubleHelixLib/nn4na_utils.py:176,200,287,352; lib/python3.11/site-packages/doubleHelixLib/doublehelix_nnmodel.so; SHA-256 pinned shipped binary; lib/python3.11/site-packages/doubleHelix-5.6.3-py3.11.egg-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:core:doublehelix","env":"core","topic":"runtime","status":"verified","detail":"Primary neural-inference omission. Program model2sequence creates nn4na_predict; predictor loads doublehelix_nnmodel.so and calls predict. torch imports only on initial CDLL failure; fallback refers to naive4na without a definition/import in that module, so fallback operation is unresolved. nn4na_utils includes training; export2onnx/import2tf are conversion, not proof of runtime engines. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/doubleHelix/__main__.py:493,573; lib/python3.11/site-packages/doubleHelixLib/sequence_utils.py:25,139,258; lib/python3.11/site-packages/doubleHelixLib/nn4na_predict.py:27,74,77,80,92,96; lib/python3.11/site-packages/doubleHelixLib/nn4na_utils.py:176,200,287,352; lib/python3.11/site-packages/doubleHelixLib/doublehelix_nnmodel.so; SHA-256 pinned shipped binary; lib/python3.11/site-packages/doubleHelix-5.6.3-py3.11.egg-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:core:dxtbx","env":"core","topic":"runtime","status":"verified","detail":"Optional sklearn import; multi-panel detector projection uses DBSCAN if sklearn is available. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/dxtbx/model/detector_helpers.py:18,20,372,378; lib/python3.11/site-packages/dxtbx-3.30.0.dist-info/RECORD; distribution/package ownership; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:findmysequence","env":"core","topic":"runtime","status":"verified","detail":"Instantiates fmslib.sequence_utils.model2sequence, which constructs nn_predict.nn_predict and calls its predict method. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/findmysequence/__main__.py:20,21,22,153,216; lib/python3.11/site-packages/fmslib/sequence_utils.py:34,90,487; lib/python3.11/site-packages/findmysequence-1.0.28-py3.11.egg-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:core:metalcoordanalysis","env":"core","topic":"runtime","status":"verified","detail":"GaussianMixture clustering and DBSCAN ring identification. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/metalCoord/analysis/cluster.py:3,129; lib/python3.11/site-packages/metalCoord/correspondense/procrustes.py:5,150; lib/python3.11/site-packages/metalcoordanalysis-0.2.15.dist-info/RECORD; distribution/package ownership; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:modelcraft","env":"core","topic":"runtime","status":"verified","detail":"Additional consumer, not a new neural engine: NucleoFindPredict runs nucleofind core model with --gpu; NucleoFindBuild runs nucleofind-build. Both X-ray and EM workflows call these jobs. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/modelcraft/jobs/nucleofind.py:22,57; lib/python3.11/site-packages/modelcraft/modelcraftxray.py:184,189; lib/python3.11/site-packages/modelcraft/modelcraftem.py:51,150; lib/python3.11/site-packages/modelcraft/job.py:13,15,36,59,62,63; lib/python3.11/site-packages/modelcraft-6.1.1.dist-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:core:nucleofind","env":"core","topic":"external","status":"verified","detail":"The separate install command can fetch models/database. The inspected prediction path uses local ONNX files.","evidence":"lib/python3.11/site-packages/nucleofind/prediction/model.py:101-130,133-163; lib/python3.11/site-packages/nucleofind/install.py:26"},{"component_id":"pydist:core:nucleofind","env":"core","topic":"models","status":"verified","detail":"Two byte-identical core ONNX copies ship; loader searches site-packages and CLIBD. Exact selected path depends on arguments/environment; nano is not shipped.","evidence":"lib/python3.11/site-packages/nucleofind/prediction/load.py:6,58-73; lib/python3.11/site-packages/nucleofind/prediction/model.py:133-163,180-204; lib/python3.11/site-packages/nucleofind/prediction/predict.py:133,235-243; lib/python3.11/site-packages/nucleofind/build.py:110-116"},{"component_id":"pydist:core:nucleofind","env":"core","topic":"provenance","status":"unresolved","detail":"Installed metadata gives a local build-origin path, but exact training/export lineage and model producer/opset were not established.","evidence":"lib/python3.11/site-packages/nucleofind-1.3.2.dist-info/METADATA; lib/python3.11/site-packages/nucleofind/prediction/model.py:133-163,180-204"},{"component_id":"pydist:core:nucleofind","env":"core","topic":"runtime","status":"verified","detail":"Source imports ONNX Runtime and creates InferenceSession; installed onnxruntime is 1.19.2. Linux METADATA instead requests onnxruntime-gpu; GPU operation is untested.","evidence":"lib/python3.11/site-packages/nucleofind/prediction/load.py:6,58-73; lib/python3.11/site-packages/nucleofind/prediction/model.py:133-163,180-204; lib/python3.11/site-packages/nucleofind/prediction/predict.py:133,235-243; lib/python3.11/site-packages/nucleofind/build.py:110-116"},{"component_id":"pydist:core:panddas","env":"core","topic":"runtime","status":"verified","detail":"DBSCAN and Gaussian-mixture fitting methods, separate core package identity from PanDDA2 environment. Static source evidence only; runtime operation was not tested. Same panddas distribution also owns Pandemic ADP TLS-group identification (separate claim, no duplicate coverage topic).","evidence":"lib/python3.11/site-packages/giant/structure/ensembles/cluster_waters.py:345,347,352,457; lib/python3.11/site-packages/panddas-1.0.0-py3.11.egg-info/top_level.txt; distribution/package ownership; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:ridl","env":"core","topic":"runtime","status":"verified","detail":"perAtomClusterAnalysis fits KMeans; mapsToDensityMetrics StandardScaler occurs specifically in makeTrainingSet, and nearby old KMeans block is commented out. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/ridl/perAtomClusterAnalysis.py:3,371,372,418,419; lib/python3.11/site-packages/ridl/mapsToDensityMetrics.py:697,698; lib/python3.11/site-packages/ridl-0.0.1.dist-info/top_level.txt; distribution/package ownership; lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/top_level.txt; installed scikit-learn 1.4.2 owns sklearn"},{"component_id":"pydist:core:xia2","env":"core","topic":"runtime","status":"verified","detail":"MultiCrystalAnalysis creates DialsCorrelationMatrix and runs it; wrapper imports dials.algorithms.correlation.analysis.CorrelationMatrix. Thus source-backed transitive classical-ML reach. Static source evidence only; runtime operation was not tested.","evidence":"lib/python3.11/site-packages/xia2/Modules/MultiCrystalAnalysis.py:29,162; lib/python3.11/site-packages/xia2/Wrappers/Dials/Functional/CorrelationMatrix.py:9,126; lib/python3.11/site-packages/xia2-3.29.0-py3.11.egg-info/top_level.txt; distribution/package ownership"},{"component_id":"pydist:share/mamba/envs/abcfold:abcfold","env":"share/mamba/envs/abcfold","topic":"external","status":"verified","detail":"Five conditional backends: AlphaFold3 container; Boltz 2.2.1, Chai-lab 0.6.1, Protenix 0.7.3 and OpenFold3 0.3.1 in separately created environments.","evidence":"share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/abcfold.py:139,175-176,192-193,216-217,235-236; share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/backend_envs.py:88-105"},{"component_id":"pydist:share/mamba/envs/abcfold:abcfold","env":"share/mamba/envs/abcfold","topic":"models","status":"not-applicable","detail":"No backend model weights ship in this environment; backend paths refer to user-provided or externally downloaded models.","evidence":"share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/abcfold.py:139,175-176,192-193,216-217,235-236; share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/backend_envs.py:88-105"},{"component_id":"pydist:share/mamba/envs/abcfold:abcfold","env":"share/mamba/envs/abcfold","topic":"provenance","status":"unresolved","detail":"Backend install pins describe requested external versions, not versions actually installed or used; AlphaFold3 container version is unknown.","evidence":"share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/abcfold.py:139,175-176,192-193,216-217,235-236; share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/backend_envs.py:88-105"},{"component_id":"pydist:share/mamba/envs/abcfold:abcfold","env":"share/mamba/envs/abcfold","topic":"runtime","status":"verified","detail":"ABCFold 1.1.1 dispatches optional external backends; no ML runtime is installed in its environment. Launcher interpreter resolution remains untested.","evidence":"share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/abcfold.py:139,175-176,192-193,216-217,235-236; share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold/backend_envs.py:88-105"},{"component_id":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","env":"share/mamba/envs/pandda2","topic":"external","status":"verified","detail":"Missing checkpoint/config files trigger gdown downloads; this includes the unshipped no-ligand checkpoint.","evidence":"share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/get_scoring_models.py:85-96,110-120,135-144"},{"component_id":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","env":"share/mamba/envs/pandda2","topic":"models","status":"verified","detail":"Default ligand-aware path selects shipped event/build checkpoints. The no-ligand path requests an absent checkpoint; legacy model.pt/model_event_build.pt loaders remain untraced.","evidence":"share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/pandda.py:44; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/get_scoring_models.py:78-159; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/base.py:97-108; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/args/args.py:14"},{"component_id":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","env":"share/mamba/envs/pandda2","topic":"provenance","status":"unresolved","detail":"Checkpoint training/export lineage and numerical contents were not established; no deserialization or model execution was performed.","evidence":"share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/pandda.py:44; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/get_scoring_models.py:78-159; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/base.py:97-108; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/args/args.py:14"},{"component_id":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","env":"share/mamba/envs/pandda2","topic":"runtime","status":"verified","detail":"pandda_2_gemmi 0.0.1 source calls torch checkpoint loading in the dedicated Python 3.9 environment; installed torch is 1.13.1. Launcher re-execs ccp4-python; actual interpreter resolution is untested.","evidence":"share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/pandda.py:44; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/get_scoring_models.py:78-159; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/base.py:97-108; share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/args/args.py:14"},{"component_id":"pydist:share/mamba/envs/pandda2:rdkit","env":"share/mamba/envs/pandda2","topic":"models","status":"verified","detail":"Shipped NP score table has a static default loader and fragment-scoring routine. This is not asserted to be a neural network; application-level use, training provenance and successful deserialization remain unverified.","evidence":"share/mamba/envs/pandda2/lib/python3.9/site-packages/rdkit/Contrib/NP_Score/npscorer.py:27-33,36-74"}],"reach":[{"node_id":"component:core:arcimboldo aleph","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"component:core:arcimboldo aleph -> pydist:core:scikit-learn"},{"node_id":"component:core:buccaneer nn","env":"core","ml_family":"native-ml","framework_major":"","direct":"y","path":"component:core:buccaneer nn -> native_lib:core:bin/cbuccaneerNN"},{"node_id":"component:core:coot chemical feature clustering","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"component:core:coot chemical feature clustering -> pydist:core:scikit-learn"},{"node_id":"component:core:fmslib","env":"core","ml_family":"native-ml","framework_major":"","direct":"y","path":"component:core:fmslib -> native_lib:core:lib/python3.11/site-packages/fmslib/fms_nnmodel.so"},{"node_id":"component:core:libtbx covariance helpers","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"component:core:libtbx covariance helpers -> pydist:core:scikit-learn"},{"node_id":"component:core:phasertng matthews ml","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"component:core:phasertng matthews ml -> pydist:core:scikit-learn"},{"node_id":"component:core:phasertng matthews ml","env":"core","ml_family":"native-ml","framework_major":"","direct":"y","path":"component:core:phasertng matthews ml -> native_lib:core:lib/python3.11/lib-dynload/phasertng_ext.so"},{"node_id":"component:core:slicendice","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"component:core:slicendice -> pydist:core:scikit-learn"},{"node_id":"component:core:struvolpy","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"component:core:struvolpy -> pydist:core:scikit-learn"},{"node_id":"native_lib:core:bin/cbuccaneerNN","env":"core","ml_family":"native-ml","framework_major":"","direct":"n","path":"native_lib:core:bin/cbuccaneerNN"},{"node_id":"native_lib:core:lib/python3.11/lib-dynload/phasertng_ext.so","env":"core","ml_family":"native-ml","framework_major":"","direct":"n","path":"native_lib:core:lib/python3.11/lib-dynload/phasertng_ext.so"},{"node_id":"native_lib:core:lib/python3.11/site-packages/doubleHelixLib/doublehelix_nnmodel.so","env":"core","ml_family":"native-ml","framework_major":"","direct":"n","path":"native_lib:core:lib/python3.11/site-packages/doubleHelixLib/doublehelix_nnmodel.so"},{"node_id":"native_lib:core:lib/python3.11/site-packages/fmslib/fms_nnmodel.so","env":"core","ml_family":"native-ml","framework_major":"","direct":"n","path":"native_lib:core:lib/python3.11/site-packages/fmslib/fms_nnmodel.so"},{"node_id":"pydist:core:checkmysequence","env":"core","ml_family":"native-ml","framework_major":"","direct":"n","path":"pydist:core:checkmysequence -> component:core:fmslib -> native_lib:core:lib/python3.11/site-packages/fmslib/fms_nnmodel.so"},{"node_id":"pydist:core:conkit","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"pydist:core:conkit -> pydist:core:scikit-learn"},{"node_id":"pydist:core:dials","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"pydist:core:dials -> pydist:core:scikit-learn"},{"node_id":"pydist:core:dials","env":"core","ml_family":"ml-ecosystem","framework_major":"4","direct":"y","path":"pydist:core:dials -> pydist:core:optuna"},{"node_id":"pydist:core:doublehelix","env":"core","ml_family":"native-ml","framework_major":"","direct":"y","path":"pydist:core:doublehelix -> native_lib:core:lib/python3.11/site-packages/doubleHelixLib/doublehelix_nnmodel.so"},{"node_id":"pydist:core:findmysequence","env":"core","ml_family":"native-ml","framework_major":"","direct":"n","path":"pydist:core:findmysequence -> component:core:fmslib -> native_lib:core:lib/python3.11/site-packages/fmslib/fms_nnmodel.so"},{"node_id":"pydist:core:metalcoordanalysis","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"pydist:core:metalcoordanalysis -> pydist:core:scikit-learn"},{"node_id":"pydist:core:modelcraft","env":"core","ml_family":"onnxruntime","framework_major":"1","direct":"n","path":"pydist:core:modelcraft -> pydist:core:nucleofind -> pydist:core:onnxruntime"},{"node_id":"pydist:core:nucleofind","env":"core","ml_family":"onnxruntime","framework_major":"1","direct":"y","path":"pydist:core:nucleofind -> pydist:core:onnxruntime"},{"node_id":"pydist:core:onnxruntime","env":"core","ml_family":"onnxruntime","framework_major":"1","direct":"n","path":"pydist:core:onnxruntime"},{"node_id":"pydist:core:optuna","env":"core","ml_family":"ml-ecosystem","framework_major":"4","direct":"n","path":"pydist:core:optuna"},{"node_id":"pydist:core:panddas","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"pydist:core:panddas -> pydist:core:scikit-learn"},{"node_id":"pydist:core:ridl","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"pydist:core:ridl -> pydist:core:scikit-learn"},{"node_id":"pydist:core:scikit-learn","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"n","path":"pydist:core:scikit-learn"},{"node_id":"pydist:core:xia2","env":"core","ml_family":"classical-ml","framework_major":"1","direct":"n","path":"pydist:core:xia2 -> pydist:core:dials -> pydist:core:scikit-learn"},{"node_id":"pydist:core:xia2","env":"core","ml_family":"ml-ecosystem","framework_major":"4","direct":"n","path":"pydist:core:xia2 -> pydist:core:dials -> pydist:core:optuna"},{"node_id":"pydist:share/mamba/envs/pandda2:hdbscan","env":"share/mamba/envs/pandda2","ml_family":"classical-ml","framework_major":"0","direct":"n","path":"pydist:share/mamba/envs/pandda2:hdbscan"},{"node_id":"pydist:share/mamba/envs/pandda2:hdbscan","env":"share/mamba/envs/pandda2","ml_family":"classical-ml","framework_major":"1","direct":"y","path":"pydist:share/mamba/envs/pandda2:hdbscan -> pydist:share/mamba/envs/pandda2:scikit-learn"},{"node_id":"pydist:share/mamba/envs/pandda2:nvidia-cublas-cu11","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"11","direct":"n","path":"pydist:share/mamba/envs/pandda2:nvidia-cublas-cu11"},{"node_id":"pydist:share/mamba/envs/pandda2:nvidia-cuda-nvrtc-cu11","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"11","direct":"n","path":"pydist:share/mamba/envs/pandda2:nvidia-cuda-nvrtc-cu11"},{"node_id":"pydist:share/mamba/envs/pandda2:nvidia-cuda-runtime-cu11","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"11","direct":"n","path":"pydist:share/mamba/envs/pandda2:nvidia-cuda-runtime-cu11"},{"node_id":"pydist:share/mamba/envs/pandda2:nvidia-cudnn-cu11","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"11","direct":"y","path":"pydist:share/mamba/envs/pandda2:nvidia-cudnn-cu11 -> pydist:share/mamba/envs/pandda2:nvidia-cublas-cu11"},{"node_id":"pydist:share/mamba/envs/pandda2:nvidia-cudnn-cu11","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"8","direct":"n","path":"pydist:share/mamba/envs/pandda2:nvidia-cudnn-cu11"},{"node_id":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"11","direct":"n","path":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi -> pydist:share/mamba/envs/pandda2:torch -> pydist:share/mamba/envs/pandda2:nvidia-cublas-cu11"},{"node_id":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","env":"share/mamba/envs/pandda2","ml_family":"accelerator","framework_major":"8","direct":"n","path":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi -> pydist:share/mamba/envs/pandda2:torch -> 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environment=share/mamba/envs/abcfold; shipped=y; version=84.0.0"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"conda:share/mamba/envs/abcfold:tk","disposition":"installed Conda runtime/build-support record","rationale":"The exact ABCFold environment record supplies Tcl/Tk GUI/runtime libraries; no ML function is indicated.","evidence":["share/mamba/envs/abcfold/conda-meta/tk-8.6.13-noxft_h1df4ec4_4.json; build=noxft_h1df4ec4_4; channel=conda-forge","share/mamba/envs/abcfold/conda-meta/tk-8.6.13-noxft_h1df4ec4_4.json: installed Conda JSON; build=noxft_h1df4ec4_4; declared depends=['libgcc >=15', '__glibc >=2.17,<3.0.a0', 'libzlib >=1.3.2,<2.0a0']; package file list count=520"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"conda:share/mamba/envs/abcfold:tzdata","disposition":"non-ML environment infrastructure","rationale":"Installed Conda record identifies IANA time-zone data. 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Dependencies were checked against the same environment; this package is infrastructure, not an ML model.","evidence":["share/mamba/envs/abcfold/conda-meta/wheel-0.48.0-pyhd8ed1ab_0.json","build=pyhd8ed1ab_0","channel=conda-forge","cpu64 installed record share/mamba/envs/abcfold/conda-meta/wheel-0.48.0-pyhd8ed1ab_0.json; sha256=28395650cca2b3f9d9be42ddf0cfe9f39a7b5477bab0c4f7829a333b496aee7d; record exists=True","Conda record identity=wheel 0.48.0 build=pyhd8ed1ab_0; depends=['packaging >=24.0', 'python >=3.10']"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"conda:share/mamba/envs/abcfold:zstd","disposition":"compression runtime","rationale":"The conda record supplies zstd in ABCFold and has zlib/GCC/glibc dependencies; data compression support.","evidence":["share/mamba/envs/abcfold/conda-meta/zstd-1.5.7-hb78ec9c_7.json; build=hb78ec9c_7; channel=conda-forge","conda-meta JSON share/mamba/envs/abcfold/conda-meta/zstd-1.5.7-hb78ec9c_7.json; SHA-256 0909e436679c8981b8706c02716d20364836a5254b774b6aedbebd9c05f69f8a; file entries=18"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"conda:share/mamba/envs/pandda2:-openmp-mutex","disposition":"non-ML-conda-runtime-infrastructure","rationale":"Installed Conda record identifies -openmp-mutex 4.5 (20_gnu) in share/mamba/envs/pandda2; role is OpenMP runtime selector/constraint. 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This is environment/package infrastructure, not a learned model or training artifact.","evidence":["share/mamba/envs/pandda2/conda-meta/bzip2-1.0.8-hda65f42_10.json; build=hda65f42_10; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"conda:share/mamba/envs/pandda2:ca-certificates","disposition":"tls_trust_store_infrastructure","rationale":"Installed Conda record for ca-certificates 2026.7.22 in share/mamba/envs/pandda2; role is tls trust store infrastructure. 1 assigned conda dependency edges were reviewed separately with exact target environment/version.","evidence":["installed conda record share/mamba/envs/pandda2/conda-meta/ca-certificates-2026.7.22-hbd8a1cb_0.json sha256=e21dc5fe280f869601e24a029f05b8f663275cad0b9d3899848d35be4da9218c bytes=1965","record identity name=ca-certificates version=2026.7.22 build=hbd8a1cb_0 channel=conda-forge","record depends=[\"__unix\"]"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"conda:share/mamba/envs/pandda2:colorama","disposition":"Conda runtime infrastructure dependency","rationale":"Installed colorama 0.4.6 is a support package in share/mamba/envs/pandda2; its conda record/build/channel and declared depends were reviewed. 1 assigned conda dependency edge(s) are assessed separately; no learned model functionality is attributed to this package.","evidence":["share/mamba/envs/pandda2/conda-meta/colorama-0.4.6-pyhd8ed1ab_1.json; build=pyhd8ed1ab_1; channel=conda-forge","share/mamba/envs/pandda2/conda-meta record: name=colorama, version=0.4.6; build=pyhd8ed1ab_1; channel=conda-forge","Assigned dependency edges from this node: 1; exact targets and constraints are in dependency_edges.","Installed conda-meta exact depends=[\"python >=3.9\"]; build=pyhd8ed1ab_1; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"conda:share/mamba/envs/pandda2:exceptiongroup","disposition":"exception compatibility library","rationale":"Exception-group helpers for Python exception handling.","evidence":["installed Conda record: share/mamba/envs/pandda2/conda-meta/exceptiongroup-1.3.0-pyhd8ed1ab_0.json; exceptiongroup=1.3.0; build=pyhd8ed1ab_0; channel=conda-forge; depends=[\"python >=3.9\", \"typing_extensions >=4.6.0\"]","Conda file ownership: 20 files; examples=[\"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/INSTALLER\", \"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/METADATA\", \"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/RECORD\", \"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/REQUESTED\", \"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/WHEEL\", \"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/direct_url.json\", \"lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/licenses/LICENSE\", \"lib/python3.9/site-packages/exceptiongroup/__init__.py\"]","static source/data scan from Conda-owned files: 6 files/40507 bytes; matched review terms=0; examples=[]","node identity=conda:share/mamba/envs/pandda2:exceptiongroup; environment=share/mamba/envs/pandda2; shipped=y; version=1.3.0"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"conda:share/mamba/envs/pandda2:iniconfig","disposition":"installed Conda runtime/build-support record","rationale":"The exact PandDA environment record supplies Python test configuration support; no ML/model function is indicated.","evidence":["share/mamba/envs/pandda2/conda-meta/iniconfig-2.0.0-pyhd8ed1ab_1.json; build=pyhd8ed1ab_1; channel=conda-forge","share/mamba/envs/pandda2/conda-meta/iniconfig-2.0.0-pyhd8ed1ab_1.json: installed Conda JSON; build=pyhd8ed1ab_1; declared depends=['python >=3.9']; package file list count=16"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"conda:share/mamba/envs/pandda2:ld-impl-linux-64","disposition":"non-ML environment infrastructure","rationale":"Installed Conda record identifies GNU ELF linker implementation. 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Its declared dependency list is retained and checked against same-environment target records.","evidence":["share/mamba/envs/pandda2/conda-meta/libgcc-16.2.0-ha9f2e26_7.json; build=ha9f2e26_7; channel=conda-forge","share/mamba/envs/pandda2/conda-meta/libgcc-16.2.0-ha9f2e26_7.json; record={\"build\": \"ha9f2e26_7\", \"build_number\": 7, \"channel\": \"conda-forge\", \"constrains\": [\"libgcc-ng ==16.2.0 *_7\", \"libgomp 16.2.0 he0feb66_7\"], \"depends\": [\"__glibc >=2.17,<3.0.a0\", \"_openmp_mutex >=4.5\"], \"name\": \"libgcc\", \"subdir\": \"linux-64\", \"version\": \"16.2.0\"}"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"conda:share/mamba/envs/pandda2:libgomp","disposition":"conda-runtime-or-tool-infrastructure","rationale":"Installed libgomp 16.2.0 in share/mamba/envs/pandda2 is OpenMP runtime library. 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Dependencies were checked against the same environment; this package is infrastructure, not an ML model.","evidence":["share/mamba/envs/pandda2/conda-meta/libzlib-1.3.2-h25fd6f3_3.json","build=h25fd6f3_3","channel=conda-forge","cpu64 installed record share/mamba/envs/pandda2/conda-meta/libzlib-1.3.2-h25fd6f3_3.json; sha256=3ff179f0f3541257836a4e2cafea3735919e7ad4165a6711238214ca89312888; record exists=True","Conda record identity=libzlib 1.3.2 build=h25fd6f3_3; depends=['__glibc >=2.17,<3.0.a0']"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"conda:share/mamba/envs/pandda2:ncurses","disposition":"terminal UI runtime","rationale":"The PandDA2 conda record supplies ncurses and its support files; not an ML runtime.","evidence":["share/mamba/envs/pandda2/conda-meta/ncurses-6.6-hdb14827_1.json; build=hdb14827_1; channel=conda-forge","conda-meta JSON share/mamba/envs/pandda2/conda-meta/ncurses-6.6-hdb14827_1.json; SHA-256 32f47c1448877a78d53deaa9ece3ec0a948b7e26f90157fcdb29456137e7fd39; file entries=3014"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"conda:share/mamba/envs/pandda2:openssl","disposition":"non-ML-conda-runtime-infrastructure","rationale":"Installed Conda record identifies openssl 3.6.5 (h781a0a9_0) in share/mamba/envs/pandda2; role is TLS/cryptography library. Its declared dependency list is retained and checked against same-environment target records.","evidence":["share/mamba/envs/pandda2/conda-meta/openssl-3.6.5-h781a0a9_0.json; build=h781a0a9_0; channel=conda-forge","share/mamba/envs/pandda2/conda-meta/openssl-3.6.5-h781a0a9_0.json; record={\"build\": \"h781a0a9_0\", \"build_number\": 0, \"channel\": \"conda-forge\", \"constrains\": [], \"depends\": [\"__glibc >=2.17,<3.0.a0\", \"ca-certificates\", \"libgcc >=15\"], \"name\": \"openssl\", \"subdir\": \"linux-64\", \"version\": \"3.6.5\"}"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"conda:share/mamba/envs/pandda2:packaging","disposition":"conda-runtime-or-tool-infrastructure","rationale":"Installed packaging 26.3 in share/mamba/envs/pandda2 is Python version/specifier utility. This is environment/package infrastructure, not a learned model or training artifact.","evidence":["share/mamba/envs/pandda2/conda-meta/packaging-26.3-pyhc364b38_0.json; build=pyhc364b38_0; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"conda:share/mamba/envs/pandda2:pip","disposition":"python_packaging_or_compatibility_infrastructure","rationale":"Installed Conda record for pip 25.2 in share/mamba/envs/pandda2; role is python packaging or compatibility infrastructure. 3 assigned conda dependency edges were reviewed separately with exact target environment/version.","evidence":["installed conda record share/mamba/envs/pandda2/conda-meta/pip-25.2-pyh8b19718_0.json sha256=21e408be200675d5b9a24a85068852ee50bc7eaea26944688f11639fe053c44a bytes=328728","record identity name=pip version=25.2 build=pyh8b19718_0 channel=conda-forge","record depends=[\"python >=3.9,<3.13.0a0\",\"setuptools\",\"wheel\"]"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"conda:share/mamba/envs/pandda2:pluggy","disposition":"Conda runtime infrastructure dependency","rationale":"Installed pluggy 1.6.0 is a support package in share/mamba/envs/pandda2; its conda record/build/channel and declared depends were reviewed. 2 assigned conda dependency edge(s) are assessed separately; no learned model functionality is attributed to this package.","evidence":["share/mamba/envs/pandda2/conda-meta/pluggy-1.6.0-pyhf9edf01_1.json; build=pyhf9edf01_1; channel=conda-forge","share/mamba/envs/pandda2/conda-meta record: name=pluggy, version=1.6.0; build=pyhf9edf01_1; channel=conda-forge","Assigned dependency edges from this node: 2; exact targets and constraints are in dependency_edges.","Installed conda-meta exact depends=[\"python >=3.9\", \"python\"]; build=pyhf9edf01_1; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"conda:share/mamba/envs/pandda2:pygments","disposition":"syntax highlighting library","rationale":"Syntax-highlighting/lexer library; broad network/transformer/regression vocabulary comes from lexer token tables, not ML.","evidence":["installed Conda record: share/mamba/envs/pandda2/conda-meta/pygments-2.19.2-pyhd8ed1ab_0.json; pygments=2.19.2; build=pyhd8ed1ab_0; channel=conda-forge; depends=[\"python >=3.9\"]","Conda file ownership: 686 files; examples=[\"lib/python3.9/site-packages/pygments-2.19.2.dist-info/INSTALLER\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/METADATA\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/RECORD\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/REQUESTED\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/WHEEL\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/direct_url.json\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/entry_points.txt\", \"lib/python3.9/site-packages/pygments-2.19.2.dist-info/licenses/AUTHORS\"]","static source/data scan from Conda-owned files: 160 files/2719599 bytes; matched review terms=30; examples=[{\"path\": \"lib/python3.9/site-packages/pygments/__init__.py\", \"line\": 12, \"text\": \"* special attention is paid to details, increasing quality by a fair amount\"}, {\"path\": \"lib/python3.9/site-packages/pygments/lexers/_lilypond_builtins.py\", \"line\": 1506, \"text\": \"\\\"with-string-transformer\\\",\"}, {\"path\": \"lib/python3.9/site-packages/pygments/lexers/_lilypond_builtins.py\", \"line\": 2419, \"text\": \"\\\"grob-transformer\\\",\"}]","node identity=conda:share/mamba/envs/pandda2:pygments; environment=share/mamba/envs/pandda2; shipped=y; version=2.19.2"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"conda:share/mamba/envs/pandda2:pytest","disposition":"installed Conda runtime/build-support record","rationale":"The exact PandDA environment record is test infrastructure and declares Python/test-support dependencies; it is not a model.","evidence":["share/mamba/envs/pandda2/conda-meta/pytest-8.4.1-pyhd8ed1ab_0.json; build=pyhd8ed1ab_0; channel=conda-forge","share/mamba/envs/pandda2/conda-meta/pytest-8.4.1-pyhd8ed1ab_0.json: installed Conda JSON; build=pyhd8ed1ab_0; declared depends=['colorama >=0.4', 'exceptiongroup >=1', 'iniconfig >=1', 'packaging >=20', 'pluggy >=1.5,<2', 'pygments >=2.7.2', 'python >=3.9', 'tomli >=1']; package file list count=158"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"conda:share/mamba/envs/pandda2:python","disposition":"non-ML environment infrastructure","rationale":"Installed Conda record identifies Python 3.9 runtime for the isolated pandda2 environment. Declared dependencies are retained as separate edges below; this runtime/build support package is not itself a trained model.","evidence":["share/mamba/envs/pandda2/conda-meta/python-3.9.23-hc30ae73_0_cpython.json; build=hc30ae73_0_cpython; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"conda:share/mamba/envs/pandda2:readline","disposition":"Conda runtime infrastructure","rationale":"Installed Conda runtime/build-support record. Dependencies were checked against the same environment; this package is infrastructure, not an ML model.","evidence":["share/mamba/envs/pandda2/conda-meta/readline-8.3-hd6e31c0_1.json","build=hd6e31c0_1","channel=conda-forge","cpu64 installed record share/mamba/envs/pandda2/conda-meta/readline-8.3-hd6e31c0_1.json; sha256=8753d1af79e1c052eb4041998b96bf378921e7cec4ce353d7ac7c0e0ef80a7d4; record exists=True","Conda record identity=readline 8.3 build=hd6e31c0_1; depends=['__glibc >=2.17,<3.0.a0', 'libgcc >=15', 'ncurses >=6.6,<7.0a0']"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"conda:share/mamba/envs/pandda2:setuptools","disposition":"Python packaging/build runtime","rationale":"The PandDA2 environment contains setuptools and its bundled/vendored helper dependencies; build/install support.","evidence":["share/mamba/envs/pandda2/conda-meta/setuptools-79.0.1-pyhff2d567_0.json; build=pyhff2d567_0; channel=conda-forge","conda-meta JSON share/mamba/envs/pandda2/conda-meta/setuptools-79.0.1-pyhff2d567_0.json; SHA-256 cbffb94a6d5220f7e725304644d4a613c5768ebeaa2a235956259908c953decd; file entries=871"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"conda:share/mamba/envs/pandda2:tk","disposition":"non-ML-conda-runtime-infrastructure","rationale":"Installed Conda record identifies tk 8.6.13 (noxft_h1df4ec4_4) in share/mamba/envs/pandda2; role is GUI toolkit. Its declared dependency list is retained and checked against same-environment target records.","evidence":["share/mamba/envs/pandda2/conda-meta/tk-8.6.13-noxft_h1df4ec4_4.json; build=noxft_h1df4ec4_4; channel=conda-forge","share/mamba/envs/pandda2/conda-meta/tk-8.6.13-noxft_h1df4ec4_4.json; record={\"build\": \"noxft_h1df4ec4_4\", \"build_number\": 104, \"channel\": \"conda-forge\", \"constrains\": [\"xorg-libx11 >=1.8.13,<2.0a0\"], \"depends\": [\"libgcc >=15\", \"__glibc >=2.17,<3.0.a0\", \"libzlib >=1.3.2,<2.0a0\"], \"name\": \"tk\", \"subdir\": \"linux-64\", \"version\": \"8.6.13\"}"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"conda:share/mamba/envs/pandda2:tomli","disposition":"conda-runtime-or-tool-infrastructure","rationale":"Installed tomli 2.2.1 in share/mamba/envs/pandda2 is TOML parser. This is environment/package infrastructure, not a learned model or training artifact.","evidence":["share/mamba/envs/pandda2/conda-meta/tomli-2.2.1-pyhe01879c_2.json; build=pyhe01879c_2; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"conda:share/mamba/envs/pandda2:typing-extensions","disposition":"python_packaging_or_compatibility_infrastructure","rationale":"Installed Conda record for typing_extensions 4.14.1 in share/mamba/envs/pandda2; role is python packaging or compatibility infrastructure. 2 assigned conda dependency edges were reviewed separately with exact target environment/version.","evidence":["installed conda record share/mamba/envs/pandda2/conda-meta/typing_extensions-4.14.1-pyhe01879c_0.json sha256=fd215972a14c428dd10cfe99e91b30a6d404cd36f9d082444632c551ce0c5f54 bytes=5404","record identity name=typing_extensions version=4.14.1 build=pyhe01879c_0 channel=conda-forge","record depends=[\"python >=3.9\",\"python\"]"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"conda:share/mamba/envs/pandda2:tzdata","disposition":"Conda runtime infrastructure dependency","rationale":"Installed tzdata 2026c is a support package in share/mamba/envs/pandda2; its conda record/build/channel and declared depends were reviewed. 0 assigned conda dependency edge(s) are assessed separately; no learned model functionality is attributed to this package.","evidence":["share/mamba/envs/pandda2/conda-meta/tzdata-2026c-h151e31d_0.json; build=h151e31d_0; channel=conda-forge","share/mamba/envs/pandda2/conda-meta record: name=tzdata, version=2026c; build=h151e31d_0; channel=conda-forge","Assigned dependency edges from this node: 0; exact targets and constraints are in dependency_edges.","Installed conda-meta exact depends=[]; build=h151e31d_0; channel=conda-forge"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"conda:share/mamba/envs/pandda2:wheel","disposition":"Python wheel build tooling","rationale":"Wheel packaging/build tooling.","evidence":["installed Conda record: share/mamba/envs/pandda2/conda-meta/wheel-0.45.1-pyhd8ed1ab_1.json; wheel=0.45.1; build=pyhd8ed1ab_1; channel=conda-forge; depends=[\"python >=3.9\"]","Conda file ownership: 66 files; examples=[\"lib/python3.9/site-packages/wheel-0.45.1.dist-info/LICENSE.txt\", \"lib/python3.9/site-packages/wheel-0.45.1.dist-info/METADATA\", \"lib/python3.9/site-packages/wheel-0.45.1.dist-info/RECORD\", \"lib/python3.9/site-packages/wheel-0.45.1.dist-info/WHEEL\", \"lib/python3.9/site-packages/wheel-0.45.1.dist-info/entry_points.txt\", \"lib/python3.9/site-packages/wheel/__init__.py\", \"lib/python3.9/site-packages/wheel/__main__.py\", \"lib/python3.9/site-packages/wheel/_bdist_wheel.py\"]","static source/data scan from Conda-owned files: 28 files/205586 bytes; matched review terms=0; examples=[]","node identity=conda:share/mamba/envs/pandda2:wheel; environment=share/mamba/envs/pandda2; shipped=y; version=0.45.1"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"conda:share/mamba/envs/pandda2:zstd","disposition":"installed Conda runtime/build-support record","rationale":"This is a low-level parsing, cryptographic, identifier or compression runtime record; no ML/model function is indicated.","evidence":["share/mamba/envs/pandda2/conda-meta/zstd-1.5.7-hb78ec9c_7.json; build=hb78ec9c_7; channel=conda-forge","share/mamba/envs/pandda2/conda-meta/zstd-1.5.7-hb78ec9c_7.json: installed Conda JSON; build=hb78ec9c_7; declared depends=['__glibc >=2.17,<3.0.a0', 'libzlib >=1.3.2,<2.0a0']; package file list count=18"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"js_manifest:javascript/lib/python3.11/site-packages:jquery-ui:lib/python3.11/site-packages/ccp4i2/docs/report_files/0.1.0/jquery-ui-1.10.4.custom/development-bundle/package.json","disposition":"application_manifest_surface_only","rationale":"The manifest metadata alone is not evidence of a trained model. The bounded application source scan and the separate FitLigand source leads are retained elsewhere in this report.","evidence":{"byte_length":1774,"entrypoint_audit":{"entrypoint_fields":{},"static_file_targets":[],"target_count_truncated":false},"locked_manifest_sha256":"40a698559878bb1e2fff47e73f38830bb010f72ff9f40356a094834c26d4680d","locked_manifest_validation":"match","manifest_path":"lib/python3.11/site-packages/ccp4i2/docs/report_files/0.1.0/jquery-ui-1.10.4.custom/development-bundle/package.json","metadata_object_preserved_in_full":true,"metadata_raw_sha256":"40a698559878bb1e2fff47e73f38830bb010f72ff9f40356a094834c26d4680d","role":"application_or_vendored_manifest","top_level_metadata_fields":["author","bugs","dependencies","description","devDependencies","homepage","keywords","licenses","maintainers","name","repository","scripts","title","version"]},"review_file":"audits/ccp4-10.0.001/full-review/supplemental-packages.json"},{"identity":"js_manifest:javascript/share/jscofe:ccp4cloud:share/jscofe/package.json","disposition":"application_manifest_surface_only","rationale":"The manifest metadata alone is not evidence of a trained model. The bounded application source scan and the separate FitLigand source leads are retained elsewhere in this report.","evidence":{"byte_length":749,"entrypoint_audit":{"entrypoint_fields":{},"static_file_targets":[],"target_count_truncated":false},"locked_manifest_sha256":"63c4e62e4565dd79c12a6b469db19252463a1290d01860dec3fa6e7cbd004703","locked_manifest_validation":"match","manifest_path":"share/jscofe/package.json","metadata_object_preserved_in_full":true,"metadata_raw_sha256":"63c4e62e4565dd79c12a6b469db19252463a1290d01860dec3fa6e7cbd004703","role":"application_or_vendored_manifest","top_level_metadata_fields":["dependencies","name","version"]},"review_file":"audits/ccp4-10.0.001/full-review/supplemental-packages.json"},{"identity":"js_manifest:javascript/share/jscofe:cofe-browser:share/jscofe/cofe-browser/package.json","disposition":"application_manifest_surface_only","rationale":"The manifest metadata alone is not evidence of a trained model. The bounded application source scan and the separate FitLigand source leads are retained elsewhere in this report.","evidence":{"byte_length":672,"entrypoint_audit":{"entrypoint_fields":{"main":"cofe-browser.mjs"},"static_file_targets":[],"target_count_truncated":false},"locked_manifest_sha256":"fd5eb9f33180b1edf838c37116598b392997cd7ca86222c31097079424aed2c6","locked_manifest_validation":"match","manifest_path":"share/jscofe/cofe-browser/package.json","metadata_object_preserved_in_full":true,"metadata_raw_sha256":"fd5eb9f33180b1edf838c37116598b392997cd7ca86222c31097079424aed2c6","role":"application_or_vendored_manifest","top_level_metadata_fields":["author","build","dependencies","description","devDependencies","keywords","license","main","name","productName","scripts","type","version"]},"review_file":"audits/ccp4-10.0.001/full-review/supplemental-packages.json"},{"identity":"js_manifest:javascript/share/jscofe:jquery-ui:share/jscofe/js-lib/jquery-ui/package.json","disposition":"application_manifest_surface_only","rationale":"The manifest metadata alone is not evidence of a trained model. The bounded application source scan and the separate FitLigand source leads are retained elsewhere in this report.","evidence":{"byte_length":2122,"entrypoint_audit":{"entrypoint_fields":{"main":"ui/widget.js"},"static_file_targets":[],"target_count_truncated":false},"locked_manifest_sha256":"02f0804ebb96cdbc18ecdb1fcdc511d96a8f8ec9463bc33b847cd38f50180d06","locked_manifest_validation":"match","manifest_path":"share/jscofe/js-lib/jquery-ui/package.json","metadata_object_preserved_in_full":true,"metadata_raw_sha256":"02f0804ebb96cdbc18ecdb1fcdc511d96a8f8ec9463bc33b847cd38f50180d06","role":"application_or_vendored_manifest","top_level_metadata_fields":["author","bugs","dependencies","description","devDependencies","homepage","keywords","license","main","maintainers","name","repository","scripts","title","version"]},"review_file":"audits/ccp4-10.0.001/full-review/supplemental-packages.json"},{"identity":"js_manifest:javascript/share/mamba/envs/abcfold/lib/python3.11/site-packages:jupyterlab-plotly:share/mamba/envs/abcfold/lib/python3.11/site-packages/plotly/labextension/package.json","disposition":"application_manifest_surface_only","rationale":"The manifest metadata alone is not evidence of a trained model. The bounded application source scan and the separate FitLigand source leads are retained elsewhere in this report.","evidence":{"byte_length":1389,"entrypoint_audit":{"entrypoint_fields":{"main":"lib/mimeExtension.js"},"static_file_targets":[],"target_count_truncated":false},"locked_manifest_sha256":"1d4f2700729136c5ed8fbc4680a701086b74bd8dd00b40996640f1832521125b","locked_manifest_validation":"match","manifest_path":"share/mamba/envs/abcfold/lib/python3.11/site-packages/plotly/labextension/package.json","metadata_object_preserved_in_full":true,"metadata_raw_sha256":"1d4f2700729136c5ed8fbc4680a701086b74bd8dd00b40996640f1832521125b","role":"application_or_vendored_manifest","top_level_metadata_fields":["author","dependencies","description","devDependencies","jupyterlab","license","main","name","repository","scripts","version"]},"review_file":"audits/ccp4-10.0.001/full-review/supplemental-packages.json"},{"identity":"js_manifest:javascript/share/mamba:jupyterlab-plotly:share/mamba/envs/abcfold/share/jupyter/labextensions/jupyterlab-plotly/package.json","disposition":"application_manifest_surface_only","rationale":"The manifest metadata alone is not evidence of a trained model. The bounded application source scan and the separate FitLigand source leads are retained elsewhere in this report.","evidence":{"byte_length":1389,"entrypoint_audit":{"entrypoint_fields":{"main":"lib/mimeExtension.js"},"static_file_targets":[],"target_count_truncated":false},"locked_manifest_sha256":"1d4f2700729136c5ed8fbc4680a701086b74bd8dd00b40996640f1832521125b","locked_manifest_validation":"match","manifest_path":"share/mamba/envs/abcfold/share/jupyter/labextensions/jupyterlab-plotly/package.json","metadata_object_preserved_in_full":true,"metadata_raw_sha256":"1d4f2700729136c5ed8fbc4680a701086b74bd8dd00b40996640f1832521125b","role":"application_or_vendored_manifest","top_level_metadata_fields":["author","dependencies","description","devDependencies","jupyterlab","license","main","name","repository","scripts","version"]},"review_file":"audits/ccp4-10.0.001/full-review/supplemental-packages.json"},{"identity":"npm:javascript/dnatco:canvas:dnatco/bin/node_modules/canvas/package.json","disposition":"no_ml_surface_identified_in_bounded_npm_review","rationale":"No ML, trained-model, ResNet, or diffusion evidence surfaced in this package metadata, declared entrypoint targets, or bounded static source-token review. 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No separate learned model is identified by this package review.","evidence":["lib/python3.11/site-packages/acedrg-0.334.0.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:adding-stats-to-mmcif","disposition":"crystallographic_coordinate_metadata_statistics_utility","rationale":"The package adds statistics to mmCIF metadata; its 14-file installed source group and declared dependencies were reviewed, with no trained-model path or weights found.","evidence":["installed metadata lib/python3.11/site-packages/adding_stats_to_mmcif-0.5-py3.11.egg-info/PKG-INFO sha256=a1b926155432b22c8b8a691217b55067602014f525e87104eb0b1e941072a691 bytes=332 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/adding_stats_to_mmcif-0.5-py3.11.egg-info/SOURCES.txt rows=80; sample=[\".coveragerc\", \".gitattributes\", \".gitignore\", \".travis.yml\"]","top_level lib/python3.11/site-packages/adding_stats_to_mmcif-0.5-py3.11.egg-info/top_level.txt=[\"adding_stats_to_mmcif\"]","static Python audit group package=adding_stats_to_mmcif env=core: 14 files, 61067 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:alembic","disposition":"database migration framework; no crystallographic ML path found","rationale":"database schema migrations and environment support; no model artifact or CCP4 scientific inference path identified","evidence":["lib/python3.11/site-packages/alembic-1.15.2.dist-info/METADATA:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/alembic-1.15.2.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"SQLAlchemy>=1.4.0\", \"Mako\", \"typing-extensions>=4.12\", \"tzdata; extra == \\\"tz\\\"\"]; ownership={\"entry_points.txt\": \"[console_scripts]\\nalembic = alembic.config:main\\n\", \"record_file_count\": 152, \"top_level.txt\": \"alembic\\n\"}","audits/ccp4-10.0.001/python.json AST group package=alembic root=lib/python3.11/site-packages files=65 hit_files=3 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:antlr4-python3-runtime","disposition":"parser runtime","rationale":"ANTLR parser runtime; no fitted model evidence.","evidence":["installed metadata: lib/python3.11/site-packages/antlr4_python3_runtime-4.9.3-py3.11.egg-info/PKG-INFO; SHA-256=bf325e5155318385a2fcc4680742da710bbadf13a3d1c0979a98b3487980f261; Name=antlr4-python3-runtime; Version=4.9.3; Summary=ANTLR 4.9.3 runtime for Python 3.7","declared Requires-Dist (1): [\"typing; python_version < \\\"3.5\\\"\"]","ownership: top_level metadata path candidate=lib/python3.11/site-packages/antlr4_python3_runtime-4.9.3-py3.11.egg-info/top_level.txt; top_level=[\"antlr4\"]; RECORD rows=0; RECORD sample=[]; empty top_level list means no import-root claim from that metadata file","static source scan: 0 files, 0 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:antlr4-python3-runtime; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:ascii-graph","disposition":"utility / text graph rendering","rationale":"Installed ASCII graph formatter. No model or fitting source surfaced in this distribution scan. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/ascii_graph-1.5.1-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/ascii_graph-1.5.1-py3.11.egg-info/PKG-INFO: installed metadata ['Name: ascii_graph', 'Version: 1.5.1']","metadata-owned top_level/RECORD roots: top_level=['ascii_graph']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/ascii_graph']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:asgiref","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: ASGI protocol and async/web framework support. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/asgiref-3.6.0-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/asgiref-3.6.0-py3.11.egg-info/PKG-INFO: Name: asgiref","lib/python3.11/site-packages/asgiref-3.6.0-py3.11.egg-info/PKG-INFO: Version: 3.6.0","lib/python3.11/site-packages/asgiref-3.6.0-py3.11.egg-info/PKG-INFO: Summary: ASGI specs, helper code, and adapters"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:bcrypt","disposition":"general runtime/development infrastructure","rationale":"Password hashing implementation package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/bcrypt-3.1.7-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/bcrypt-3.1.7-py3.11.egg-info/PKG-INFO; sha256=de9a9aa54ee034ae5600cfb5838c5bdfde398c809631fe048c5a5e8cf6fa8fe3; record exists=True","top_level.txt roots (metadata-derived): _bcrypt, bcrypt","metadata-derived source roots ['lib/python3.11/site-packages/bcrypt']; bounded scan files=2, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:beniget","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["lib/python3.11/site-packages/beniget-0.4.1-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/beniget-0.4.1-py3.11.egg-info/PKG-INFO; metadata SHA-256 b7d21c91e2280ba6816b514bab2a07dd2460f93f36b36f94b3edafb624ca6cda","top_level.txt roots=['beniget']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 2 Python files / 34816 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:beniget; environment=core; version=0.4.1"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:biopython","disposition":"scientific-biology-toolkit-with-legacy-classifier-algorithms","rationale":"The installed biology toolkit includes legacy NaiveBayes, kNN, logistic-regression and maximum-entropy classifier/train APIs in Bio.*. This is algorithm capability, not evidence of an application consumer or a fitted model in this shard.","evidence":["lib/python3.11/site-packages/biopython-1.80-py3.11.egg-info/PKG-INFO; Name: biopython | Version: 1.80 | Summary: Freely available tools for computational molecular biology.","owner: top_level=['Bio', 'BioSQL']; source_roots_from_METADATA_or_RECORD=['Bio', 'BioSQL']; RECORD_rows=not provided; RECORD_sample=[]","declared dependencies: Requires-Dist: numpy","lib/python3.11/site-packages/Bio/NaiveBayes.py:14 is hardly ever true, the classifier works well enough in practice.","lib/python3.11/site-packages/Bio/NaiveBayes.py:21  - NaiveBayes - Holds information for a naive Bayes classifier.","lib/python3.11/site-packages/Bio/NaiveBayes.py:24  - train     - Train a new naive Bayes classifier.","lib/python3.11/site-packages/Bio/pairwise2.py:984         # Attention: This may fail, if the gap-penalties for both strands are","lib/python3.11/site-packages/Bio/kNN.py:18  - kNN           Holds information for a nearest neighbors classifier.","lib/python3.11/site-packages/Bio/kNN.py:22  - train        Train a new kNN classifier.","lib/python3.11/site-packages/Bio/kNN.py:59     \"\"\"Train a k nearest neighbors classifier on a training set.","lib/python3.11/site-packages/Bio/bgzf.py:130 attention to the file offsets which will be explained below:","lib/python3.11/site-packages/Bio/LogisticRegression.py:11  - LogisticRegression    Holds information for a LogisticRegression classifier.","lib/python3.11/site-packages/Bio/LogisticRegression.py:14  - train        Train a new classifier.","lib/python3.11/site-packages/Bio/LogisticRegression.py:28      - beta - List of the weights for each dimension.","lib/python3.11/site-packages/Bio/MaxEntropy.py:26     \"\"\"Hold information for a Maximum Entropy classifier.","lib/python3.11/site-packages/Bio/MaxEntropy.py:30     alphas       List of the weights for each feature.","lib/python3.11/site-packages/Bio/MaxEntropy.py:33     Car data from example Naive Bayes Classifier example by Eric Meisner November 22, 2003","lib/python3.11/site-packages/Bio/SeqRecord.py:52     pickled, for example for use in the multiprocessing library, we need to","lib/python3.11/site-packages/Bio/SeqRecord.py:53     be able to pickle the restricted dictionary objects.","lib/python3.11/site-packages/Bio/SeqRecord.py:57     >>> import pickle","lib/python3.11/site-packages/Bio/Data/IUPACData.py:170 unambiguous_dna_weights = {\"A\": 331.2218, \"C\": 307.1971, \"G\": 347.2212, \"T\": 322.2085}","lib/python3.11/site-packages/Bio/Data/IUPACData.py:173 monoisotopic_unambiguous_dna_weights = {","lib/python3.11/site-packages/Bio/Data/IUPACData.py:180 unambiguous_dna_weight_ranges = _make_ranges(unambiguous_dna_weights)","lib/python3.11/site-packages/Bio/AlignIO/MsfIO.py:158         weights = []","lib/python3.11/site-packages/Bio/AlignIO/MsfIO.py:180                     weights.append(float(weight.strip()))","lib/python3.11/site-packages/Bio/AlignIO/MsfIO.py:318             for (i, s, w) in zip(ids, seqs, weights)","lib/python3.11/site-packages/Bio/SearchIO/_model/hit.py:130             # This makes it easier to work with file formats with unpredictable"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:bokeh","disposition":"plotting-and-web-visualization-library","rationale":"Bokeh provides visualization support and owns sample plot data in the assigned archive set; package presence is not a CCP4 learned-model consumer.","evidence":["lib/python3.11/site-packages/bokeh-2.4.3-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:calver","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/calver-2022.6.26.dist-info/METADATA sha256=91c81e901207e36519cb898cf6e14fe2a9ac2e273e87e22e070a0cb06b5c99b7 bytes=2260 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/calver-2022.6.26.dist-info/RECORD rows=13; sample=[\"calver-2022.6.26.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"calver-2022.6.26.dist-info/METADATA,sha256=kcgekBIH42UZy4mM9uFP4qmsLic-h-IuBwoMsGtcmbc,2260\", \"calver-2022.6.26.dist-info/RECORD,,\", \"calver-2022.6.26.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0\"]","top_level lib/python3.11/site-packages/calver-2022.6.26.dist-info/top_level.txt=[\"calver\"]","static Python audit group package=calver env=core: 2 files, 1058 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:ccp4mg","disposition":"molecular graphics and user-interface package; no inference backend identified","rationale":"CCP4MG color/download code references AlphaFold database metadata but does not implement AlphaFold inference","evidence":["lib/python3.11/site-packages/ccp4mg-2.11.0-py3.11.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/ccp4mg-2.11.0-py3.11.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"SOURCES.txt\": \"AUTHORS\\nCOPYING\\nCOPYING.GPL\\nsetup.py\\n./ArrayToB64.py\\n./COPYING\\n./__init__.py\\n./atom_util.py\\n./ccp4mg_icon.png\\n./ccp4srs.py\\n./cprim.py\\n./crash_handler.py\\n./enm_util.py\\n./field.py\\n./glShaders.py\\n./headers.py\\n./hklfile.py\\n./hydrophobicity_util.py\\n./image_info.py\\n./mapview.py\\n./mgapp.py\\n./mginterrupt.py\\n./mmdb2.py\\n./mmut.py\\n./opengl.py\\n./paramsmanager.py\\n./pixieInterface.py\\n./point_funcs.py\\n./prosmart_util.py\\n./psutil.py\\n./pygl_coord.py\\n./redirect.py\\n./sequence_util.py\\n./setup-standalone.py\\n./splash.png\\n./streams.py\\n./surface.py\\n./svgPrimitive.py\\n./symmetry.py\\n./uddBFactorSize.py\\n./xmapview.py\\n./WebGL/CIsoSurface.js\\n./WebGL/MNUI.js\\n./WebGL/TODO.txt\\n./WebGL/ascene.scene.xml\\n./WebGL/ascene2.scene.xml\\n./WebGL/calculateSurface.js\\n./WebGL/canvas2D-map-webworker-big.html\\n./WebGL/canvas2D-map.html\\n./WebGL/client-only-5a3h.html\\n./WebGL/client-only.html\\n./WebGL/contacts.scene.xml\\n./WebGL/edtsurf.js\\n./WebGL/ener_lib.js\\n./WebGL/fog.html\\n./WebGL/fogandclip.js\\n./WebGL/fontHeight.js\\n./WebGL/get_monomer.html\\n./WebGL/glMatrix.js\\n./WebGL/icon.ico\\n./WebGL/icosa_sphere.js\\n./WebGL/jquery-1.11.0.min.js\\n./WebGL/jquery-1.11.0.min.map\\n./WebGL/jquery-3.3.1.min.js\\n./WebGL/jquery-ui.css\\n./WebGL/js-pimple-simple.html\\n./WebGL/js-pimple.html\\n./WebGL/jscolor.js\\n./WebGL/jspimple.css\\n./WebGL/jspimple.js\\n./WebGL/lines-fragment-shader.glsl\\n./WebGL/lines-fragment-shader.js\\n./WebGL/lines-vertex-shader.glsl\\n./WebGL/lines-vertex-shader.js\\n./WebGL/load_scene.html\\n./WebGL/mgBase64.js\\n./WebGL/mgMaths.js\\n./WebGL/mgMiniMol\", \"top_level.txt\": \"ccp4mg\\n\"}","audits/ccp4-10.0.001/python.json AST group package=ccp4mg root=lib/python3.11/site-packages files=356 hit_files=25 imports={}","lib/python3.11/site-packages/ccp4mg/mgapp.py:252,319; python/ui/model_colour.py; AlphaFold DB color/download references"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:certifi","disposition":"certificate trust store","rationale":"CA certificate bundle provider; no scientific/model code.","evidence":["installed metadata: lib/python3.11/site-packages/certifi-2026.1.4.dist-info/METADATA; SHA-256=1527c911f2ae328e9b265a1f52bb51a67e0f15362d6d8c97a4737f037645a486; Name=certifi; Version=2026.1.4; Summary=Python package for providing Mozilla's CA Bundle.","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=lib/python3.11/site-packages/certifi-2026.1.4.dist-info/top_level.txt; top_level=[\"certifi\"]; RECORD rows=13; RECORD sample=[\"certifi-2026.1.4.dist-info/INSTALLER\", \"certifi-2026.1.4.dist-info/METADATA\", \"certifi-2026.1.4.dist-info/RECORD\", \"certifi-2026.1.4.dist-info/REQUESTED\", \"certifi-2026.1.4.dist-info/WHEEL\", \"certifi-2026.1.4.dist-info/direct_url.json\", \"certifi-2026.1.4.dist-info/licenses/LICENSE\", \"certifi-2026.1.4.dist-info/top_level.txt\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 3 files, 3731 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:certifi; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:cffi","disposition":"native binding infrastructure","rationale":"Python-to-C foreign-function interface; not a model implementation. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/cffi-1.14.6-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/cffi-1.14.6-py3.11.egg-info/PKG-INFO: installed metadata ['Name: cffi', 'Version: 1.14.6', 'Requires-Dist: pycparser']","metadata-owned top_level/RECORD roots: top_level=['_cffi_backend', 'cffi']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/cffi']","Installed source scan examples: lib/python3.11/site-packages/cffi/api.py:832 backendlib = _load_backend_lib(backend, libname, flags); lib/python3.11/site-packages/cffi/api.py:838 value = backendlib.load_function(BType, name); lib/python3.11/site-packages/cffi/api.py:845 read_variable = backendlib.read_variable; lib/python3.11/site-packages/cffi/api.py:846 write_variable = backendlib.write_variable"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:chardet","disposition":"statistical text heuristic","rationale":"Installed package role from metadata and static implementation review: heuristic charset detector with frequency tables; statistical language profiles, not a neural model runtime. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/chardet-3.0.4-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/chardet-3.0.4-py3.11.egg-info/PKG-INFO: Name: chardet","lib/python3.11/site-packages/chardet-3.0.4-py3.11.egg-info/PKG-INFO: Version: 3.0.4","lib/python3.11/site-packages/chardet-3.0.4-py3.11.egg-info/PKG-INFO: Summary: Universal encoding detector for Python 2 and 3","lib/python3.11/site-packages/chardet/sbcsgroupprober.py:31: from .langcyrillicmodel import (Win1251CyrillicModel, Koi8rModel,","lib/python3.11/site-packages/chardet/sbcsgroupprober.py:32: Latin5CyrillicModel, MacCyrillicModel,","lib/python3.11/site-packages/chardet/sbcsgroupprober.py:33: Ibm866Model, Ibm855Model)","lib/python3.11/site-packages/chardet/sbcsgroupprober.py:34: from .langgreekmodel import Latin7GreekModel, Win1253GreekModel","lib/python3.11/site-packages/chardet/sbcsgroupprober.py:35: from .langbulgarianmodel import Latin5BulgarianModel, Win1251BulgarianModel"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:charset-normalizer","disposition":"general runtime/development infrastructure","rationale":"Text encoding detection package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/charset_normalizer-2.0.7-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/charset_normalizer-2.0.7-py3.11.egg-info/PKG-INFO; sha256=b863ba405ea1ef09175c25b66bd179a0964efd59e47723167cbd20d74097a9e6; record exists=True","top_level.txt roots (metadata-derived): charset_normalizer","metadata-derived source roots ['lib/python3.11/site-packages/charset_normalizer']; bounded scan files=12, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:checkmysequence","disposition":"shipped neural sequence-model consumer","rationale":"Its CLI constructs FMSLib model2sequence for sequence prediction; the actual engine is supplied by the sibling FMSLib package.","evidence":["lib/python3.11/site-packages/checkmysequence-1.5.2-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/checkmysequence-1.5.2-py3.11.egg-info/PKG-INFO; metadata SHA-256 67309fb652bf7c4c87dfdf65f03b528bce7290359f06e38269221979c4ad9bf9","top_level.txt roots=['checkmysequence']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 3 Python files / 66588 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:checkmysequence; environment=core; version=1.5.2","lib/python3.11/site-packages/checkmysequence/__main__.py:242-245"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:colorlog","disposition":"logging-utility","rationale":"Installed colorlog 4.1.0 in core is logging-utility; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["lib/python3.11/site-packages/colorlog-4.1.0-py3.11.egg-info/PKG-INFO; Name: colorlog | Version: 4.1.0 | Summary: Log formatting with colors!","owner: top_level=['colorlog']; source_roots_from_METADATA_or_RECORD=['colorlog']; RECORD_rows=not provided; RECORD_sample=[]","declared dependencies: Requires-Dist: colorama; sys_platform == \"win32\""],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:conkit","disposition":"classical-ML-consumer-with-shipped-SVC-and-scaler","rationale":"ConKit model validation statically loads shipped joblib assets and applies SVC predict_proba to scaled residue/contact-map features. The package metadata requires scikit-learn <=0.24.2, while same-core metadata identifies 1.4.2; therefore artifact compatibility and successful execution remain unresolved.","evidence":["lib/python3.11/site-packages/conkit-0.13.2-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:contourpy","disposition":"graphics_or_visualization_infrastructure","rationale":"Installed graphics/font/contour infrastructure; static source review found no shipped trained model consumer in the distribution.","evidence":["installed metadata lib/python3.11/site-packages/contourpy-1.0.7.dist-info/METADATA sha256=30deb9d9ef48b681fc81575aedebbd5feaebb04133b448829b70e77bc05a64bd bytes=3818 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/contourpy-1.0.7.dist-info/RECORD rows=32; sample=[\"contourpy-1.0.7.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"contourpy-1.0.7.dist-info/METADATA,sha256=MN652e9ItoH8gVda7eu9X-rrsEEztEiCm3Dne8BaZL0,3818\", \"contourpy-1.0.7.dist-info/RECORD,,\", \"contourpy-1.0.7.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0\"]","top_level lib/python3.11/site-packages/contourpy-1.0.7.dist-info/top_level.txt=[\"contourpy\"]","static Python audit group package=contourpy env=core: 11 files, 63328 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:coot-headless-api","disposition":"headless Coot application API and structure-building helpers","rationale":"installed ownership includes coot_headless_api and rcrane trees; native Coot science remains in application libraries; this package is API/build glue, not itself a trained model","evidence":["lib/python3.11/site-packages/coot_headless_api-1.3.3-py3.11.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/coot_headless_api-1.3.3-py3.11.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"SOURCES.txt\": \".clang-format\\nABOUT-NLS\\nAUTHORS\\nBUGS\\nCMakeLists-gemmi.txt\\nCMakeLists.txt\\nCOPYING\\nCOPYING.LESSERv3\\nChangeLog\\nCoot-style-guide\\nDONE\\nGemfile\\nINSTALL\\nMakefile.am\\nNEWS\\nREADME\\nREADME.md\\nRELEASE-NOTES\\nTODO\\n_config.yml\\nacconfig.h\\nautogen-mac.sh\\nautogen.sh\\nbldnotes\\nbldnotes-2008\\nbldnotes-2009\\nbuild-it\\nbuild-it-3-3\\nbuild-it-gtk3\\nbuild-it-win\\nbuild-python.sh\\ncod-types-db-normalized.bin\\ncompare_versions.sh\\nconfig.guess\\nconfig.sub\\nconfigure.ac\\ncoot-gtk2-try2.glade\\ncoot-gtk2.glade\\ncoot-gtk4-converted.ui\\ncoot.appdata.xml\\ncoot.desktop\\ncootrc.template\\ncopyright-disclaimer.txt\\ncount-loc\\ncycle-page-builder.scm\\ndepcomp\\ndnotes\\ndnotes-2008\\nfind-==-assignments.sh\\nfind-duplicates.sh\\nfind-in-code.sh\\nfix-cif-loops.awk\\nfix-fsf-address.sh\\nfunction-notes\\ngenerate-git-revision-count-cc.sh\\ngenerate-svn-revision-cc.sh\\nget-the-git-commit-count.sh\\nget-the-git-commit.sh\\nhappy-coot-diary.html\\nifdef-for-create-aboutdialog.awk\\ninstall-sh\\nintltool-extract.in\\nintltool-merge.in\\nintltool-update.in\\nltmain.sh-unneeded\\nmake-patches\\nmake-scheme-tar\\nmapview.glade\\nmissing\\nmkinstalldirs\\nmmdb-graph-matching-for-gemmi.md\\nmmdb-selection-doc\\nporting-to-gtk4\\nprocess-greg-log.awk\\nrel-todo\\nrel-todo-0.6\\nrel-todo-gtk4\\nset-git-prompt\\nsetup-flycheck-gtk4-macos.el\\nsetup-flycheck-gtk4.el\\nsetup-greg\\nsetup.py\\nstandard-residues.pdb\\ntest-with-greg.scm\\ntest7.cmb\\nvalgrind-python.supp\\n.github/workflows/build-coot-macos.yml-aside\\n.github/workflows/build-coot-ubuntu.yml-disabled\\n.github/workflows/build-coot-windows.yml-disabled\\n.github/workflows\", \"top_level.txt\": \"coot_headless_api\\nrcrane\\n\"}","coot_headless_api-1.3.3 installed egg-info top-level/RECORD ownership; coot_headless_api and rcrane source roots"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:cryptography","disposition":"cryptographic primitives","rationale":"Cryptographic primitives and recipes; no ML model evidence in package-local scan.","evidence":["installed metadata: lib/python3.11/site-packages/cryptography-2.8-py3.11.egg-info/PKG-INFO; SHA-256=e95de153c9d3cb084feb537552559f4ebbfd34052146230aa9309a3386e8f4ca; Name=cryptography; Version=2.8; Summary=cryptography is a package which provides cryptographic recipes and primitives to Python developers.","declared Requires-Dist (19): [\"six>=1.4.1\",\"cffi!=1.11.3,>=1.8\",\"enum34; python_version < \\\"3\\\"\",\"ipaddress; python_version < \\\"3\\\"\",\"pytest!=3.9.0,!=3.9.1,!=3.9.2,>=3.6.0; extra == \\\"test\\\"\",\"pretend; extra == \\\"test\\\"\",\"iso8601; extra == \\\"test\\\"\",\"pytz; extra == \\\"test\\\"\",\"hypothesis!=3.79.2,>=1.11.4; extra == \\\"test\\\"\",\"sphinx!=1.8.0,>=1.6.5; 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no fixed trained model or CCP4 consumer was established in this review. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/csb-1.2.5-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/csb-1.2.5-py3.11.egg-info/PKG-INFO: installed metadata ['Name: csb', 'Version: 1.2.5', 'Requires-Dist: numpy', 'Requires-Dist: scipy', 'Requires-Dist: matplotlib']","metadata-owned top_level/RECORD roots: top_level=['csb']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/csb']","lib/python3.11/site-packages/csb/statistics/mixtures.py:11-14,24,193-211,330-370 (Gaussian mixtures, parameter estimation and BIC selection)","lib/python3.11/site-packages/csb/bio/hmm/__init__.py:1-7,42-49 (profile-HMM APIs)"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:cycler","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: small style-cycle utility. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/cycler-0.10.0-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/cycler-0.10.0-py3.11.egg-info/PKG-INFO: Name: cycler","lib/python3.11/site-packages/cycler-0.10.0-py3.11.egg-info/PKG-INFO: Version: 0.10.0","lib/python3.11/site-packages/cycler-0.10.0-py3.11.egg-info/PKG-INFO: Summary: Composable style cycles"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:cython","disposition":"installed Python support package; ML role not established","rationale":"Installed Python distribution; inspected metadata, declared dependencies, ownership/top-level roots, and bounded text-only package source search. No trained model or in-tree scientific ML caller was established for this package in the reviewed evidence.","evidence":["lib/python3.11/site-packages/Cython-3.0.8-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/Cython-3.0.8-py3.11.egg-info/PKG-INFO; sha256=da54a0e33ebd5676edac8b39353f5d7ba497d745b50c15e5150f2e96ccaa31f0; record exists=True","top_level.txt roots (metadata-derived): Cython, cython, pyximport","metadata-derived source roots ['lib/python3.11/site-packages/Cython', 'lib/python3.11/site-packages/pyximport']; bounded scan files=293, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:dials","disposition":"classical unsupervised/statistical ML and scientific analytics package","rationale":"Static review found OPTICS clustering and silhouette scoring in correlation analysis and PCA plus nearest-neighbor features in cosym. 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Its clustering/graph methods are classical graph analysis; no trained model weights or supervised inference path were found in the installed source scan.","evidence":["installed metadata lib/python3.11/site-packages/igraph-0.9.10-py3.11.egg-info/PKG-INFO sha256=98783d17fdf4d5f745fe0e27dd74631e8fc963c306845cfbd008d9af75e27598 bytes=3148 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/igraph-0.9.10-py3.11.egg-info/SOURCES.txt rows=2185; sample=[\"LICENSE\", \"MANIFEST.in\", \"README.md\", \"setup.cfg\"]","top_level lib/python3.11/site-packages/igraph-0.9.10-py3.11.egg-info/top_level.txt=[\"igraph\"]","static Python audit group package=igraph env=core: 29 files, 727877 bytes, 2 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/igraph/drawing/utils.py sha256=a4e1404266fab7a87455b7de2b14f04ac0c9065c33299e3537adefc127123330"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:imageio","disposition":"image input/output plugin framework","rationale":"installed implementation is an image I/O library; source mention of Kohonen maps is documentation/example material, not an implemented shipped model","evidence":["lib/python3.11/site-packages/imageio-2.34.2-py3.11.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/imageio-2.34.2-py3.11.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"numpy\", \"pillow>=8.3.2\", \"wheel; extra == \\\"build\\\"\", \"black; extra == \\\"linting\\\"\", \"flake8; extra == \\\"linting\\\"\", \"pytest; extra == \\\"test\\\"\", \"pytest-cov; extra == \\\"test\\\"\", \"fsspec[github]; extra == \\\"test\\\"\", \"sphinx<6; extra == \\\"docs\\\"\", \"numpydoc; extra == \\\"docs\\\"\", \"pydata-sphinx-theme; extra == \\\"docs\\\"\", \"imageio-ffmpeg; extra == \\\"ffmpeg\\\"\", \"psutil; extra == \\\"ffmpeg\\\"\", \"tifffile; extra == \\\"tifffile\\\"\", \"av; extra == \\\"pyav\\\"\", \"pillow-heif; extra == \\\"pillow-heif\\\"\", \"astropy; extra == \\\"fits\\\"\", \"gdal; extra == \\\"gdal\\\"\", \"itk; extra == \\\"itk\\\"\", \"astropy; extra == \\\"full\\\"\", \"av; extra == \\\"full\\\"\", \"black; extra == \\\"full\\\"\", \"flake8; extra == \\\"full\\\"\", \"fsspec[github]; extra == \\\"full\\\"\", \"gdal; extra == \\\"full\\\"\", \"imageio-ffmpeg; extra == \\\"full\\\"\", \"itk; extra == \\\"full\\\"\", \"numpydoc; extra == \\\"full\\\"\", \"pillow-heif; extra == \\\"full\\\"\", \"psutil; extra == \\\"full\\\"\", \"pydata-sphinx-theme; extra == \\\"full\\\"\", \"pytest; extra == \\\"full\\\"\", \"pytest-cov; extra == \\\"full\\\"\", \"sphinx<6; extra == \\\"full\\\"\", \"tifffile; extra == \\\"full\\\"\", \"wheel; extra == \\\"full\\\"\", \"pytest; extra == \\\"dev\\\"\", \"pytest-cov; extra == \\\"dev\\\"\", \"fsspec[github]; extra == \\\"dev\\\"\", \"black; extra == \\\"dev\\\"\", \"flake8; extra == \\\"dev\\\"\", \"astropy; extra == \\\"all-plugins\\\"\", \"av; extra == \\\"all-plugins\\\"\", \"imageio-ffmpeg; extra == \\\"all-plugins\\\"\", \"pillow-heif; extra == \\\"all-plugins\\\"\", \"psutil; extra == \\\"all-plugins\\\"\", \"tifffile; extra == \\\"all-plugins\\\"\", \"av; extra == \\\"all-plugins-pypy\\\"\", \"imageio-ffmpeg; extra == \\\"all-plugins-pypy\\\"\", \"pillow-heif; extra == \\\"all-plugins-pypy\\\"\", \"psutil; extra == \\\"all-plugins-pypy\\\"\", \"tifffile; extra == \\\"all-plugins-pypy\\\"\"]; ownership={\"SOURCES.txt\": \"CONTRIBUTORS.txt\\nLICENSE\\nMANIFEST.in\\nREADME.md\\nsetup.cfg\\nsetup.py\\ndocs/Makefile\\ndocs/conf.py\\ndocs/examples.rst\\ndocs/imageio_ext.py\\ndocs/index.rst\\ndocs/make.bat\\ndocs/_static/imageio_logo.png\\ndocs/_templates/better_class.rst\\ndocs/_templates/formats.rst.template\\ndocs/_templates/plugin.rst\\ndocs/development/index.rst\\ndocs/development/plugins.rst\\ndocs/formats/formats_by_plugin.rst\\ndocs/formats/index.rst\\ndocs/formats/video_formats.rst\\ndocs/reference/core_v3.rst\\ndocs/reference/index.rst\\ndocs/reference/userapi.rst\\ndocs/user_guide/cmdlinescripts.rst\\ndocs/user_guide/drop27.rst\\ndocs/user_guide/envvariables.rst\\ndocs/user_guide/freezing.rst\\ndocs/user_guide/index.rst\\ndocs/user_guide/installation.rst\\ndocs/user_guide/overview.rst\\ndocs/user_guide/requests.rst\\ndocs/user_guide/scipy.rst\\ndocs/user_guide/standardimages.rst\\nimageio/__init__.py\\nimageio/__main__.py\\nimageio/freeze.py\\nimageio/py.typed\\nimageio/testing.py\\nimageio/typing.py\\nimageio/v2.py\\nimageio/v2.pyi\\nimageio/v3.py\\nimageio/v3.pyi\\nimageio.egg-info/PKG-INFO\\nimageio.egg-info/SOURCES.txt\\nimageio.egg-info/dependency_links.txt\\nimageio.egg-info/entry_points.txt\\nimageio.egg-info/not-zip-safe\\nimageio.egg-info/requires.txt\\nimageio.egg-info/top_level.txt\\nimageio/config/__init__.py\\nimageio/config/extensions.py\\nimageio/config/extensions.pyi\\nimageio/config/plugins.py\\nimageio/config/plugins.pyi\\nimageio/core/__init__.py\\nimageio/core/fetching.py\\nimageio/core/findlib.py\\nimageio/core/format.py\\nimageio/core/format.pyi\\nimageio/core/imopen.py\\nimageio/core/imo\", \"entry_points.txt\": \"[console_scripts]\\nimageio_download_bin = imageio.__main__:download_bin_main\\nimageio_remove_bin = imageio.__main__:remove_bin_main\\n\", \"top_level.txt\": \"imageio\\n\"}","audits/ccp4-10.0.001/python.json AST group package=imageio root=lib/python3.11/site-packages files=48 hit_files=5 imports={}","Installed imageio plugin source and distribution metadata; Kohonen mention is a documentation/example match rather than an executable model implementation."],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:import-serial","disposition":"serial diffraction import utility","rationale":"Serial macromolecular diffraction data import utility.","evidence":["installed metadata: lib/python3.11/site-packages/import_serial-0.8-py3.11.egg-info/PKG-INFO; SHA-256=5ceb69d5fe3790ef4d6396ce9256798ca2b04533ca62a301403146955eead98c; Name=import_serial; Version=0.8; Summary=Import diffractio data from serial macromolecular crystallography","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=lib/python3.11/site-packages/import_serial-0.8-py3.11.egg-info/top_level.txt; top_level=[\"import_serial\"]; RECORD rows=0; RECORD sample=[]; empty top_level list means no import-root claim from that metadata file","static source scan: 0 files, 0 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:import-serial; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:importlib-resources","disposition":"Python resource-access compatibility library","rationale":"Resource reader/adapter utilities; no ML role identified. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/importlib_resources-6.3.2.dist-info/METADATA:L2","lib/python3.11/site-packages/importlib_resources-6.3.2.dist-info/METADATA: installed metadata ['Name: importlib_resources', 'Version: 6.3.2', 'Requires-Dist: zipp>=3.1.0; python_version < \"3.10\"', 'Requires-Dist: pytest>=6; extra == \"testing\"', 'Requires-Dist: pytest-checkdocs>=2.4; extra == \"testing\"', 'Requires-Dist: pytest-cov; extra == \"testing\"', 'Requires-Dist: pytest-mypy; platform_python_implementation != \"PyPy\" and extra == \"testing\"', 'Requires-Dist: pytest-enabler>=2.2; extra == \"testing\"', 'Requires-Dist: pytest-ruff>=0.2.1; extra == \"testing\"', 'Requires-Dist: zipp>=3.17; extra == \"testing\"', 'Requires-Dist: jaraco.collections; extra == \"testing\"', 'Requires-Dist: sphinx>=3.5; extra == \"docs\"', 'Requires-Dist: sphinx<7.2.5; extra == \"docs\"', 'Requires-Dist: jaraco.packaging>=9.3; extra == \"docs\"', 'Requires-Dist: rst.linker>=1.9; extra == \"docs\"', 'Requires-Dist: furo; extra == \"docs\"', 'Requires-Dist: sphinx-lint; extra == \"docs\"', 'Requires-Dist: jaraco.tidelift>=1.4; extra == \"docs\"']","metadata-owned top_level/RECORD roots: top_level=['importlib_resources']; RECORD roots=['importlib_resources']; RECORD rows=86; resolved roots=['lib/python3.11/site-packages/importlib_resources']","Installed source scan examples: lib/python3.11/site-packages/importlib_resources/future/adapters.py:59 over stdlib readers."],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:iniconfig","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: test/configuration parser. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/iniconfig-1.1.1-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/iniconfig-1.1.1-py3.11.egg-info/PKG-INFO: Name: iniconfig","lib/python3.11/site-packages/iniconfig-1.1.1-py3.11.egg-info/PKG-INFO: Version: 1.1.1","lib/python3.11/site-packages/iniconfig-1.1.1-py3.11.egg-info/PKG-INFO: Summary: iniconfig: brain-dead simple config-ini parsing"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:iris-validation","disposition":"protein structural-validation package; not an ML model package","rationale":"Protein-structure validation UI; “model” refers to structural models. Inspected package roots did not establish an ML estimator or trained model.","evidence":["lib/python3.11/site-packages/iris_validation-0.3.3.dist-info/METADATA:L2","cpu64 installed record lib/python3.11/site-packages/iris_validation-0.3.3.dist-info/METADATA; sha256=0a5eb3ab915ca69854a17cdb60667bf7c0435aebce943d0ccaef33faa7bbad7a; record exists=True","top_level.txt roots (metadata-derived): iris_validation","metadata-derived source roots ['lib/python3.11/site-packages/iris_validation']; bounded scan files=9, truncated=True","lib/python3.11/site-packages/iris_validation/__init__.py:4 describes interactive validation of 3D protein models; :31 exposes metrics_model_series_from_files."],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:jinja2","disposition":"template engine","rationale":"Source review supports template rendering and AST optimizer/visitor utilities, not ML inference.","evidence":["lib/python3.11/site-packages/Jinja2-3.1.4.dist-info/METADATA:L2","lib/python3.11/site-packages/Jinja2-3.1.4.dist-info/METADATA; metadata SHA-256 47f6ebce93d0541be919cb26f966ebb60a2d3bbb2e4350f417eaa4853cde11f6","top_level.txt roots=[]; RECORD=lib/python3.11/site-packages/Jinja2-3.1.4.dist-info/RECORD; RECORD existing=34/59","read-only source scan: 25 Python files / 484629 bytes; 2 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:jinja2; environment=core; version=3.1.4","bounded hit review: 2 hit files were parser/build/test/support contexts; no scientific model consumer identified"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:joblib","disposition":"parallelism-and-python-object-serialization-infrastructure","rationale":"Joblib provides parallel execution and pickle-based persistence used by scikit-learn; bundled joblib pickle files in this shard are test fixtures. Package capability does not make every serialized payload a model.","evidence":["lib/python3.11/site-packages/joblib-1.3.2-py3.11.egg-info/PKG-INFO; Name: joblib | Version: 1.3.2 | Summary: Lightweight pipelining with Python functions","owner: top_level=['joblib']; source_roots_from_METADATA_or_RECORD=['joblib']; RECORD_rows=not provided; RECORD_sample=[]","lib/python3.11/site-packages/joblib/_dask.py:136 def _joblib_probe_task():","lib/python3.11/site-packages/joblib/_dask.py:137     # Noop used by the joblib connector to probe when workers are ready.","lib/python3.11/site-packages/joblib/_dask.py:153             msg = (\"You are trying to use 'dask' as a joblib parallel backend \"","lib/python3.11/site-packages/joblib/numpy_pickle.py:7 import pickle","lib/python3.11/site-packages/joblib/numpy_pickle.py:18 from .numpy_pickle_utils import Unpickler, Pickler","lib/python3.11/site-packages/joblib/numpy_pickle.py:19 from .numpy_pickle_utils import _read_fileobject, _write_fileobject","lib/python3.11/site-packages/joblib/_store_backends.py:3 from pickle import PicklingError","lib/python3.11/site-packages/joblib/_store_backends.py:18 from . import numpy_pickle","lib/python3.11/site-packages/joblib/_store_backends.py:176                 item = numpy_pickle.load(f)","lib/python3.11/site-packages/joblib/backports.py:2 Backports of fixes for joblib dependencies","lib/python3.11/site-packages/joblib/backports.py:145             \"'joblib.backports.make_memmap' should not be used \"","lib/python3.11/site-packages/joblib/backports.py:150     # https://github.com/joblib/joblib/issues/540","lib/python3.11/site-packages/joblib/compressor.py:5 from joblib.backports import LooseVersion","lib/python3.11/site-packages/joblib/compressor.py:36 _ZFILE_PREFIX = b'ZF'  # used with pickle files created before 0.9.3.","lib/python3.11/site-packages/joblib/__init__.py:1 \"\"\"Joblib is a set of tools to provide **lightweight pipelining in","lib/python3.11/site-packages/joblib/__init__.py:9 Joblib is optimized to be **fast** and **robust** on large","lib/python3.11/site-packages/joblib/__init__.py:15     **Documentation:**       https://joblib.readthedocs.io","lib/python3.11/site-packages/joblib/pool.py:1 \"\"\"Custom implementation of multiprocessing.Pool with custom pickler.","lib/python3.11/site-packages/joblib/pool.py:26 from pickle import Pickler","lib/python3.11/site-packages/joblib/pool.py:28 from pickle import HIGHEST_PROTOCOL","lib/python3.11/site-packages/joblib/_memmapping_reducer.py:21 from pickle import whichmodule, loads, dumps, HIGHEST_PROTOCOL, PicklingError","lib/python3.11/site-packages/joblib/_memmapping_reducer.py:34 from .numpy_pickle import dump, load, load_temporary_memmap","lib/python3.11/site-packages/joblib/_memmapping_reducer.py:53 # Set used in joblib workers, referencing the filenames of temporary memmaps","lib/python3.11/site-packages/joblib/_cloudpickle_wrapper.py:2 Small shim of loky's cloudpickle_wrapper to avoid failure when","lib/python3.11/site-packages/joblib/numpy_pickle_utils.py:7 import pickle","lib/python3.11/site-packages/joblib/numpy_pickle_utils.py:21 Unpickler = pickle._Unpickler","lib/python3.11/site-packages/joblib/numpy_pickle_utils.py:22 Pickler = pickle._Pickler","lib/python3.11/site-packages/joblib/parallel.py:36 # Make sure that those two classes are part of the public joblib.parallel API","lib/python3.11/site-packages/joblib/parallel.py:206                 f\"joblib backend instead of {backend.__class__.__name__} \"","lib/python3.11/site-packages/joblib/parallel.py:218     \"\"\"Set the default backend or configuration for :class:`~joblib.Parallel`.","lib/python3.11/site-packages/joblib/numpy_pickle_compat.py:1 \"\"\"Numpy pickle compatibility functions.\"\"\"","lib/python3.11/site-packages/joblib/numpy_pickle_compat.py:3 import pickle","lib/python3.11/site-packages/joblib/numpy_pickle_compat.py:10 from .numpy_pickle_utils import _ZFILE_PREFIX"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:kiwisolver","disposition":"plotting-layout-dependency","rationale":"KiwiSolver is a plotting/layout dependency, not a model consumer.","evidence":["lib/python3.11/site-packages/kiwisolver-1.0.1-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:lazy-loader","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/lazy_loader-0.4.dist-info/METADATA sha256=98310f39300952c13265e416e7f51c96529a007b25ac20942a36f98741683350 bytes=7614 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/lazy_loader-0.4.dist-info/RECORD rows=21; sample=[\"lazy_loader-0.4.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"lazy_loader-0.4.dist-info/METADATA,sha256=mDEPOTAJUsEyZeQW5_UcllKaAHslrCCUKjb5h0FoM1A,7614\", \"lazy_loader-0.4.dist-info/RECORD,,\", \"lazy_loader-0.4.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0\"]","top_level lib/python3.11/site-packages/lazy_loader-0.4.dist-info/top_level.txt=[\"lazy_loader\"]","static Python audit group package=lazy_loader env=core: 6 files, 17240 bytes, 2 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/lazy_loader/__init__.py sha256=2c8871de3ea5d0715a9ae831b20267a1749bac31b1ae691317f406d829a2f2cb"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:libtbx-dials","disposition":"CCTBX/DIALS integration metadata and bridge","rationale":"no learned-model implementation attributed to this distribution in the inspected source group","evidence":["lib/python3.11/site-packages/libtbx.dials.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/libtbx.dials.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"SOURCES.txt\": \"libtbx.dials.egg-info/PKG-INFO\\nlibtbx.dials.egg-info/SOURCES.txt\\nlibtbx.dials.egg-info/dependency_links.txt\\nlibtbx.dials.egg-info/top_level.txt\\n\", \"top_level.txt\": \"\"}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:libtbx-scitbx","disposition":"scientific package entry-point metadata","rationale":"libtbx entry point manager for scitbx; package metadata only, so behavior outside this distribution remains unreviewed.","evidence":["installed metadata: lib/python3.11/site-packages/libtbx.scitbx.egg-info/PKG-INFO; SHA-256=1b9ec8caa1df19422313598393b7dec6f547f567ce5e7d381a6573a193180b1b; Name=libtbx.scitbx; Version=0.0.0; Summary=libtbx entry point manager for scitbx","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=lib/python3.11/site-packages/libtbx.scitbx.egg-info/top_level.txt; top_level=[\"\"]; RECORD rows=0; RECORD sample=[]; empty top_level list means no import-root claim from that metadata file","static source scan: 0 files, 0 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:libtbx-scitbx; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:lxml","disposition":"XML/HTML parsing and transformation","rationale":"Compiled libxml/libxslt binding; the optional `source` extra has a Cython constraint that differs from the installed version (tracked on the edge). This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/lxml-4.9.4-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/lxml-4.9.4-py3.11.egg-info/PKG-INFO: installed metadata ['Name: lxml', 'Version: 4.9.4', 'Requires-Dist: Cython==0.29.37; extra == \"source\"', 'Requires-Dist: cssselect>=0.7; extra == \"cssselect\"', 'Requires-Dist: html5lib; extra == \"html5\"', 'Requires-Dist: BeautifulSoup4; extra == \"htmlsoup\"']","metadata-owned top_level/RECORD roots: top_level=['lxml']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/lxml']","Installed source scan examples: lib/python3.11/site-packages/lxml/etree.pyx:60 from libc cimport limits, stdio, stdlib; lib/python3.11/site-packages/lxml/etree.pyx:61 from libc cimport string as cstring_h   # not to be confused with stdlib 'string'; lib/python3.11/site-packages/lxml/objectify.pyx:21 cimport libc.string as cstring_h   # not to be confused with stdlib 'string'; lib/python3.11/site-packages/lxml/includes/xslt.pxd:121 cdef void xsltSetTransformErrorFunc("],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:mako","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: text templating engine. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/mako-1.3.9.dist-info/METADATA:L2","lib/python3.11/site-packages/mako-1.3.9.dist-info/METADATA: Name: Mako","lib/python3.11/site-packages/mako-1.3.9.dist-info/METADATA: Version: 1.3.9","lib/python3.11/site-packages/mako-1.3.9.dist-info/METADATA: Summary: A super-fast templating language that borrows the best ideas from the existing templating languages.","lib/python3.11/site-packages/mako/_ast_util.py:118: traversing.  For this a special visitor exists (`NodeTransformer`) that","lib/python3.11/site-packages/mako/_ast_util.py:149: class NodeTransformer(NodeVisitor):","lib/python3.11/site-packages/mako/_ast_util.py:154: The `NodeTransformer` will walk the AST and use the return value of the","lib/python3.11/site-packages/mako/_ast_util.py:161: Here an example transformer that rewrites all `foo` to `data['foo']`::","lib/python3.11/site-packages/mako/_ast_util.py:163: class RewriteName(NodeTransformer):"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:markupsafe","disposition":"general runtime/development infrastructure","rationale":"Html escaping package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/MarkupSafe-2.0.1-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/MarkupSafe-2.0.1-py3.11.egg-info/PKG-INFO; sha256=fe204c6c0a2d28f96baf0845b9dc3c28eb708de82d500f6446907e9b23a27692; record exists=True","top_level.txt roots (metadata-derived): markupsafe","metadata-derived source roots ['lib/python3.11/site-packages/markupsafe']; bounded scan files=3, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:matplotlib","disposition":"plotting and scientific numerical utility","rationale":"The scanned code includes compatibility spectral and kernel-density helpers; those functions are general visualization/statistics utilities, not a trained model.","evidence":["lib/python3.11/site-packages/matplotlib-3.6.3-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/matplotlib-3.6.3-py3.11.egg-info/PKG-INFO; metadata SHA-256 71f2731749d44924919ad543931c5f361e5cce0d91629fbe108321a01fc8f328","top_level.txt roots=['matplotlib', 'mpl_toolkits', 'pylab']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 281 Python files / 6602138 bytes; 16 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:matplotlib; environment=core; version=3.6.3","lib/python3.11/site-packages/matplotlib/mlab.py:1-6,10-25"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:meson-python","disposition":"python-build-or-test-infrastructure","rationale":"Installed meson-python 0.17.1 in core is python-build-or-test-infrastructure; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["lib/python3.11/site-packages/meson_python-0.17.1.dist-info/METADATA; Name: meson-python | Version: 0.17.1 | Summary: Meson Python build backend (PEP 517)","owner: top_level=(absent); source_roots_from_METADATA_or_RECORD=['mesonpy']; RECORD_rows=21; RECORD_sample=['meson_python-0.17.1.dist-info/INSTALLER', 'meson_python-0.17.1.dist-info/METADATA', 'meson_python-0.17.1.dist-info/MIT.txt', 'meson_python-0.17.1.dist-info/RECORD', 'meson_python-0.17.1.dist-info/REQUESTED', 'meson_python-0.17.1.dist-info/WHEEL', 'meson_python-0.17.1.dist-info/direct_url.json', 'mesonpy/__init__.py']","declared dependencies: Requires-Dist: meson>=0.63.3; python_version < \"3.12\"; Requires-Dist: meson>=1.2.3; python_version >= \"3.12\"; Requires-Dist: packaging>=19.0; Requires-Dist: pyproject-metadata>=0.7.1; Requires-Dist: tomli>=1.0.0; python_version < \"3.11\"; Requires-Dist: build; extra == \"test\"; Requires-Dist: packaging>=23.1; extra == \"test\"; Requires-Dist: pytest>=6.0; extra == \"test\"; Requires-Dist: pytest-cov[toml]; extra == \"test\"; Requires-Dist: pytest-mock; extra == \"test\"; Requires-Dist: cython>=3.0.3; extra == \"test\"; Requires-Dist: wheel; extra == \"test\""],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:metalcoordanalysis","disposition":"scientific-statistical-clustering-library","rationale":"Static source calls sklearn GaussianMixture in metalCoord/analysis/cluster.py and DBSCAN in metalCoord/correspondense/procrustes.py. These are unsupervised statistical/geometry operations; no fitted model asset or default CCP4 application invocation is established.","evidence":["lib/python3.11/site-packages/metalcoordanalysis-0.2.15.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:mock","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/mock-3.0.5-py3.11.egg-info/PKG-INFO sha256=fb944154740e422e94e5a89ad09b493242c28abd68516bd2775c6cc7936b6924 bytes=3188 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/mock-3.0.5-py3.11.egg-info/SOURCES.txt rows=13; sample=[\"CHANGELOG.rst\", \"LICENSE.txt\", \"MANIFEST.in\", \"README.rst\"]","top_level lib/python3.11/site-packages/mock-3.0.5-py3.11.egg-info/top_level.txt=[\"mock\"]","static Python audit group package=mock env=core: 2 files, 86446 bytes, 1 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/mock/mock.py sha256=b6856a2cba3de51599a836c094bd0166cba923dafc88d8849427419909aa352e"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:modelcraft","disposition":"crystallographic model-building workflow that conditionally launches NucleoFind","rationale":"modelcraft/jobs/nucleofind.py:22,57 and modelcraft/jobs/modelcraft{em,xray}.py launch nucleofind/nucleofind-build; modelcraftxray.py:184,189 and modelcraftem.py:51,150 show conditional nucleic-acid route; GPU execution untested","evidence":["lib/python3.11/site-packages/modelcraft-6.1.1.dist-info/METADATA:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/modelcraft-6.1.1.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"gemmi>=0.5.5\", \"numpy\", \"pandas\", \"requests\", \"scipy\", \"tabulate\"]; ownership={\"entry_points.txt\": \"[console_scripts]\\nmodelcraft = modelcraft.scripts.modelcraft:main\\nmodelcraft-contents = modelcraft.scripts.contents:main\\nmodelcraft-copies = modelcraft.scripts.copies:main\\nmodelcraft-sidechains = modelcraft.scripts.sidechains:main\\nmodelcraft-validate = modelcraft.scripts.validate:main\\n\", \"record_file_count\": 173, \"top_level.txt\": \"modelcraft\\n\"}","audits/ccp4-10.0.001/python.json AST group package=modelcraft root=lib/python3.11/site-packages files=80 hit_files=8 imports={}","lib/python3.11/site-packages/modelcraft/jobs/nucleofind.py:22,57; modelcraft/jobs/modelcraftxray.py:184,189; modelcraft/jobs/modelcraftem.py:51,150"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:mpi4py","disposition":"MPI bindings","rationale":"Python MPI bindings, infrastructure.","evidence":["installed metadata: lib/python3.11/site-packages/mpi4py-3.1.5-py3.11.egg-info/PKG-INFO; SHA-256=023f19d48c0d040edf6e74e2f9c74ecf79b652752af354c0b87413ce1cbe1888; Name=mpi4py; Version=3.1.5; Summary=Python bindings for MPI","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=lib/python3.11/site-packages/mpi4py-3.1.5-py3.11.egg-info/top_level.txt; top_level=[\"mpi4py\"]; RECORD rows=0; RECORD sample=[]; empty top_level list means no import-root claim from that metadata file","static source scan: 0 files, 0 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:mpi4py; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:mrcfile","disposition":"MRC/CCP4 map I/O","rationale":"Reads and writes MRC/CCP4 map files; no model artifact identified. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/mrcfile-1.3.0-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/mrcfile-1.3.0-py3.11.egg-info/PKG-INFO: installed metadata ['Name: mrcfile', 'Version: 1.3.0', 'Requires-Dist: numpy>=1.12.0']","metadata-owned top_level/RECORD roots: top_level=['mrcfile']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/mrcfile']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:msgpack","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: MessagePack serialization. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/msgpack-1.0.8-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/msgpack-1.0.8-py3.11.egg-info/PKG-INFO: Name: msgpack","lib/python3.11/site-packages/msgpack-1.0.8-py3.11.egg-info/PKG-INFO: Version: 1.0.8","lib/python3.11/site-packages/msgpack-1.0.8-py3.11.egg-info/PKG-INFO: Summary: MessagePack serializer"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:nanobind","disposition":"C++ binding infrastructure with generic tensor interoperability","rationale":"C++ binding/runtime infrastructure. TensorFlow/Torch strings are generic DLPack and stub-generation interoperability, not model code or a trained model.","evidence":["lib/python3.11/site-packages/nanobind-2.7.0.dist-info/METADATA:L2","cpu64 installed record lib/python3.11/site-packages/nanobind-2.7.0.dist-info/METADATA; sha256=5acd68d5a1bbf1f45d6e77d6c8b8a85018db154ca14329a6a035c90ed9def85b; record exists=True","metadata-derived source roots ['lib/python3.11/site-packages/nanobind']; bounded scan files=80, truncated=False","lib/python3.11/site-packages/nanobind/stubgen.py:256 parses torch.Tensor type spellings; gemmi_ext DLPack string window at native offset 5745662 contains generic torch/tensorflow/jax/cupy adapters."],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:natsort","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["lib/python3.11/site-packages/natsort-7.1.1-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/natsort-7.1.1-py3.11.egg-info/PKG-INFO; metadata SHA-256 144a52d7f8a14620663736ada03ea2f4c1e85a9cfc6fd395e0973ea036ebe294","top_level.txt roots=['natsort']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 11 Python files / 93845 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:natsort; environment=core; version=7.1.1"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:networkx","disposition":"graph-algorithm-library-with-node-classification-apis","rationale":"NetworkX is a graph-algorithm library; source includes algorithms/node_classification.py, a graph label-propagation/classification API, and its optional integrations are declared as extras. 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extra == \"developer\"; Requires-Dist: mypy>=1.1; extra == \"developer\"; Requires-Dist: rtoml; extra == \"developer\"; Requires-Dist: sphinx>=7; extra == \"doc\"; Requires-Dist: pydata-sphinx-theme>=0.14; extra == \"doc\"; Requires-Dist: sphinx-gallery>=0.14; extra == \"doc\"; Requires-Dist: numpydoc>=1.6; extra == \"doc\"","lib/python3.11/site-packages/networkx/convert_matrix.py:68         An operator that determines how weights in multigraphs are handled.","lib/python3.11/site-packages/networkx/convert_matrix.py:69         The default is to sum the weights of the multiple edges.","lib/python3.11/site-packages/networkx/convert_matrix.py:193     Simple integer weights on edges:","lib/python3.11/site-packages/networkx/algorithms/sparsifiers.py:190     \"\"\"Setup residual graph as a copy of G with unique edges weights.","lib/python3.11/site-packages/networkx/algorithms/sparsifiers.py:196     This function associates distinct weights to the edges of the","lib/python3.11/site-packages/networkx/algorithms/sparsifiers.py:215     # establish unique edge weights, even for unweighted graphs","lib/python3.11/site-packages/networkx/algorithms/chordal.py:428                 # y_weight will be bigger than node weights between y and z","lib/python3.11/site-packages/networkx/algorithms/chordal.py:436         # during calculation of paths the weights should not be updated","lib/python3.11/site-packages/networkx/algorithms/cuts.py:29     *cut size* is the sum of the weights of the edges \"between\" the two","lib/python3.11/site-packages/networkx/algorithms/bridges.py:163         If function, used to compute edge weights for the span.","lib/python3.11/site-packages/networkx/algorithms/cluster.py:328     as the geometric average of the subgraph edge weights [2]_,","lib/python3.11/site-packages/networkx/algorithms/cluster.py:335     The edge weights :math:`\\hat{w}_{uv}` are normalized by the maximum weight","lib/python3.11/site-packages/networkx/algorithms/cluster.py:340     Additionally, this weighted definition has been generalized to support negative edge weights [3]_.","lib/python3.11/site-packages/networkx/algorithms/node_classification.py:43         name of target labels to predict","lib/python3.11/site-packages/networkx/algorithms/node_classification.py:47     predicted : list","lib/python3.11/site-packages/networkx/algorithms/node_classification.py:48         List of length ``len(G)`` with the predicted labels for each node.","lib/python3.11/site-packages/networkx/algorithms/simple_paths.py:453     If a weighted shortest path search is to be used, no negative weights","lib/python3.11/site-packages/networkx/algorithms/simple_paths.py:843     This algorithm is not guaranteed to work if edge weights","lib/python3.11/site-packages/networkx/algorithms/simple_paths.py:963                     raise ValueError(\"Contradictory paths found: negative weights?\")","lib/python3.11/site-packages/networkx/algorithms/time_dependent.py:141         weights = [G.nodes[i].get(weight, 1) for i in pred]","lib/python3.11/site-packages/networkx/algorithms/time_dependent.py:142         return round(sum(bi / wt for bi, wt in zip(b, weights)) / n, 2)","lib/python3.11/site-packages/networkx/algorithms/cycles.py:121     attention to strongly connected components of G, generate all simple cycles","lib/python3.11/site-packages/networkx/algorithms/cycles.py:124     restrict our attention to biconnected components, generate all simple cycles","lib/python3.11/site-packages/networkx/algorithms/cycles.py:1049         name of the edge attribute to use for edge weights","lib/python3.11/site-packages/networkx/algorithms/__init__.py:29 from networkx.algorithms.link_prediction import *","lib/python3.11/site-packages/networkx/algorithms/matching.py:266     Use the maximum-weight algorithm with edge weights subtracted","lib/python3.11/site-packages/networkx/algorithms/matching.py:270     The weight of a matching is the sum of the weights of its edges.","lib/python3.11/site-packages/networkx/algorithms/matching.py:274     This method replaces the edge weights with 1 plus the maximum edge weight"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:nucleofind","disposition":"ONNX-model-inference-and-model-fetcher","rationale":"NucleoFind statically imports ONNX Runtime and has model download/install routines; a shipped ONNX model is recorded elsewhere in the full inventory and its loader accepts core model paths. The installed package also exposes external model/database download behavior; no runtime session was created.","evidence":["lib/python3.11/site-packages/nucleofind-1.3.2.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:numpy","disposition":"numerical_or_dataframe_infrastructure","rationale":"Installed numerical array/dataframe infrastructure; source marker hits were reviewed in context and did not establish trained weights or an application ML path for this distribution.","evidence":["installed metadata lib/python3.11/site-packages/numpy-1.26.4.dist-info/METADATA sha256=4f151eefd36459b2a4b1831a4faaf673f3fa95a0397c27c52dc4cd2591202f66 bytes=7335 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/numpy-1.26.4.dist-info/RECORD rows=1407; sample=[\"../../../bin/f2py,sha256=RxzmTeYN1TwdyLMIlsjKrPOM7hndFty81bbJ09G7RHU,257\", \"numpy-1.26.4.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"numpy-1.26.4.dist-info/LICENSE.txt,sha256=JjIjOQxDqdSghB4CCSZf2SehmPjonI7ugJt0N9fl6MI,1543\", \"numpy-1.26.4.dist-info/METADATA,sha256=TxUe79NkWbKksYMaT6r2c_P6laA5fCfFLcTNJZEgL2Y,7335\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=numpy env=core: 489 files, 8673614 bytes, 44 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/numpy/lib/utils.py sha256=e8d76579a10b662a8045d8fe102663c6dc0b7f56ea92539c2b8de6f72a1979fb"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:nxmx","disposition":"NeXus/NXmx metadata and data parsing support","rationale":"Python package handles HDF5/NeXus data and metadata; no model inference path identified","evidence":["lib/python3.11/site-packages/nxmx-0.0.5.dist-info/METADATA:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/nxmx-0.0.5.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"h5py\", \"pint\", \"python-dateutil\", \"scipy\", \"numpy\"]; ownership={\"record_file_count\": 13, \"top_level.txt\": \"nxmx\\n\"}","audits/ccp4-10.0.001/python.json AST group package=nxmx root=lib/python3.11/site-packages files=2 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:omegaconf","disposition":"configuration library","rationale":"Hierarchical configuration library.","evidence":["installed metadata: lib/python3.11/site-packages/omegaconf-2.3.0.dist-info/METADATA; SHA-256=ececbf74319384a59702bd4bfc4ea269167a0be1608b6ae3facb7a70763a8b8d; Name=omegaconf; Version=2.3.0; Summary=A flexible configuration library","declared Requires-Dist (3): [\"antlr4-python3-runtime==4.9.*\",\"PyYAML>=5.1.0\",\"dataclasses; python_version == \\\"3.6\\\"\"]","ownership: top_level metadata path candidate=lib/python3.11/site-packages/omegaconf-2.3.0.dist-info/top_level.txt; top_level=[\"omegaconf\", \"pydevd_plugins\"]; RECORD rows=34; RECORD sample=[\"omegaconf-2.3.0.dist-info/INSTALLER\", \"omegaconf-2.3.0.dist-info/METADATA\", \"omegaconf-2.3.0.dist-info/RECORD\", \"omegaconf-2.3.0.dist-info/REQUESTED\", \"omegaconf-2.3.0.dist-info/WHEEL\", \"omegaconf-2.3.0.dist-info/direct_url.json\", \"omegaconf-2.3.0.dist-info/licenses/LICENSE\", \"omegaconf-2.3.0.dist-info/top_level.txt\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 25 files, 342296 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:omegaconf; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:onedep-api","disposition":"PDBe OneDep API client","rationale":"Network/API client; metadata extras cover test/development, not model inference. 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package metadata and owned files were reviewed without invoking it.","evidence":["lib/python3.11/site-packages/pip-24.3.1.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:pkgconfig","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/pkgconfig-1.5.5-py3.11.egg-info/PKG-INFO sha256=acb9c47405fa891700e199e7f8f446827bce582b45b8c3a9cc83708ada0efd50 bytes=3535 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/pkgconfig-1.5.5-py3.11.egg-info/SOURCES.txt rows=10; sample=[\"LICENSE\", \"README.rst\", \"pyproject.toml\", \"setup.py\"]","top_level lib/python3.11/site-packages/pkgconfig-1.5.5-py3.11.egg-info/top_level.txt=[\"pkgconfig\"]","static Python audit group package=pkgconfig env=core: 2 files, 9054 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:pluggy","disposition":"Python plugin-registration infrastructure","rationale":"plugin hook dispatch only; 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Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/prettytable-3.3.0-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/prettytable-3.3.0-py3.11.egg-info/PKG-INFO; sha256=de450b778265c3a70eb9ff26fb6b541ba4ee233d519208a673a680bebc7472b5; record exists=True","top_level.txt roots (metadata-derived): prettytable","metadata-derived source roots ['lib/python3.11/site-packages/prettytable']; bounded scan files=3, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:privateer","disposition":"C++ glycan analysis package; RECORD archive discrepancy","rationale":"This distribution has no Python source and records a native executable, extension and glycomics/torsion JSON data. Its RECORD also lists lib64/libprivateer_lib.a (12,279,182 bytes), but the path is absent from the bundle; a bounded bundle find found no matching archive. Treat this as a package-record/file-presence lead pending install-layout clarification.","evidence":["lib/python3.11/site-packages/privateer-0.5.dist-info/METADATA:L2","lib/python3.11/site-packages/privateer-0.5.dist-info/METADATA; metadata SHA-256 7417baeae6c515cd1a5e2a88f3baae77fe20cbc2dc97c8a15b3b799e55fbcc79","top_level.txt roots=[]; RECORD=lib/python3.11/site-packages/privateer-0.5.dist-info/RECORD; RECORD existing=12/13","read-only source scan: 0 Python files / 0 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:privateer; environment=core; version=0.5","lib/python3.11/site-packages/privateer-0.5.dist-info/RECORD:1-13","lib/python3.11/site-packages/privateer-0.5.dist-info/METADATA","RECORD entry lib64/libprivateer_lib.a has SHA-256 base64 hQXBMBt2rgBb8dyVzVdOTnyrw3aBRUYFpu54mFSMvCs and size 12,279,182; no such path found under bundle root","lib/python3.11/site-packages/privateer/privateer_data/glycomics/privateer_glycomics_database.json","lib/python3.11/site-packages/privateer/privateer_data/linkage_torsions/privateer_torsion_database.json"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:procrunner","disposition":"process-launch-utility","rationale":"Installed procrunner 2.3.3 in core is process-launch-utility; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["lib/python3.11/site-packages/procrunner-2.3.3-py3.11.egg-info/PKG-INFO; Name: procrunner | Version: 2.3.3 | Summary: Versatile utility function to run external processes","owner: top_level=['procrunner']; source_roots_from_METADATA_or_RECORD=['procrunner']; RECORD_rows=not provided; RECORD_sample=[]"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:psutil","disposition":"process-and-system-utility","rationale":"psutil provides process/system information and is not an ML consumer.","evidence":["lib/python3.11/site-packages/psutil-5.7.2-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:py","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/py-1.11.0-py3.11.egg-info/PKG-INFO sha256=5fd9f4203818ca82030bea46a79eb866f8a55fefbe80ff29d4aa16933f62d223 bytes=3028 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/py-1.11.0-py3.11.egg-info/SOURCES.txt rows=152; sample=[\".flake8\", \".gitattributes\", \".gitignore\", \"AUTHORS\"]","top_level lib/python3.11/site-packages/py-1.11.0-py3.11.egg-info/top_level.txt=[\"py\"]","static Python audit group package=py env=core: 36 files, 269152 bytes, 7 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/py/_std.py sha256=267cd378f0c5d133733ca8d81c844c2b0bb0cc4e9bbcb395f2af6bec594b659f"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:py-cpuinfo","disposition":"CPU feature reporting utility","rationale":"hardware metadata only; no learned-model path","evidence":["lib/python3.11/site-packages/py_cpuinfo-9.0.0.dist-info/METADATA:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/py_cpuinfo-9.0.0.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"entry_points.txt\": \"[console_scripts]\\ncpuinfo = cpuinfo:main\\n\", \"record_file_count\": 16, \"top_level.txt\": \"cpuinfo\\n\"}","audits/ccp4-10.0.001/python.json AST group package=cpuinfo root=lib/python3.11/site-packages files=3 hit_files=1 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:pybind11","disposition":"native binding headers/tooling","rationale":"C++/Python binding headers; build infrastructure.","evidence":["installed metadata: lib/python3.11/site-packages/pybind11-2.12.0-py3.11.egg-info/PKG-INFO; SHA-256=a8e09da26b4beb2030824a3a824959456164dd0ede31b964abde70a3f5d4536d; Name=pybind11; Version=2.12.0; Summary=Seamless operability between C++11 and Python","declared Requires-Dist (1): [\"pybind11_global==2.12.0; extra == \\\"global\\\"\"]","ownership: top_level metadata path candidate=lib/python3.11/site-packages/pybind11-2.12.0-py3.11.egg-info/top_level.txt; top_level=[\"pybind11\"]; RECORD rows=0; RECORD sample=[]; empty top_level list means no import-root claim from that metadata file","static source scan: 0 files, 0 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:pybind11; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:pycairo","disposition":"Cairo graphics binding","rationale":"Vector graphics binding; no ML role. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/pycairo-1.20.0-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/pycairo-1.20.0-py3.11.egg-info/PKG-INFO: installed metadata ['Name: pycairo', 'Version: 1.20.0']","metadata-owned top_level/RECORD roots: top_level=['cairo']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/cairo']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:pycparser","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: C grammar/parser infrastructure. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/pycparser-2.18-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/pycparser-2.18-py3.11.egg-info/PKG-INFO: Name: pycparser","lib/python3.11/site-packages/pycparser-2.18-py3.11.egg-info/PKG-INFO: Version: 2.18","lib/python3.11/site-packages/pycparser-2.18-py3.11.egg-info/PKG-INFO: Summary: C parser in Python","lib/python3.11/site-packages/pycparser/c_ast.py:2: # ** ATTENTION **","lib/python3.11/site-packages/pycparser/c_ast.py:112: *   Modeled after Python's own AST visiting facilities","lib/python3.11/site-packages/pycparser/_ast_gen.py:141: # ** ATTENTION **","lib/python3.11/site-packages/pycparser/_ast_gen.py:253: *   Modeled after Python's own AST visiting facilities","lib/python3.11/site-packages/pycparser/ply/cpp.py:698: if ifstack[-1][0]:     # We only pay attention if outer \"if\" allows this"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:pyfftw","disposition":"numerical/runtime infrastructure","rationale":"FFT backend; numerical transform library, not a model.","evidence":["lib/python3.11/site-packages/pyFFTW-0.15.0-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/pyFFTW-0.15.0-py3.11.egg-info/PKG-INFO; sha256=3036ecedf443da0d6a624d85c8857b1e755823a4e29644dabd78f65acb469e18; record exists=True","top_level.txt roots (metadata-derived): pyfftw","metadata-derived source roots ['lib/python3.11/site-packages/pyfftw']; bounded scan files=17, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:pygobject","disposition":"GTK language binding","rationale":"Metadata and source ownership identify GUI bindings; the bounded Python scan found no model inference code.","evidence":["lib/python3.11/site-packages/PyGObject-3.42.2-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/PyGObject-3.42.2-py3.11.egg-info/PKG-INFO; metadata SHA-256 4ad16738f62b767fbf185a86922ba293426a1cb04d7cd4622cb503ac00036fcb","top_level.txt roots=['gi', 'pygtkcompat']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 27 Python files / 308826 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:pygobject; environment=core; version=3.42.2"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:pyjob","disposition":"CCP4-job-orchestration-utility","rationale":"Installed pyjob 0.3.0 in core is CCP4-job-orchestration-utility; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["lib/python3.11/site-packages/pyjob-0.3.0-py3.11.egg-info/PKG-INFO; Name: pyjob | Version: 0.3.0 | Summary: Job Management Controller","owner: top_level=['pyjob']; source_roots_from_METADATA_or_RECORD=['pyjob']; RECORD_rows=not provided; RECORD_sample=[]","declared dependencies: Requires-Dist: chardet>=3.0.4; Requires-Dist: enum34; python_version < \"3.4\"; Requires-Dist: pyyaml>=3.13"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:pynacl","disposition":"cryptography-utility","rationale":"PyNaCl supplies cryptographic primitives and is not an ML consumer.","evidence":["lib/python3.11/site-packages/PyNaCl-1.3.0-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:pyopengl","disposition":"graphics_or_visualization_infrastructure","rationale":"Installed graphics/font/contour infrastructure; static source review found no shipped trained model consumer in the distribution.","evidence":["installed metadata lib/python3.11/site-packages/PyOpenGL-3.1.5-py3.11.egg-info/PKG-INFO sha256=9438e2ab8d40515c82783ede9417fdaecd78da08f1a29d59387320615651b987 bytes=3352 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/PyOpenGL-3.1.5-py3.11.egg-info/SOURCES.txt rows=2918; sample=[\"MANIFEST.in\", \"license.txt\", \"readme.rst\", \"setup.cfg\"]","top_level lib/python3.11/site-packages/PyOpenGL-3.1.5-py3.11.egg-info/top_level.txt=[\"OpenGL\"]","static Python audit group package=OpenGL env=core: 2821 files, 5682114 bytes, 1 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/OpenGL/plugins.py sha256=d0729bc975319220786bdfb0f62c4a6717e8fd069a576af34c16ba04dedce1c4"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:pyparsing","disposition":"grammar and text parser library","rationale":"parser infrastructure only; no model path","evidence":["lib/python3.11/site-packages/pyparsing-3.1.4.dist-info/METADATA:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/pyparsing-3.1.4.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"railroad-diagrams ; extra == \\\"diagrams\\\"\", \"jinja2 ; extra == \\\"diagrams\\\"\"]; ownership={\"record_file_count\": 30}","audits/ccp4-10.0.001/python.json AST group package=pyparsing root=lib/python3.11/site-packages files=11 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:pyproject-metadata","disposition":"build metadata parser","rationale":"PEP 621/pyproject metadata tooling.","evidence":["installed metadata: lib/python3.11/site-packages/pyproject_metadata-0.8.0.dist-info/METADATA; SHA-256=4a5a534d727e71a9a344454fa262e360934f35c7f83211c5858f5672c453218a; Name=pyproject_metadata; Version=0.8.0; Summary=PEP 621 metadata parsing","declared Requires-Dist (7): [\"packaging>=19.0\",\"furo>=2023.9.10 ; extra == \\\"docs\\\"\",\"sphinx-autodoc-typehints>=1.10.0 ; extra == \\\"docs\\\"\",\"sphinx~=7.0 ; extra == \\\"docs\\\"\",\"pytest-cov[toml]>=2 ; extra == \\\"test\\\"\",\"pytest>=6.2.4 ; extra == \\\"test\\\"\",\"tomli>=1.0.0 ; extra == \\\"test\\\" and (python_version<\\\"3.11\\\")\"]","ownership: top_level metadata path candidate=lib/python3.11/site-packages/pyproject_metadata-0.8.0.dist-info/top_level.txt; top_level=[]; RECORD rows=9; RECORD sample=[\"pyproject_metadata-0.8.0.dist-info/INSTALLER\", \"pyproject_metadata-0.8.0.dist-info/LICENSE\", \"pyproject_metadata-0.8.0.dist-info/METADATA\", \"pyproject_metadata-0.8.0.dist-info/RECORD\", \"pyproject_metadata-0.8.0.dist-info/REQUESTED\", \"pyproject_metadata-0.8.0.dist-info/WHEEL\", \"pyproject_metadata-0.8.0.dist-info/direct_url.json\", \"pyproject_metadata/__init__.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 1 files, 20882 bytes, 0 skipped/overflow; ML vocabulary hits=2","representative broad-term source hits: [{\"path\": \"pyproject_metadata/__init__.py\", \"line\": 310, \"text\": \"for classifier in self.classifiers:\"}, {\"path\": \"pyproject_metadata/__init__.py\", \"line\": 311, \"text\": \"message['Classifier'] = classifier\"}]","node identity: pydist:core:pyproject-metadata; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:pyqt-builder","disposition":"Qt binding build tooling","rationale":"Build backend for PyQt extensions; no ML role. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/PyQt_builder-1.12.1-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/PyQt_builder-1.12.1-py3.11.egg-info/PKG-INFO: installed metadata ['Name: PyQt-builder', 'Version: 1.12.1', 'Requires-Dist: packaging', 'Requires-Dist: sip<7,>=6.3']","metadata-owned top_level/RECORD roots: top_level=['pyqtbuild']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/pyqtbuild']","Installed source scan examples: lib/python3.11/site-packages/pyqtbuild/project.py:109 pylib_shlib = ducfg.get('LDLIBRARY', '')"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:pyqt5","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: Qt GUI bindings. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/PyQt5-5.15.4.dist-info/METADATA:L2","lib/python3.11/site-packages/PyQt5-5.15.4.dist-info/METADATA: Name: PyQt5","lib/python3.11/site-packages/PyQt5-5.15.4.dist-info/METADATA: Version: 5.15.4","lib/python3.11/site-packages/PyQt5-5.15.4.dist-info/METADATA: Summary: Python bindings for the Qt cross platform application toolkit","lib/python3.11/site-packages/PyQt5/uic/Compiler/qtproxies.py:105: # ATTENTION: currently, classes can either be literal or normal. If a class"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:pyqt5-sip","disposition":"general runtime/development infrastructure","rationale":"Qt python bindings/runtime package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/PyQt5_sip-12.15.0-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/PyQt5_sip-12.15.0-py3.11.egg-info/PKG-INFO; sha256=d7576dd294ea179eb608adb849390adc434bb0410d62474c55e0e65ddaab97a7; record exists=True","top_level.txt roots (metadata-derived): PyQt5","metadata-derived source roots ['lib/python3.11/site-packages/PyQt5']; bounded scan files=65, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:pyside2","disposition":"Qt GUI binding with bundled OpenCV example","rationale":"The only ML-adjacent source hits include examples/external/opencv/webcam_pattern_detection.py; that is an example tree, not evidence of CCP4 application-level pattern detection or a model asset.","evidence":["lib/python3.11/site-packages/PySide2-5.15.11-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/PySide2-5.15.11-py3.11.egg-info/PKG-INFO; metadata SHA-256 2f3ddda2d041b50989118172d2041c1e1751c1d05473a6cbd8030d91805207de","top_level.txt roots=['PySide2', 'QtCore']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 192 Python files / 2230337 bytes; 11 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:pyside2; environment=core; version=5.15.11","lib/python3.11/site-packages/PySide2/examples/external/opencv/webcam_pattern_detection.py","package tree: 192 Python files / 2,230,337 bytes read; 11 files matched broad terms"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:pytest","disposition":"python-build-or-test-infrastructure","rationale":"Installed pytest 7.3.2 in core is python-build-or-test-infrastructure; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["lib/python3.11/site-packages/pytest-7.3.2-py3.11.egg-info/PKG-INFO; Name: pytest | Version: 7.3.2 | Summary: pytest: simple powerful testing with Python","owner: top_level=['_pytest', 'py', 'pytest']; source_roots_from_METADATA_or_RECORD=['_pytest', 'py', 'pytest']; RECORD_rows=not provided; RECORD_sample=[]","declared dependencies: Requires-Dist: iniconfig; Requires-Dist: packaging; Requires-Dist: pluggy<2.0,>=0.12; Requires-Dist: colorama; sys_platform == \"win32\"; Requires-Dist: exceptiongroup>=1.0.0rc8; python_version < \"3.11\"; Requires-Dist: importlib-metadata>=0.12; python_version < \"3.8\"; Requires-Dist: tomli>=1.0.0; python_version < \"3.11\"; Requires-Dist: argcomplete; extra == \"testing\"; Requires-Dist: attrs>=19.2.0; extra == \"testing\"; Requires-Dist: hypothesis>=3.56; extra == \"testing\"; Requires-Dist: mock; extra == \"testing\"; Requires-Dist: nose; extra == \"testing\""],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:pytest-faulthandler","disposition":"test-runner-support","rationale":"pytest-faulthandler is test-runner support; not application inference evidence.","evidence":["lib/python3.11/site-packages/pytest_faulthandler-2.0.1-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:pytest-forked","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/pytest_forked-1.5.0-py3.11.egg-info/PKG-INFO sha256=893b160232e259445d17e98bd7f561a9e831dfe1d91cb9eb7ec333143cbdee60 bytes=3736 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/pytest_forked-1.5.0-py3.11.egg-info/SOURCES.txt rows=23; sample=[\".gitignore\", \".pre-commit-config.yaml\", \"CHANGELOG.rst\", \"LICENSE\"]","top_level lib/python3.11/site-packages/pytest_forked-1.5.0-py3.11.egg-info/top_level.txt=[\"pytest_forked\"]","static Python audit group package=pytest_forked env=core: 1 files, 3665 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:pytest-mock","disposition":"test-only mocking support","rationale":"test support, not a runtime scientific dependency","evidence":["lib/python3.11/site-packages/pytest_mock-1.13.0-py3.11.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from lib/python3.11/site-packages/pytest_mock-1.13.0-py3.11.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"pytest>=2.7\", \"mock; python_version < \\\"3.0\\\"\", \"pre-commit; extra == \\\"dev\\\"\", \"tox; extra == \\\"dev\\\"\"]; ownership={\"SOURCES.txt\": \".gitignore\\n.pre-commit-config.yaml\\nCHANGELOG.rst\\nHOWTORELEASE.rst\\nLICENSE\\nREADME.rst\\nsetup.cfg\\nsetup.py\\ntox.ini\\n.github/FUNDING.yml\\n.github/workflows/main.yml\\nsrc/pytest_mock/__init__.py\\nsrc/pytest_mock/_version.py\\nsrc/pytest_mock/plugin.py\\nsrc/pytest_mock.egg-info/PKG-INFO\\nsrc/pytest_mock.egg-info/SOURCES.txt\\nsrc/pytest_mock.egg-info/dependency_links.txt\\nsrc/pytest_mock.egg-info/entry_points.txt\\nsrc/pytest_mock.egg-info/requires.txt\\nsrc/pytest_mock.egg-info/top_level.txt\\ntests/test_pytest_mock.py\", \"entry_points.txt\": \"[pytest11]\\npytest_mock = pytest_mock\\n\", \"top_level.txt\": \"pytest_mock\\n\"}","audits/ccp4-10.0.001/python.json AST group package=pytest_mock root=lib/python3.11/site-packages files=3 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:python-dateutil","disposition":"date/time utility","rationale":"Date/time parsing and timezone utilities.","evidence":["installed metadata: lib/python3.11/site-packages/python_dateutil-2.8.2-py3.11.egg-info/PKG-INFO; SHA-256=7e068951fadd6a8c3f66d358560aeb86e7a7380d4e0525c722076213628160e0; Name=python-dateutil; Version=2.8.2; Summary=Extensions to the standard Python datetime module","declared Requires-Dist (1): [\"six>=1.5\"]","ownership: top_level metadata path candidate=lib/python3.11/site-packages/python_dateutil-2.8.2-py3.11.egg-info/top_level.txt; top_level=[\"dateutil\"]; RECORD rows=0; RECORD sample=[]; empty top_level list means no import-root claim from that metadata file","static source scan: 0 files, 0 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:python-dateutil; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:python-docx","disposition":"Word document I/O","rationale":"Document parser/writer; no ML role. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/python_docx-0.8.11-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/python_docx-0.8.11-py3.11.egg-info/PKG-INFO: installed metadata ['Name: python-docx', 'Version: 0.8.11', 'Requires-Dist: lxml>=2.3.2']","metadata-owned top_level/RECORD roots: top_level=['docx']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/docx']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:pythran","disposition":"numerical compiler/runtime","rationale":"Installed package role from metadata and static implementation review: ahead-of-time compiler for numerical Python kernels. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/pythran-0.15.0-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/pythran-0.15.0-py3.11.egg-info/PKG-INFO: Name: pythran","lib/python3.11/site-packages/pythran-0.15.0-py3.11.egg-info/PKG-INFO: Version: 0.15.0","lib/python3.11/site-packages/pythran-0.15.0-py3.11.egg-info/PKG-INFO: Summary: Ahead of Time compiler for numeric kernels","lib/python3.11/site-packages/pythran/tables.py:3987: # We currently don't accurately model the fact that the return of ravel","lib/python3.11/site-packages/pythran/passmanager.py:178: class Transformation(ContextManager, ast.NodeTransformer):","lib/python3.11/site-packages/pythran/intrinsic.py:1: \"\"\" This module contains all classes used to model intrinsics behavior.  \"\"\"","lib/python3.11/site-packages/pythran/intrinsic.py:38: Model any Method/Function.","lib/python3.11/site-packages/pythran/transformations/normalize_static_if.py:63: class PatchReturn(ast.NodeTransformer):"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:pytz","disposition":"general runtime/development infrastructure","rationale":"Timezone data/runtime package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/pytz-2020.5-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/pytz-2020.5-py3.11.egg-info/PKG-INFO; sha256=393d87dfff5ccbc19f926e0be229e1dffc1212b30ee25d1ffcb534bf2ca79fe0; record exists=True","top_level.txt roots (metadata-derived): pytz","metadata-derived source roots ['lib/python3.11/site-packages/pytz']; bounded scan files=6, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:pyyaml","disposition":"YAML parser","rationale":"Metadata/source ownership indicate serialization/config support, with no model source hit.","evidence":["lib/python3.11/site-packages/PyYAML-6.0.2-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/PyYAML-6.0.2-py3.11.egg-info/PKG-INFO; metadata SHA-256 c7cb799996ddca9d1b37e4c9cdbe8df12f4d6139ebd0aac5e9bd4c64e5b7886c","top_level.txt roots=['_yaml', 'yaml']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 18 Python files / 218908 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:pyyaml; environment=core; version=6.0.2"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:rabdam","disposition":"radiation-damage-analysis-and-tabular-output-tool","rationale":"RABDAM is an X-ray radiation-damage analysis tool. Its source pickles pandas output/dataframes for persistence; the focused source scan found no fitted estimator or neural inference path.","evidence":["lib/python3.11/site-packages/rabdam-2.0-py3.11.egg-info/PKG-INFO; Name: rabdam | Version: 2.0 | Summary: RABDAM: A program to identify and quantify specific radiation damage within individual protein crystal structures","owner: top_level=['rabdam', 'tests']; source_roots_from_METADATA_or_RECORD=['rabdam', 'tests']; RECORD_rows=not provided; RECORD_sample=[]","declared dependencies: Requires-Dist: numpy>=1.15.0; Requires-Dist: matplotlib>=2.2.0; Requires-Dist: scipy>=1.1.0; Requires-Dist: pandas>=0.24.1; Requires-Dist: requests; Requires-Dist: setuptools","lib/python3.11/site-packages/rabdam/Subroutines/CalculateBDamage.py:63         import pickle","lib/python3.11/site-packages/rabdam/Subroutines/CalculateBDamage.py:668         # required for subsequent analysis, are then pickled - this allows","lib/python3.11/site-packages/rabdam/Subroutines/CalculateBDamage.py:678         df.to_pickle(storage_file + '_dataframe.pkl')","lib/python3.11/site-packages/rabdam/Subroutines/output.py:666         # Save output scores as a csv file and as a pickled dataframe","lib/python3.11/site-packages/rabdam/Subroutines/output.py:681             old_out_df = pd.read_pickle('Logfiles/Bnet_{}.pkl'.format(prot_or_na))","lib/python3.11/site-packages/rabdam/Subroutines/output.py:689         new_out_df.to_pickle('Logfiles/Bnet_{}.pkl'.format(prot_or_na))"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:reciprocalspaceship","disposition":"crystallographic-data-library-with-two-version-conflicts","rationale":"ReciprocalSpaceship is a crystallographic data-analysis library. Its installed metadata requires Gemmi <=0.7.3 and pandas >=2.2.2 (<=2.3.3); same-core versions are Gemmi 0.7.5 and pandas 2.1.4, violating both declared ranges. No ML model consumer is identified by the bounded source scan.","evidence":["lib/python3.11/site-packages/reciprocalspaceship-1.0.7-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:requests","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/requests-2.28.2-py3.11.egg-info/PKG-INFO sha256=82fcb1df699bff8012c884b1199dd8ee6882ad212f4a11f6a8fc7a0130b007fe bytes=4882 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/requests-2.28.2-py3.11.egg-info/SOURCES.txt rows=47; sample=[\"HISTORY.md\", \"LICENSE\", \"MANIFEST.in\", \"NOTICE\"]","top_level lib/python3.11/site-packages/requests-2.28.2-py3.11.egg-info/top_level.txt=[\"requests\"]","static Python audit group package=requests env=core: 18 files, 180249 bytes, 1 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/requests/packages.py sha256=0d782ff852487336484e6bf4bc40408568f85bee4218220dfe4b2f811d7b0efb"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:ridl","disposition":"RIDL density interpretation package using optional classical learning utilities","rationale":"ridl/perAtomClusterAnalysis.py:3,371-372,418-419 fits KMeans for positive/negative density clustering; 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mapsToDensityMetrics.py:624-625,697"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:scikit-build-core","disposition":"build backend","rationale":"CMake-based Python build backend; build tooling, not a model.","evidence":["installed metadata: lib/python3.11/site-packages/scikit_build_core-0.10.4.dist-info/METADATA; SHA-256=3f575e2238c162cf1e15dbc3a0e398e2a7c7f8236fe50bbfdae452fe7ce4965c; Name=scikit_build_core; Version=0.10.4; Summary=Build backend for CMake based projects","declared Requires-Dist (43): [\"exceptiongroup>=1.0; python_version < '3.11'\",\"importlib-metadata>=4.13; python_version < '3.8'\",\"importlib-resources>=1.3; python_version < '3.9'\",\"packaging>=21.3\",\"pathspec>=0.10.1\",\"tomli>=1.2.2; python_version < '3.11'\",\"typing-extensions>=3.10.0; python_version < '3.9'\",\"pytest-cov[toml]; extra == 'cov'\",\"rich; extra == 'dev'\",\"furo; extra == 'docs'\",\"hatchling; extra == 'docs'\",\"myst-parser>=0.13; extra == 'docs'\",\"setuptools; 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empty top_level list means no import-root claim from that metadata file","static source scan: 75 files, 279024 bytes, 0 skipped/overflow; ML vocabulary hits=2","representative broad-term source hits: [{\"path\": \"scikit_build_core/_vendor/pyproject_metadata/__init__.py\", \"line\": 310, \"text\": \"for classifier in self.classifiers:\"}, {\"path\": \"scikit_build_core/_vendor/pyproject_metadata/__init__.py\", \"line\": 311, \"text\": \"message['Classifier'] = classifier\"}]","node identity: pydist:core:scikit-build-core; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:scikit-image","disposition":"scientific image-processing and feature algorithms","rationale":"Includes restoration/denoising methods, HOG and Fisher-vector features and geometric estimators; these are algorithm capabilities, not evidence of trained weights or CCP4 runtime reach. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/scikit_image-0.22.0.dist-info/METADATA:L2","lib/python3.11/site-packages/scikit_image-0.22.0.dist-info/METADATA: installed metadata ['Name: scikit-image', 'Version: 0.22.0', 'Requires-Dist: numpy>=1.22', 'Requires-Dist: scipy>=1.8', 'Requires-Dist: networkx>=2.8', 'Requires-Dist: pillow>=9.0.1', 'Requires-Dist: imageio>=2.27', 'Requires-Dist: tifffile>=2022.8.12', 'Requires-Dist: packaging>=21', 'Requires-Dist: lazy_loader>=0.3', 'Requires-Dist: meson-python>=0.14; extra == \"build\"', 'Requires-Dist: wheel; extra == \"build\"', 'Requires-Dist: setuptools>=67; extra == \"build\"', 'Requires-Dist: packaging>=21; extra == \"build\"', 'Requires-Dist: ninja; extra == \"build\"', 'Requires-Dist: Cython>=0.29.32; extra == \"build\"', 'Requires-Dist: pythran; extra == \"build\"', 'Requires-Dist: numpy>=1.22; extra == \"build\"']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['skimage']; RECORD rows=818; resolved roots=['lib/python3.11/site-packages/skimage']","lib/python3.11/site-packages/skimage/__init__.py:35 (restoration/denoising APIs)","lib/python3.11/site-packages/skimage/feature/_hog.py:293; feature/_fisher_vector.py:49,239; measure/fit.py:30-32 (feature/estimation methods)"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:scikit-learn","disposition":"classical machine-learning framework","rationale":"Installed scikit-learn provides classical estimators, clustering, ensemble methods, and SVM implementations. This is model-building/inference capability, not proof that any bundled CCP4 task uses every estimator; previously known classical consumers remain outside this package-only disposition.","evidence":["lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/PKG-INFO: Name: scikit-learn","lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/PKG-INFO: Version: 1.4.2","lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/PKG-INFO: Summary: A set of python modules for machine learning and data mining","lib/python3.11/site-packages/sklearn/calibration.py:23: BaseEstimator,","lib/python3.11/site-packages/sklearn/calibration.py:24: ClassifierMixin,","lib/python3.11/site-packages/sklearn/calibration.py:25: MetaEstimatorMixin,","lib/python3.11/site-packages/sklearn/calibration.py:30: from .isotonic import IsotonicRegression","lib/python3.11/site-packages/sklearn/calibration.py:31: from .model_selection import check_cv, cross_val_predict","lib/python3.11/site-packages/scikit_learn-1.4.2-py3.11.egg-info/PKG-INFO:L2 (installed Name/Version)","lib/python3.11/site-packages/sklearn/calibration.py (BaseEstimator, ClassifierMixin, IsotonicRegression source)"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:scipy","disposition":"numerical/statistical scientific infrastructure","rationale":"Numerical/statistical scientific library. Keyword hits resolve to numerical routines and test interoperability, not a bundled trained model.","evidence":["lib/python3.11/site-packages/scipy-1.13.1.dist-info/METADATA:L2","cpu64 installed record lib/python3.11/site-packages/scipy-1.13.1.dist-info/METADATA; sha256=daa3b9481a7879f190a33428547728d6b5d3151996b2bf2b8c64c5d9dd5820ee; record exists=True","metadata-derived source roots ['lib/python3.11/site-packages/scipy']; bounded scan files=45, truncated=True","lib/python3.11/site-packages/scipy/conftest.py:119-120 mentions PyTorch only in array-API test backend setup; scipy/__init__.py:26 lists Orthogonal Distance Regression."],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:seaborn","disposition":"statistical visualization and regression plotting","rationale":"Source implements linear-model plots and optional statsmodels integration. 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no application model role is evidenced.","evidence":["lib/python3.11/site-packages/setuptools-79.0.1.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:setuptools-scm","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/setuptools_scm-8.3.1.dist-info/METADATA sha256=a4a5a66c7dd5f9113d3ae03392ca0918174fdeac4f1b261e63d259f9756df741 bytes=7000 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/setuptools_scm-8.3.1.dist-info/RECORD rows=68; sample=[\"setuptools_scm-8.3.1.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"setuptools_scm-8.3.1.dist-info/METADATA,sha256=pKWmbH3V-RE9OuAzksoJGBdP3qxPGyYeY9JZ-XVt90E,7000\", \"setuptools_scm-8.3.1.dist-info/RECORD,,\", \"setuptools_scm-8.3.1.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0\"]","top_level lib/python3.11/site-packages/setuptools_scm-8.3.1.dist-info/top_level.txt=[\"setuptools_scm\"]","static Python audit group package=setuptools_scm env=core: 29 files, 97041 bytes, 3 files with broad ML/loader marker hits","representative package source lib/python3.11/site-packages/setuptools_scm/_run_cmd.py sha256=0bf5fe2b7132029c3f9b3533dea25a26431e2a197f10cf29746d31019eb4dff3"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:core:shiboken2","disposition":"Qt Python binding generator/runtime support","rationale":"binding infrastructure only; 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The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/six-1.12.0-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/six-1.12.0-py3.11.egg-info/PKG-INFO: Name: six","lib/python3.11/site-packages/six-1.12.0-py3.11.egg-info/PKG-INFO: Version: 1.12.0","lib/python3.11/site-packages/six-1.12.0-py3.11.egg-info/PKG-INFO: Summary: Python 2 and 3 compatibility utilities"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:sqlalchemy","disposition":"general runtime/development infrastructure","rationale":"Database toolkit package. 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source_roots_from_METADATA_or_RECORD=['tornado']; RECORD_rows=not provided; RECORD_sample=[]"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:tqdm","disposition":"progress-reporting-utility","rationale":"tqdm is progress UI; a generic optional Keras adapter is not evidence of an application model consumer.","evidence":["lib/python3.11/site-packages/tqdm-4.66.6.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:trove-classifiers","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/trove_classifiers-2023.11.29.dist-info/METADATA sha256=5fcaf9a1731d22d331648c5347f2a5255f1c653743cfc2595405c09c864d29c6 bytes=2348 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/trove_classifiers-2023.11.29.dist-info/RECORD rows=13; 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Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"record_file_count\": 9}","audits/ccp4-10.0.001/python.json AST group package=typing_extensions.py root=lib/python3.11/site-packages files=1 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:core:tzdata","disposition":"timezone database","rationale":"Timezone database.","evidence":["installed metadata: lib/python3.11/site-packages/tzdata-2022.1.dist-info/METADATA; SHA-256=0d02bf82fb87be291ab464f9e05d277672e77d094f670b0d4663cd33dd495a19; Name=tzdata; Version=2022.1; Summary=Provider of IANA time zone data","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=lib/python3.11/site-packages/tzdata-2022.1.dist-info/top_level.txt; top_level=[\"tzdata\"]; RECORD rows=632; RECORD sample=[\"tzdata-2022.1.dist-info/INSTALLER\", \"tzdata-2022.1.dist-info/METADATA\", \"tzdata-2022.1.dist-info/RECORD\", \"tzdata-2022.1.dist-info/REQUESTED\", \"tzdata-2022.1.dist-info/WHEEL\", \"tzdata-2022.1.dist-info/direct_url.json\", \"tzdata-2022.1.dist-info/licenses/LICENSE\", \"tzdata-2022.1.dist-info/licenses/licenses/LICENSE_APACHE\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 22 files, 252 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:core:tzdata; environment=core; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:core:urllib3","disposition":"HTTP transport library","rationale":"Network transport. Optional secure/SOCKS extras are declarations, not proof of selected use. This is a distinct installed record in the core environment; no identity was borrowed from another environment.","evidence":["lib/python3.11/site-packages/urllib3-1.26.7-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/urllib3-1.26.7-py3.11.egg-info/PKG-INFO: installed metadata ['Name: urllib3', 'Version: 1.26.7', 'Requires-Dist: brotlipy>=0.6.0; extra == \"brotli\"', 'Requires-Dist: pyOpenSSL>=0.14; extra == \"secure\"', 'Requires-Dist: cryptography>=1.3.4; extra == \"secure\"', 'Requires-Dist: idna>=2.0.0; extra == \"secure\"', 'Requires-Dist: certifi; extra == \"secure\"', 'Requires-Dist: ipaddress; python_version == \"2.7\" and extra == \"secure\"', 'Requires-Dist: PySocks!=1.5.7,<2.0,>=1.5.6; extra == \"socks\"']","metadata-owned top_level/RECORD roots: top_level=['urllib3']; RECORD roots=None; RECORD rows=None; resolved roots=['lib/python3.11/site-packages/urllib3']","Installed source scan examples: lib/python3.11/site-packages/urllib3/util/wait.py:83 # sockets for both conditions. (The stdlib selectors module does the same; lib/python3.11/site-packages/urllib3/contrib/pyopenssl.py:103 _stdlib_to_openssl_verify = {; lib/python3.11/site-packages/urllib3/contrib/pyopenssl.py:109 _openssl_to_stdlib_verify = dict((v, k) for k, v in _stdlib_to_openssl_verify.items()); lib/python3.11/site-packages/urllib3/contrib/pyopenssl.py:171 def _dnsname_to_stdlib(name):"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:core:versioneer","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: build-time version metadata helper. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["lib/python3.11/site-packages/versioneer-0.29.dist-info/METADATA:L2","lib/python3.11/site-packages/versioneer-0.29.dist-info/METADATA: Name: versioneer","lib/python3.11/site-packages/versioneer-0.29.dist-info/METADATA: Version: 0.29","lib/python3.11/site-packages/versioneer-0.29.dist-info/METADATA: Summary: Easy VCS-based management of project version strings"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:core:websockets","disposition":"general runtime/development infrastructure","rationale":"Network protocol library package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["lib/python3.11/site-packages/websockets-10.4-py3.11.egg-info/PKG-INFO:L2","cpu64 installed record lib/python3.11/site-packages/websockets-10.4-py3.11.egg-info/PKG-INFO; sha256=d1a241235b14f2f89d18a5a029945ea3b302cc05b04194a82bf91d6c74b8d739; record exists=True","top_level.txt roots (metadata-derived): websockets, websockets/extensions, websockets/legacy","metadata-derived source roots ['lib/python3.11/site-packages/websockets', 'lib/python3.11/site-packages/websockets/extensions', 'lib/python3.11/site-packages/websockets/legacy']; bounded scan files=43, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:core:wget","disposition":"download utility","rationale":"The top-level module is a single wget.py file; its source describes a general HTTP download helper. The package scan initially looks empty only because the module is a file rather than a directory.","evidence":["lib/python3.11/site-packages/wget-3.2-py3.11.egg-info/PKG-INFO:L2","lib/python3.11/site-packages/wget-3.2-py3.11.egg-info/PKG-INFO; metadata SHA-256 b6f51d8060127c28c284fc78b704cbc5611b83e9afc4ee87406e067bdcb08526","top_level.txt roots=['wget']; RECORD=legacy egg-info (no RECORD); RECORD existing=None/None","read-only source scan: 0 Python files / 0 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:core:wget; environment=core; version=3.2","lib/python3.11/site-packages/wget.py:1-24","lib/python3.11/site-packages/wget-3.2-py3.11.egg-info/top_level.txt"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:core:wxpython","disposition":"GUI-binding","rationale":"Installed wxpython 4.2.2 in core is GUI-binding; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["lib/python3.11/site-packages/wxPython-4.2.2-py3.11.egg-info/PKG-INFO; Name: wxPython | Version: 4.2.2 | Summary: Cross platform GUI toolkit for Python, \"Phoenix\" version","owner: top_level=['wx']; source_roots_from_METADATA_or_RECORD=['wx']; RECORD_rows=not provided; RECORD_sample=[]","declared dependencies: Requires-Dist: numpy<1.17; python_version <= \"2.7\"; Requires-Dist: numpy; python_version >= \"3.0\" and python_version < \"3.12\"; Requires-Dist: six"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:core:xia2","disposition":"crystallographic-integration-with-correlation-clustering","rationale":"xia2 MultiCrystalAnalysis statically constructs a DIALS CorrelationMatrix clustering workflow and invokes it when the clustering path is selected. This is correlation-based experiment analysis; the package source contains no separate fitted ML weight asset in the assigned evidence.","evidence":["lib/python3.11/site-packages/xia2-3.29.0-py3.11.egg-info/PKG-INFO:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:core:xyzservices","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata lib/python3.11/site-packages/xyzservices-2021.9.1-py3.11.egg-info/PKG-INFO sha256=1652c3f6ef8a19169cc0dec1f5d58425d3c1c705d2fbf6db860b6a876179ddb8 bytes=4194 (manifest metadata hash matches)","ownership file lib/python3.11/site-packages/xyzservices-2021.9.1-py3.11.egg-info/SOURCES.txt rows=19; sample=[\"LICENSE\", \"MANIFEST.in\", \"README.md\", \"setup.cfg\"]","top_level lib/python3.11/site-packages/xyzservices-2021.9.1-py3.11.egg-info/top_level.txt=[\"tests\", \"xyzservices\"]","static Python audit group package=xyzservices env=core: 5 files, 22674 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/abcfold:abcfold","disposition":"protein-folding workflow wrapper around optional external structure-prediction backends","rationale":"wrapper source enumerates AlphaFold3/Boltz/Chai1/OpenFold3/Protenix launch paths; those backend packages are not confirmed as installed here","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold-1.1.1.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold-1.1.1.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"numpy==1.26.4\", \"colorama\", \"tqdm\", \"biopython==1.84\", \"requests\", \"types-requests\", \"pandas==2.2.3\", \"plotly\", \"jinja2\", \"pyarrow==19.0.1\"]; ownership={\"entry_points.txt\": \"[console_scripts]\\nabcfold = abcfold.abcfold:main\\ncustom_templates = abcfold.scripts.add_custom_template:main\\nipsae = abcfold.scripts.ipsae:main\\nmmseqs2msa = abcfold.scripts.add_mmseqs_msa:main\\n\", \"record_file_count\": 170, \"top_level.txt\": \"abcfold\\n\"}","audits/ccp4-10.0.001/python.json AST group package=abcfold root=share/mamba/envs/abcfold/lib/python3.11/site-packages files=37 hit_files=31 imports={}","share/mamba/envs/abcfold/lib/python3.11/site-packages/abcfold launcher/wrapper source for AlphaFold3, Boltz, Chai1, OpenFold3 and Protenix backends"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/abcfold:biopython","disposition":"computational biology algorithms library","rationale":"Source scan includes legacy classifier APIs and clustering references; this is algorithm/training capability, with no fitted predictor asset or application consumer established by this package record.","evidence":["installed metadata: share/mamba/envs/abcfold/lib/python3.11/site-packages/biopython-1.84.dist-info/METADATA; SHA-256=7aedff296f719719d20dcb701b951b61f3a2a9cb210ebc4f43575a40a671fd0e; Name=biopython; Version=1.84; Summary=Freely available tools for computational molecular biology.","declared Requires-Dist (1): [\"numpy\"]","ownership: top_level metadata path candidate=share/mamba/envs/abcfold/lib/python3.11/site-packages/biopython-1.84.dist-info/top_level.txt; top_level=[\"Bio\", \"BioSQL\"]; RECORD rows=682; RECORD sample=[\"Bio/Affy/CelFile.py\", \"Bio/Affy/__init__.py\", \"Bio/Align/AlignInfo.py\", \"Bio/Align/Applications/_ClustalOmega.py\", \"Bio/Align/Applications/_Clustalw.py\", \"Bio/Align/Applications/_Dialign.py\", \"Bio/Align/Applications/_MSAProbs.py\", \"Bio/Align/Applications/_Mafft.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 62 files, 1745578 bytes, 0 skipped/overflow; ML vocabulary hits=80","representative broad-term source hits: [{\"path\": \"Bio/Align/Applications/_ClustalOmega.py\", \"line\": 111, \"text\": \"# Clustering\"}, {\"path\": \"Bio/Align/Applications/_ClustalOmega.py\", \"line\": 126, \"text\": \"\\\"Guide tree input file (skips distance computation and guide-tree clustering step).\\\",\"}, {\"path\": \"Bio/Align/Applications/_ClustalOmega.py\", \"line\": 150, \"text\": \"[\\\"--clustering-out\\\", \\\"clusteringout\\\"],\"}, {\"path\": \"Bio/Align/Applications/_ClustalOmega.py\", \"line\": 151, \"text\": \"\\\"Clustering output file\\\",\"}, {\"path\": \"Bio/Align/Applications/_Clustalw.py\", \"line\": 477, \"text\": \"[\\\"-clustering\\\", \\\"-CLUSTERING\\\", \\\"CLUSTERING\\\", \\\"clustering\\\"],\"}]","targeted static implementation sources: Bio/NaiveBayes.py:62,147-174 (trained naive Bayes API); Bio/kNN.py:53,78-104 (trained k-nearest-neighbors API); Bio/LogisticRegression.py:44,58 (training/classification API); Bio/MaxEntropy.py:36,282-288 (maximum-entropy classifier/trainer); Bio/Cluster/__init__.py:115,181,252 (k-means/k-medoids/hierarchical algorithms).","node identity: pydist:share/mamba/envs/abcfold:biopython; environment=share/mamba/envs/abcfold; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/abcfold:certifi","disposition":"TLS CA certificate bundle","rationale":"Trust-store data; no ML role. This is a distinct installed record in the share/mamba/envs/abcfold environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/certifi-2026.7.22.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/certifi-2026.7.22.dist-info/METADATA: installed metadata ['Name: certifi', 'Version: 2026.7.22']","metadata-owned top_level/RECORD roots: top_level=['certifi']; RECORD roots=['certifi']; RECORD rows=18; resolved roots=['share/mamba/envs/abcfold/lib/python3.11/site-packages/certifi']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/abcfold:charset-normalizer","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: text encoding detection utility. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer-3.5.2.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer-3.5.2.dist-info/METADATA: Name: charset-normalizer","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer-3.5.2.dist-info/METADATA: Version: 3.5.2","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer-3.5.2.dist-info/METADATA: Summary: The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer/models.py:45: # __eq__ total as the data model requires (mirrors the lookup","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer/__init__.py:28: from .models import CharsetMatch, CharsetMatches","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer/api.py:22: from .models import CharsetMatch, CharsetMatches","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer/api.py:71: You may want to focus your attention to some code page or/and not others, use cp_isolation and cp_exclusion for that","share/mamba/envs/abcfold/lib/python3.11/site-packages/charset_normalizer/api.py:600: # coverage regressions by producing unrepresentative coherence scores."],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/abcfold:colorama","disposition":"general runtime/development infrastructure","rationale":"Terminal color handling package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/colorama-0.4.6.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/abcfold/lib/python3.11/site-packages/colorama-0.4.6.dist-info/METADATA; sha256=7baed29eb50c3b29bdb33ff84e3177bf1bc05784f7685ecdcaa4471c7dd810cc; record exists=True","metadata-derived source roots ['share/mamba/envs/abcfold/lib/python3.11/site-packages/colorama']; bounded scan files=13, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/abcfold:idna","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/idna-3.20.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/idna-3.20.dist-info/METADATA; metadata SHA-256 dbd8c14c1e4ca1e0c9824a6dbc7cbbf78884f38eb52d91148cd3025f671e4b85","top_level.txt roots=[]; RECORD=share/mamba/envs/abcfold/lib/python3.11/site-packages/idna-3.20.dist-info/RECORD; RECORD existing=18/28","read-only source scan: 10 Python files / 332039 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/abcfold:idna; environment=share/mamba/envs/abcfold; version=3.20"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/abcfold:jinja2","disposition":"template-engine","rationale":"Installed jinja2 3.1.6 in share/mamba/envs/abcfold is template-engine; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/jinja2-3.1.6.dist-info/METADATA; Name: Jinja2 | Version: 3.1.6 | Summary: A very fast and expressive template engine.","owner: top_level=(absent); source_roots_from_METADATA_or_RECORD=['jinja2']; RECORD_rows=57; RECORD_sample=['jinja2-3.1.6.dist-info/INSTALLER', 'jinja2-3.1.6.dist-info/METADATA', 'jinja2-3.1.6.dist-info/RECORD', 'jinja2-3.1.6.dist-info/WHEEL', 'jinja2-3.1.6.dist-info/entry_points.txt', 'jinja2-3.1.6.dist-info/licenses/LICENSE.txt', 'jinja2/__init__.py', 'jinja2/__pycache__/__init__.cpython-311.pyc']","declared dependencies: Requires-Dist: MarkupSafe>=2.0; Requires-Dist: Babel>=2.7 ; extra == \"i18n\""],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/abcfold:markupsafe","disposition":"template-escaping-utility","rationale":"MarkupSafe is HTML/template escaping support in the abcfold environment, not model code.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/markupsafe-3.0.4.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/abcfold:narwhals","disposition":"numerical_or_dataframe_infrastructure","rationale":"Installed numerical array/dataframe infrastructure; source marker hits were reviewed in context and did not establish trained weights or an application ML path for this distribution.","evidence":["installed metadata share/mamba/envs/abcfold/lib/python3.11/site-packages/narwhals-2.27.1.dist-info/METADATA sha256=5962ef236f36fe34aff21a837a0698386dcb1f0de54462aa18b73698e6ef1a4f bytes=15518 (manifest metadata hash matches)","ownership file share/mamba/envs/abcfold/lib/python3.11/site-packages/narwhals-2.27.1.dist-info/RECORD rows=332; sample=[\"narwhals-2.27.1.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"narwhals-2.27.1.dist-info/METADATA,sha256=WWLvI282_jSv8hqDegaYOG3LHw3lRGKqGLc2mObvGk8,15518\", \"narwhals-2.27.1.dist-info/RECORD,,\", \"narwhals-2.27.1.dist-info/WHEEL,sha256=xTCBFIZIIyRSxyowOv5Wqg_jFU6KsdIffuulBB09Ph8,80\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=narwhals env=share/mamba/envs/abcfold: 163 files, 2026073 bytes, 4 files with broad ML/loader marker hits","representative package source share/mamba/envs/abcfold/lib/python3.11/site-packages/narwhals/_utils.py sha256=b4b4094f9636ddc4115802a3bdf1a8b80b4c1b369f23150a1b971c12c55ec290"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/abcfold:numpy","disposition":"numerical array foundation for the ABCFold environment","rationale":"array/runtime dependency; not itself a trained model","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/numpy-1.26.4.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/abcfold/lib/python3.11/site-packages/numpy-1.26.4.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"entry_points.txt\": \"[array_api]\\nnumpy = numpy.array_api\\n\\n[pyinstaller40]\\nhook-dirs = numpy:_pyinstaller_hooks_dir\\n\\n[console_scripts]\\nf2py = numpy.f2py.f2py2e:main\\n\\n\", \"record_file_count\": 1406}","audits/ccp4-10.0.001/python.json AST group package=numpy root=lib/python3.11/site-packages files=489 hit_files=44 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/abcfold:packaging","disposition":"Python packaging utilities","rationale":"Version/specifier/metadata utilities; broad classifier hits are metadata vocabulary, not ML. The matched `classifier` hits describe PyPI metadata classifiers.","evidence":["installed metadata: share/mamba/envs/abcfold/lib/python3.11/site-packages/packaging-26.3.dist-info/METADATA; SHA-256=70fdb89fc4d4a9a043bf7372b8972bcc883fddff34ab55e9cf80d73875384763; Name=packaging; Version=26.3; Summary=Core utilities for Python packages","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=share/mamba/envs/abcfold/lib/python3.11/site-packages/packaging-26.3.dist-info/top_level.txt; top_level=[]; RECORD rows=30; RECORD sample=[\"packaging-26.3.dist-info/INSTALLER\", \"packaging-26.3.dist-info/METADATA\", \"packaging-26.3.dist-info/RECORD\", \"packaging-26.3.dist-info/WHEEL\", \"packaging-26.3.dist-info/licenses/LICENSE\", \"packaging-26.3.dist-info/licenses/LICENSE.APACHE\", \"packaging-26.3.dist-info/licenses/LICENSE.BSD\", \"packaging/__init__.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 22 files, 481499 bytes, 0 skipped/overflow; ML vocabulary hits=2","representative broad-term source hits: [{\"path\": \"packaging/metadata.py\", \"line\": 277, \"text\": \"\\\"classifier\\\": \\\"classifiers\\\",\"}, {\"path\": \"packaging/metadata.py\", \"line\": 978, \"text\": \"\\\"\\\"\\\":external:ref:`core-metadata-classifier`\\\"\\\"\\\"\"}]","node identity: pydist:share/mamba/envs/abcfold:packaging; environment=share/mamba/envs/abcfold; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/abcfold:pandas","disposition":"tabular data library","rationale":"Dataframe and numerical data handling; general-purpose algorithm-adjacent helpers, no trained model identified in package scan. This is a distinct installed record in the share/mamba/envs/abcfold environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas-2.2.3.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas-2.2.3.dist-info/METADATA: installed metadata ['Name: pandas', 'Version: 2.2.3', 'Requires-Dist: numpy>=1.22.4; python_version < \"3.11\"', 'Requires-Dist: numpy>=1.23.2; python_version == \"3.11\"', 'Requires-Dist: numpy>=1.26.0; python_version >= \"3.12\"', 'Requires-Dist: python-dateutil>=2.8.2', 'Requires-Dist: pytz>=2020.1', 'Requires-Dist: tzdata>=2022.7', 'Requires-Dist: hypothesis>=6.46.1; extra == \"test\"', 'Requires-Dist: pytest>=7.3.2; extra == \"test\"', 'Requires-Dist: pytest-xdist>=2.2.0; extra == \"test\"', 'Requires-Dist: pyarrow>=10.0.1; extra == \"pyarrow\"', 'Requires-Dist: bottleneck>=1.3.6; extra == \"performance\"', 'Requires-Dist: numba>=0.56.4; extra == \"performance\"', 'Requires-Dist: numexpr>=2.8.4; extra == \"performance\"', 'Requires-Dist: scipy>=1.10.0; extra == \"computation\"', 'Requires-Dist: xarray>=2022.12.0; extra == \"computation\"', 'Requires-Dist: fsspec>=2022.11.0; extra == \"fss\"']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['pandas']; RECORD rows=2921; resolved roots=['share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas']","Installed source scan examples: share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas/conftest.py:1801 # correctness of inference tested in tests/dtypes/test_inference.py; share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas/plotting/_misc.py:281 pandas.plotting.andrews_curves : Plot clustering visualization.; share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas/plotting/_misc.py:332 Generate a matplotlib plot for visualizing clusters of multivariate data.; share/mamba/envs/abcfold/lib/python3.11/site-packages/pandas/plotting/_core.py:1431 The method used to calculate the estimator bandwidth. This can be"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/abcfold:pip","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: Python package installer. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/pip-26.2.1.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip-26.2.1.dist-info/METADATA: Name: pip","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip-26.2.1.dist-info/METADATA: Version: 26.2.1","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip-26.2.1.dist-info/METADATA: Summary: The PyPA recommended tool for installing Python packages.","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip/_internal/self_outdated_check.py:21: from pip._internal.models.release_control import ReleaseControl","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip/_internal/self_outdated_check.py:22: from pip._internal.models.selection_prefs import SelectionPreferences","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip/_internal/wheel_builder.py:17: from pip._internal.models.link import Link","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip/_internal/wheel_builder.py:18: from pip._internal.models.wheel import Wheel","share/mamba/envs/abcfold/lib/python3.11/site-packages/pip/_internal/cache.py:16: from pip._internal.models.direct_url import DirectUrl"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/abcfold:plotly","disposition":"visualization infrastructure","rationale":"Interactive plotting/visualization library. The reviewed package sources and samples are visualization/data support, not a trained model.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/plotly-7.1.0.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/abcfold/lib/python3.11/site-packages/plotly-7.1.0.dist-info/METADATA; sha256=06b5359b97e92b0cf267237e7ec1b51fe531b6744d83810f2fb543e743687e1e; record exists=True","metadata-derived source roots ['share/mamba/envs/abcfold/lib/python3.11/site-packages/_plotly_utils', 'share/mamba/envs/abcfold/lib/python3.11/site-packages/plotly']; bounded scan files=84, truncated=True"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/abcfold:pyarrow","disposition":"columnar data and IPC support","rationale":"Broad classifier/regression matches occur in tests/conftest and test files; no trained model use was established.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/pyarrow-19.0.1.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/pyarrow-19.0.1.dist-info/METADATA; metadata SHA-256 120a17c8e006d2e1f3f4071385fd0b5f09b9c17b600043dd28b00607fb02265c","top_level.txt roots=['__dummy__', 'pyarrow']; RECORD=share/mamba/envs/abcfold/lib/python3.11/site-packages/pyarrow-19.0.1.dist-info/RECORD; RECORD existing=771/876","read-only source scan: 105 Python files / 2490290 bytes; 8 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/abcfold:pyarrow; environment=share/mamba/envs/abcfold; version=19.0.1","share/mamba/envs/abcfold/lib/python3.11/site-packages/pyarrow/conftest.py","share/mamba/envs/abcfold/lib/python3.11/site-packages/pyarrow/tests"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/abcfold:python-dateutil","disposition":"date-time-utility","rationale":"Installed python-dateutil 2.9.0.post0 in share/mamba/envs/abcfold is date-time-utility; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/python_dateutil-2.9.0.post0.dist-info/METADATA; Name: python-dateutil | Version: 2.9.0.post0 | Summary: Extensions to the standard Python datetime module","owner: top_level=['dateutil']; source_roots_from_METADATA_or_RECORD=['dateutil']; RECORD_rows=44; RECORD_sample=['dateutil/__init__.py', 'dateutil/__pycache__/__init__.cpython-311.pyc', 'dateutil/__pycache__/_common.cpython-311.pyc', 'dateutil/__pycache__/_version.cpython-311.pyc', 'dateutil/__pycache__/easter.cpython-311.pyc', 'dateutil/__pycache__/relativedelta.cpython-311.pyc', 'dateutil/__pycache__/rrule.cpython-311.pyc', 'dateutil/__pycache__/tzwin.cpython-311.pyc']","declared dependencies: Requires-Dist: six >=1.5"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/abcfold:pytz","disposition":"timezone-database-utility","rationale":"pytz supplies timezone definitions; not model code.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/pytz-2026.5.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/abcfold:requests","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-2.34.2.dist-info/METADATA sha256=8c384ba3e979480faae2859d3c5e6c1276dd2c3616e322e124d52c8cfc556f27 bytes=4806 (manifest metadata hash matches)","ownership file share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-2.34.2.dist-info/RECORD rows=46; sample=[\"requests-2.34.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"requests-2.34.2.dist-info/METADATA,sha256=jDhLo-l5SA-q4oWdPF5sEnbdLDYW4yLhJNUsjPxVbyc,4806\", \"requests-2.34.2.dist-info/RECORD,,\", \"requests-2.34.2.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91\"]","top_level share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-2.34.2.dist-info/top_level.txt=[\"requests\"]","static Python audit group package=requests env=share/mamba/envs/abcfold: 19 files, 217284 bytes, 2 files with broad ML/loader marker hits","representative package source share/mamba/envs/abcfold/lib/python3.11/site-packages/requests/compat.py sha256=5d79ba289690b5015044341a1f7bc7d24134fc13a2db3efcf852515bf9aa18b4"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/abcfold:setuptools","disposition":"Python package installation/build tooling in the ABCFold environment","rationale":"installer/build metadata only; recorded egg-info is under the Python 3.11 environment path despite the py3.10 egg-info suffix","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/setuptools-84.0.0-py3.10.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from share/mamba/envs/abcfold/lib/python3.11/site-packages/setuptools-84.0.0-py3.10.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"pytest!=8.1.*,>=6; extra == \\\"test\\\"\", \"virtualenv>=13.0.0; extra == \\\"test\\\"\", \"wheel>=0.44.0; extra == \\\"test\\\"\", \"pip>=19.1; extra == \\\"test\\\"\", \"packaging>=24.2; extra == \\\"test\\\"\", \"jaraco.envs>=2.2; extra == \\\"test\\\"\", \"pytest-xdist>=3; extra == \\\"test\\\"\", \"jaraco.path>=3.7.2; extra == \\\"test\\\"\", \"build[virtualenv]>=1.0.3; extra == \\\"test\\\"\", \"filelock>=3.4.0; extra == \\\"test\\\"\", \"ini2toml[lite]>=0.14; extra == \\\"test\\\"\", \"tomli-w>=1.0.0; extra == \\\"test\\\"\", \"pytest-timeout; extra == \\\"test\\\"\", \"pytest-perf; sys_platform != \\\"cygwin\\\" and extra == \\\"test\\\"\", \"jaraco.develop>=7.21; (python_version >= \\\"3.9\\\" and sys_platform != \\\"cygwin\\\") and extra == \\\"test\\\"\", \"pytest-home>=0.5; extra == \\\"test\\\"\", \"pytest-subprocess; extra == \\\"test\\\"\", \"pyproject-hooks!=1.1; extra == \\\"test\\\"\", \"jaraco.test>=5.5; extra == \\\"test\\\"\", \"sphinx>=3.5; extra == \\\"doc\\\"\", \"jaraco.packaging>=9.3; extra == \\\"doc\\\"\", \"rst.linker>=1.9; extra == \\\"doc\\\"\", \"furo; extra == \\\"doc\\\"\", \"sphinx-lint; extra == \\\"doc\\\"\", \"jaraco.tidelift>=1.4; extra == \\\"doc\\\"\", \"pygments-github-lexers==0.0.5; extra == \\\"doc\\\"\", \"sphinx-favicon; extra == \\\"doc\\\"\", \"sphinx-inline-tabs; extra == \\\"doc\\\"\", \"sphinx-reredirects; extra == \\\"doc\\\"\", \"sphinxcontrib-towncrier; extra == \\\"doc\\\"\", \"sphinx-notfound-page<2,>=1; extra == \\\"doc\\\"\", \"pyproject-hooks!=1.1; extra == \\\"doc\\\"\", \"towncrier<24.7; extra == \\\"doc\\\"\", \"packaging>=24.2; extra == \\\"core\\\"\", \"more_itertools>=8.8; extra == \\\"core\\\"\", \"jaraco.text>=3.7; extra == \\\"core\\\"\", \"importlib_metadata>=6; python_version < \\\"3.10\\\" and extra == \\\"core\\\"\", \"tomli>=2.0.1; python_version < \\\"3.11\\\" and extra == \\\"core\\\"\", \"wheel>=0.43.0; extra == \\\"core\\\"\", \"jaraco.functools>=4; extra == \\\"core\\\"\", \"more_itertools; extra == \\\"core\\\"\", \"pytest-checkdocs>=2.14; extra == \\\"check\\\"\", \"pytest-ruff>=0.2.1; sys_platform != \\\"cygwin\\\" and extra == \\\"check\\\"\", \"ruff>=0.13.0; sys_platform != \\\"cygwin\\\" and extra == \\\"check\\\"\", \"pytest-cov; extra == \\\"cover\\\"\", \"pytest-enabler>=3.4; extra == \\\"enabler\\\"\", \"pytest-mypy>=1.0.1; platform_python_implementation != \\\"PyPy\\\" and extra == \\\"type\\\"\", \"mypy==1.18.*; extra == \\\"type\\\"\", \"importlib_metadata>=7.0.2; python_version < \\\"3.10\\\" and extra == \\\"type\\\"\", \"jaraco.develop>=7.21; sys_platform != \\\"cygwin\\\" and extra == \\\"type\\\"\"]; ownership={\"SOURCES.txt\": \"LICENSE\\nMANIFEST.in\\nNEWS.rst\\nREADME.rst\\nconftest.py\\nexercises.py\\nlauncher.c\\nmypy.ini\\npyproject.toml\\npytest.ini\\nsetup.cfg\\nsetup.py\\ntox.ini\\n_distutils_hack/__init__.py\\n_distutils_hack/override.py\\ndocs/artwork.rst\\ndocs/build_meta.rst\\ndocs/conf.py\\ndocs/history.rst\\ndocs/index.rst\\ndocs/python 2 sunset.rst\\ndocs/roadmap.rst\\ndocs/setuptools.rst\\ndocs/deprecated/changed_keywords.rst\\ndocs/deprecated/commands.rst\\ndocs/deprecated/dependency_links.rst\\ndocs/deprecated/distutils-legacy.rst\\ndocs/deprecated/easy_install.rst\\ndocs/deprecated/functionalities.rst\\ndocs/deprecated/index.rst\\ndocs/deprecated/pkg_resources.rst\\ndocs/deprecated/python_eggs.rst\\ndocs/deprecated/resource_extraction.rst\\ndocs/deprecated/sdist-reproducibility.rst\\ndocs/deprecated/zip_safe.rst\\ndocs/deprecated/distutils/_setuptools_disclaimer.rst\\ndocs/deprecated/distutils/apiref.rst\\ndocs/deprecated/distutils/builtdist.rst\\ndocs/deprecated/distutils/commandref.rst\\ndocs/deprecated/distutils/configfile.rst\\ndocs/deprecated/distutils/examples.rst\\ndocs/deprecated/distutils/extending.rst\\ndocs/deprecated/distutils/index.rst\\ndocs/deprecated/distutils/introduction.rst\\ndocs/deprecated/distutils/packageindex.rst\\ndocs/deprecated/distutils/setupscript.rst\\ndocs/deprecated/distutils/sourcedist.rst\\ndocs/deprecated/distutils/uploading.rst\\ndocs/development/developer-guide.rst\\ndocs/development/index.rst\\ndocs/development/releases.rst\\ndocs/references/keywords.rst\\ndocs/userguide/datafiles.rst\\ndocs/userguide/declarative_config.rst\\ndocs/userguide/dependenc\", \"entry_points.txt\": \"[distutils.commands]\\nalias = setuptools.command.alias:alias\\nbdist_egg = setuptools.command.bdist_egg:bdist_egg\\nbdist_rpm = setuptools.command.bdist_rpm:bdist_rpm\\nbdist_wheel = setuptools.command.bdist_wheel:bdist_wheel\\nbuild = setuptools.command.build:build\\nbuild_clib = setuptools.command.build_clib:build_clib\\nbuild_ext = setuptools.command.build_ext:build_ext\\nbuild_py = setuptools.command.build_py:build_py\\ndevelop = setuptools.command.develop:develop\\ndist_info = setuptools.command.dist_info:dist_info\\neasy_install = setuptools.command.easy_install:easy_install\\neditable_wheel = setuptools.command.editable_wheel:editable_wheel\\negg_info = setuptools.command.egg_info:egg_info\\ninstall = setuptools.command.install:install\\ninstall_egg_info = setuptools.command.install_egg_info:install_egg_info\\ninstall_lib = setuptools.command.install_lib:install_lib\\ninstall_scripts = setuptools.command.install_scripts:install_scripts\\nrotate = setuptools.command.rotate:rotate\\nsaveopts = setuptools.command.saveopts:saveopts\\nsdist = setuptools.command.sdist:sdist\\nsetopt = setuptools.command.setopt:setopt\\n\\n[distutils.setup_keywords]\\ndependency_links = setuptools.dist:assert_string_list\\neager_resources = setuptools.dist:assert_string_list\\nentry_points = setuptools.dist:check_entry_points\\nexclude_package_data = setuptools.dist:check_package_data\\nextras_require = setuptools.dist:check_extras\\ninclude_package_data = setuptools.dist:assert_bool\\ninstall_requires = setuptools.dist:check_requirements\\nnamespace_p\", \"top_level.txt\": \"_distutils_hack\\nsetuptools\\n\"}","audits/ccp4-10.0.001/python.json AST group package=setuptools root=lib/python3.11/site-packages files=346 hit_files=44 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/abcfold:six","disposition":"compatibility utility","rationale":"Python compatibility utility.","evidence":["installed metadata: share/mamba/envs/abcfold/lib/python3.11/site-packages/six-1.17.0.dist-info/METADATA; SHA-256=562042078c2752549f6d8a7c86dbc5dd708088a7be6d80672ec7b07100b72468; Name=six; Version=1.17.0; Summary=Python 2 and 3 compatibility utilities","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=share/mamba/envs/abcfold/lib/python3.11/site-packages/six-1.17.0.dist-info/top_level.txt; top_level=[\"six\"]; RECORD rows=7; RECORD sample=[\"six-1.17.0.dist-info/INSTALLER\", \"six-1.17.0.dist-info/LICENSE\", \"six-1.17.0.dist-info/METADATA\", \"six-1.17.0.dist-info/RECORD\", \"six-1.17.0.dist-info/WHEEL\", \"six-1.17.0.dist-info/top_level.txt\", \"six.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 1 files, 34703 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:share/mamba/envs/abcfold:six; environment=share/mamba/envs/abcfold; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/abcfold:tqdm","disposition":"progress display utility","rationale":"Progress bars; contains optional Keras callback integration, but that optional adapter does not establish an installed or reached model backend. This is a distinct installed record in the share/mamba/envs/abcfold environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm-4.70.1.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm-4.70.1.dist-info/METADATA: installed metadata ['Name: tqdm', 'Version: 4.70.1', 'Requires-Dist: colorama; platform_system == \"Windows\"', 'Requires-Dist: requests; extra == \"discord\"', 'Requires-Dist: envwrap; extra == \"discord\"', 'Requires-Dist: slack-sdk; extra == \"slack\"', 'Requires-Dist: envwrap; extra == \"slack\"', 'Requires-Dist: requests; extra == \"telegram\"', 'Requires-Dist: envwrap; extra == \"telegram\"', 'Requires-Dist: ipywidgets>=6; extra == \"notebook\"']","metadata-owned top_level/RECORD roots: top_level=['tqdm']; RECORD roots=['tqdm']; RECORD rows=72; resolved roots=['share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm']","Installed source scan examples: share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm/std.py:549 # (we allow manual override since predicting time is an arcane art); share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm/std.py:609 # total is known: we can predict some stats; share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm/keras.py:10 from tensorflow import keras; share/mamba/envs/abcfold/lib/python3.11/site-packages/tqdm/keras.py:122 def _implements_predict_batch_hooks():"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/abcfold:types-requests","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: typing stub distribution for requests. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/types_requests-2.33.0.20261006.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/types_requests-2.33.0.20261006.dist-info/METADATA: Name: types-requests","share/mamba/envs/abcfold/lib/python3.11/site-packages/types_requests-2.33.0.20261006.dist-info/METADATA: Version: 2.33.0.20261006","share/mamba/envs/abcfold/lib/python3.11/site-packages/types_requests-2.33.0.20261006.dist-info/METADATA: Summary: Typing stubs for requests","share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-stubs/sessions.pyi:6: from . import adapters, auth as _auth, compat, cookies, exceptions, hooks, models, status_codes, utils","share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-stubs/sessions.pyi:7: from .models import _JSON, Response","share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-stubs/sessions.pyi:16: Request = models.Request","share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-stubs/sessions.pyi:17: PreparedRequest = models.PreparedRequest","share/mamba/envs/abcfold/lib/python3.11/site-packages/requests-stubs/sessions.pyi:18: DEFAULT_REDIRECT_LIMIT = models.DEFAULT_REDIRECT_LIMIT"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/abcfold:tzdata","disposition":"general runtime/development infrastructure","rationale":"Timezone database package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/tzdata-2026.5.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/abcfold/lib/python3.11/site-packages/tzdata-2026.5.dist-info/METADATA; sha256=e0780e8b6dc8882ce87e871a9d4589d59cb05a0c2d64f58b1ba62cde1ee91f6a; record exists=True","top_level.txt roots (metadata-derived): tzdata","metadata-derived source roots ['share/mamba/envs/abcfold/lib/python3.11/site-packages/tzdata']; bounded scan files=22, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/abcfold:urllib3","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/urllib3-2.8.0.dist-info/METADATA:L2","share/mamba/envs/abcfold/lib/python3.11/site-packages/urllib3-2.8.0.dist-info/METADATA; metadata SHA-256 10898c620e8007c030e07fa5622b68358a43010025dfbd78a1cb797699de2bb4","top_level.txt roots=[]; RECORD=share/mamba/envs/abcfold/lib/python3.11/site-packages/urllib3-2.8.0.dist-info/RECORD; RECORD existing=43/79","read-only source scan: 36 Python files / 434671 bytes; 8 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/abcfold:urllib3; environment=share/mamba/envs/abcfold; version=2.8.0","bounded hit review: 8 hit files were parser/build/test/support contexts; no scientific model consumer identified"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/abcfold:wheel","disposition":"python-build-or-test-infrastructure","rationale":"Installed wheel 0.48.0 in share/mamba/envs/abcfold is python-build-or-test-infrastructure; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/abcfold/lib/python3.11/site-packages/wheel-0.48.0.dist-info/METADATA; Name: wheel | Version: 0.48.0 | Summary: Command line tool for manipulating wheel files","owner: top_level=(absent); source_roots_from_METADATA_or_RECORD=['wheel']; RECORD_rows=21; RECORD_sample=['../../../bin/wheel', 'wheel-0.48.0.dist-info/METADATA', 'wheel-0.48.0.dist-info/RECORD', 'wheel-0.48.0.dist-info/WHEEL', 'wheel-0.48.0.dist-info/entry_points.txt', 'wheel-0.48.0.dist-info/licenses/LICENSE.txt', 'wheel/__init__.py', 'wheel/__main__.py']","declared dependencies: Requires-Dist: packaging >= 24.0"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:aiohappyeyeballs","disposition":"async-networking-utility","rationale":"aiohappyeyeballs is asyncio connection support; not model code.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/aiohappyeyeballs-2.6.1.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:aiohttp","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/aiohttp-3.13.5.dist-info/METADATA sha256=c951ddd170c8bae6abe5c8138791192369835c2444794096099f9503a816bd44 bytes=8145 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/aiohttp-3.13.5.dist-info/RECORD rows=138; sample=[\"aiohttp-3.13.5.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"aiohttp-3.13.5.dist-info/METADATA,sha256=yVHd0XDIuuar5cgTh5EZI2mDXCREeUCWCZ-VA6gWvUQ,8145\", \"aiohttp-3.13.5.dist-info/RECORD,,\", \"aiohttp-3.13.5.dist-info/WHEEL,sha256=OZLCzpIUHEX42a9RmtxH4_auVuxdXhghS0dmIdhxCRQ,184\"]","top_level share/mamba/envs/pandda2/lib/python3.9/site-packages/aiohttp-3.13.5.dist-info/top_level.txt=[\"aiohttp\"]","static Python audit group package=aiohttp env=share/mamba/envs/pandda2: 55 files, 895064 bytes, 1 files with broad ML/loader marker hits","representative package source share/mamba/envs/pandda2/lib/python3.9/site-packages/aiohttp/web.py sha256=27348d99e8e0e46e987850279088197f2b6a6d4f3ab0dbbce38c982a6a14a6ab"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:aiosignal","disposition":"async callback utility in the PanDDA2 environment","rationale":"async infrastructure only","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/aiosignal-1.4.0.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/aiosignal-1.4.0.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"frozenlist>=1.1.0\", \"typing-extensions>=4.2; python_version < \\\"3.13\\\"\"]; ownership={\"record_file_count\": 9, \"top_level.txt\": \"aiosignal\\n\"}","audits/ccp4-10.0.001/python.json AST group package=aiosignal root=share/mamba/envs/pandda2/lib/python3.9/site-packages files=1 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:async-timeout","disposition":"asyncio utility","rationale":"Timeout helper for asyncio.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/async_timeout-5.0.1.dist-info/METADATA; SHA-256=4550cd1083d820124a3ec8d38490da2915f587bf7ee1061036e04b4973c8b54f; Name=async-timeout; Version=5.0.1; Summary=Timeout context manager for asyncio programs","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/async_timeout-5.0.1.dist-info/top_level.txt; top_level=[\"async_timeout\"]; RECORD rows=9; RECORD sample=[\"async_timeout-5.0.1.dist-info/INSTALLER\", \"async_timeout-5.0.1.dist-info/LICENSE\", \"async_timeout-5.0.1.dist-info/METADATA\", \"async_timeout-5.0.1.dist-info/RECORD\", \"async_timeout-5.0.1.dist-info/WHEEL\", \"async_timeout-5.0.1.dist-info/top_level.txt\", \"async_timeout-5.0.1.dist-info/zip-safe\", \"async_timeout/__init__.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 1 files, 9186 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:share/mamba/envs/pandda2:async-timeout; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:attrs","disposition":"Python object/attribute utility","rationale":"Class construction and metadata helpers; no ML role. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/attrs-26.1.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/attrs-26.1.0.dist-info/METADATA: installed metadata ['Name: attrs', 'Version: 26.1.0']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['attr', 'attrs']; RECORD rows=55; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/attr', 'share/mamba/envs/pandda2/lib/python3.9/site-packages/attrs']","Installed source scan examples: share/mamba/envs/pandda2/lib/python3.9/site-packages/attr/_make.py:385 field_transformer,; share/mamba/envs/pandda2/lib/python3.9/site-packages/attr/_make.py:466 # Resolve default field alias before executing field_transformer, so that; share/mamba/envs/pandda2/lib/python3.9/site-packages/attr/_make.py:467 # the transformer receives fully populated Attribute objects with usable; share/mamba/envs/pandda2/lib/python3.9/site-packages/attr/_make.py:475 if field_transformer is not None:"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:beautifulsoup4","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: HTML/XML parser. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/beautifulsoup4-4.15.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/beautifulsoup4-4.15.0.dist-info/METADATA: Name: beautifulsoup4","share/mamba/envs/pandda2/lib/python3.9/site-packages/beautifulsoup4-4.15.0.dist-info/METADATA: Version: 4.15.0","share/mamba/envs/pandda2/lib/python3.9/site-packages/beautifulsoup4-4.15.0.dist-info/METADATA: Summary: Screen-scraping library","share/mamba/envs/pandda2/lib/python3.9/site-packages/bs4/builder/__init__.py:590: #: an unusual content model for them. I made this list by going"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:bokeh","disposition":"visualization infrastructure","rationale":"Interactive plotting/visualization library. The reviewed package sources and samples are visualization/data support, not a trained model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/bokeh-3.4.3.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/bokeh-3.4.3.dist-info/METADATA; sha256=222fefd9cc2606e96d2ca5fcf1f8d5ae7139f95d5e125cd827e110c59d4f0c91; record exists=True","top_level.txt roots (metadata-derived): bokeh, typings","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/bokeh', 'share/mamba/envs/pandda2/lib/python3.9/site-packages/typings']; bounded scan files=5, truncated=True"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:certifi","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/certifi-2026.7.22.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/certifi-2026.7.22.dist-info/METADATA; metadata SHA-256 ef5af1638fbb23676ac3c5777dfcfc2cd9c348fe4172ed5ba3d277655b248090","top_level.txt roots=['certifi']; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/certifi-2026.7.22.dist-info/RECORD; RECORD existing=13/18","read-only source scan: 5 Python files / 4198 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:certifi; environment=share/mamba/envs/pandda2; version=2026.7.22"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:charset-normalizer","disposition":"text-encoding-utility","rationale":"Installed charset-normalizer 3.5.2 in share/mamba/envs/pandda2 is text-encoding-utility; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/charset_normalizer-3.5.2.dist-info/METADATA; Name: charset-normalizer | Version: 3.5.2 | Summary: The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.","owner: top_level=['charset_normalizer']; source_roots_from_METADATA_or_RECORD=['charset_normalizer']; RECORD_rows=35; RECORD_sample=['../../../bin/normalizer', 'charset_normalizer-3.5.2.dist-info/INSTALLER', 'charset_normalizer-3.5.2.dist-info/METADATA', 'charset_normalizer-3.5.2.dist-info/RECORD', 'charset_normalizer-3.5.2.dist-info/WHEEL', 'charset_normalizer-3.5.2.dist-info/entry_points.txt', 'charset_normalizer-3.5.2.dist-info/licenses/LICENSE', 'charset_normalizer-3.5.2.dist-info/top_level.txt']"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:click","disposition":"command-line-interface-utility","rationale":"Click is command-line parsing support; not model code.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/click-8.1.8.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:colorama","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/colorama-0.4.6.dist-info/METADATA sha256=8de7aefdf3063ea1c12428222e85c951eb15991a4e079dcaaee157b0c02c98e7 bytes=17154 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/colorama-0.4.6.dist-info/RECORD rows=33; sample=[\"colorama-0.4.6.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"colorama-0.4.6.dist-info/METADATA,sha256=jeeu_fMGPqHBJCgiLoXJUesVmRpOB53KruFXsMAsmOc,17154\", \"colorama-0.4.6.dist-info/RECORD,,\", \"colorama-0.4.6.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=colorama env=share/mamba/envs/pandda2: 13 files, 57543 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:contourpy","disposition":"contour-generation numerical library","rationale":"plotting geometry support, not learned inference","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/contourpy-1.3.0.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/contourpy-1.3.0.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"numpy>=1.23\", \"furo; extra == \\\"docs\\\"\", \"sphinx>=7.2; extra == \\\"docs\\\"\", \"sphinx-copybutton; extra == \\\"docs\\\"\", \"bokeh; extra == \\\"bokeh\\\"\", \"selenium; extra == \\\"bokeh\\\"\", \"contourpy[bokeh,docs]; extra == \\\"mypy\\\"\", \"docutils-stubs; extra == \\\"mypy\\\"\", \"mypy==1.11.1; extra == \\\"mypy\\\"\", \"types-Pillow; extra == \\\"mypy\\\"\", \"contourpy[test-no-images]; extra == \\\"test\\\"\", \"matplotlib; extra == \\\"test\\\"\", \"Pillow; extra == \\\"test\\\"\", \"pytest; extra == \\\"test-no-images\\\"\", \"pytest-cov; extra == \\\"test-no-images\\\"\", \"pytest-rerunfailures; extra == \\\"test-no-images\\\"\", \"pytest-xdist; extra == \\\"test-no-images\\\"\", \"wurlitzer; extra == \\\"test-no-images\\\"\"]; ownership={\"record_file_count\": 42}","audits/ccp4-10.0.001/python.json AST group package=contourpy root=lib/python3.11/site-packages files=11 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:cycler","disposition":"plot style utility","rationale":"Composable plotting style cycles.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/cycler-0.12.1.dist-info/METADATA; SHA-256=23289e19b76f1e01394227696e6af2b6cd1ce79e89731209bf9195148b18ed36; Name=cycler; Version=0.12.1; Summary=Composable style cycles","declared Requires-Dist (7): [\"ipython ; extra == 'docs'\",\"matplotlib ; extra == 'docs'\",\"numpydoc ; extra == 'docs'\",\"sphinx ; extra == 'docs'\",\"pytest ; extra == 'tests'\",\"pytest-cov ; extra == 'tests'\",\"pytest-xdist ; extra == 'tests'\"]","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/cycler-0.12.1.dist-info/top_level.txt; top_level=[\"cycler\"]; RECORD rows=8; RECORD sample=[\"cycler-0.12.1.dist-info/INSTALLER\", \"cycler-0.12.1.dist-info/LICENSE\", \"cycler-0.12.1.dist-info/METADATA\", \"cycler-0.12.1.dist-info/RECORD\", \"cycler-0.12.1.dist-info/WHEEL\", \"cycler-0.12.1.dist-info/top_level.txt\", \"cycler/__init__.py\", \"cycler/py.typed\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 1 files, 16709 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:share/mamba/envs/pandda2:cycler; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:exceptiongroup","disposition":"Python exception compatibility library","rationale":"Exception grouping support; no ML role. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/exceptiongroup-1.3.0.dist-info/METADATA: installed metadata ['Name: exceptiongroup', 'Version: 1.3.0', \"Requires-Dist: typing-extensions >= 4.6.0; python_version < '3.13'\", 'Requires-Dist: pytest >= 6 ; extra == \"test\"']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['exceptiongroup']; RECORD rows=20; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/exceptiongroup']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:filelock","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: cross-process lock utility. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/filelock-3.19.1.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/filelock-3.19.1.dist-info/METADATA: Name: filelock","share/mamba/envs/pandda2/lib/python3.9/site-packages/filelock-3.19.1.dist-info/METADATA: Version: 3.19.1","share/mamba/envs/pandda2/lib/python3.9/site-packages/filelock-3.19.1.dist-info/METADATA: Summary: A platform independent file lock."],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:fire","disposition":"general runtime/development infrastructure","rationale":"Cli argument helper package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/fire-0.7.1.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/fire-0.7.1.dist-info/METADATA; sha256=fd4cf680aadcfa80f49825bcb39bd41a8fd84c4928e5325d943a4b4f0909eebe; record exists=True","top_level.txt roots (metadata-derived): fire","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/fire']; bounded scan files=47, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:fonttools","disposition":"font processing support library","rationale":"The package owns fontTools source and supports font parsing/building. Broad classifier-like tokens are general parser or test code, not inference.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/fonttools-4.60.2.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/fonttools-4.60.2.dist-info/METADATA; metadata SHA-256 eb060c3186eb7555a70d8adad6d2d3dd18c5b424a83c1b6801e55b5d14257a03","top_level.txt roots=['fontTools']; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/fonttools-4.60.2.dist-info/RECORD; RECORD existing=358/689","read-only source scan: 331 Python files / 4295151 bytes; 13 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:fonttools; environment=share/mamba/envs/pandda2; version=4.60.2","bounded hit review: 13 hit files were parser/build/test/support contexts; no scientific model consumer identified"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:frozenlist","disposition":"immutable-container-utility","rationale":"Installed frozenlist 1.8.0 in share/mamba/envs/pandda2 is immutable-container-utility; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/frozenlist-1.8.0.dist-info/METADATA; Name: frozenlist | Version: 1.8.0 | Summary: A list-like structure which implements collections.abc.MutableSequence","owner: top_level=['frozenlist']; source_roots_from_METADATA_or_RECORD=['frozenlist']; RECORD_rows=12; RECORD_sample=['frozenlist-1.8.0.dist-info/INSTALLER', 'frozenlist-1.8.0.dist-info/METADATA', 'frozenlist-1.8.0.dist-info/RECORD', 'frozenlist-1.8.0.dist-info/WHEEL', 'frozenlist-1.8.0.dist-info/licenses/LICENSE', 'frozenlist-1.8.0.dist-info/top_level.txt', 'frozenlist/__init__.py', 'frozenlist/__init__.pyi']"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:fsspec","disposition":"filesystem-abstraction","rationale":"fsspec provides filesystem abstraction and optional remote adapters; generic pickle cache references do not establish model use.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/fsspec-2025.10.0.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:gdown","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/gdown-5.2.2.dist-info/METADATA sha256=f702d9bb41e1c8b6fb10a0410d40adebc6a07679c6c2f7c41709e1df5e72256c bytes=5755 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/gdown-5.2.2.dist-info/RECORD rows=25; sample=[\"../../../bin/gdown,sha256=HMB6DXN4UwprtL3hKlYsuj1V7mY1tg4OPeK-r2n1pcY,227\", \"gdown-5.2.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"gdown-5.2.2.dist-info/METADATA,sha256=9wLZu0HhyLb7EKBBDUCt68agdnnGwvfEFwnh315yJWw,5755\", \"gdown-5.2.2.dist-info/RECORD,,\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=gdown env=share/mamba/envs/pandda2: 9 files, 41658 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:gemmi","disposition":"crystallographic file, symmetry, and geometry library","rationale":"crystallographic parsing/numerical support; no learned-model path identified","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/gemmi-0.7.5.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/gemmi-0.7.5.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"record_file_count\": 65}","audits/ccp4-10.0.001/python.json AST group package=gemmi root=lib/python3.11/site-packages files=28 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:hdbscan","disposition":"classical clustering algorithm","rationale":"HDBSCAN density-based clustering implementation, including compiled extensions; not itself a pretrained model.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/hdbscan-0.8.42.dist-info/METADATA; SHA-256=4f6a3008b5280e9fb870490e99fec6bf168b3e8c603ac609aee39a471d3a41a8; Name=hdbscan; Version=0.8.42; Summary=Clustering based on density with variable density clusters","declared Requires-Dist (4): [\"numpy<3,>=1.20\",\"scipy>=1.0\",\"scikit-learn>=1.6\",\"joblib>=1.0\"]","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/hdbscan-0.8.42.dist-info/top_level.txt; top_level=[\"hdbscan\"]; RECORD rows=28; RECORD sample=[\"../../../dist_metrics.pxd\", \"hdbscan-0.8.42.dist-info/INSTALLER\", \"hdbscan-0.8.42.dist-info/METADATA\", \"hdbscan-0.8.42.dist-info/RECORD\", \"hdbscan-0.8.42.dist-info/WHEEL\", \"hdbscan-0.8.42.dist-info/licenses/LICENSE\", \"hdbscan-0.8.42.dist-info/top_level.txt\", \"hdbscan/__init__.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 7 files, 232544 bytes, 0 skipped/overflow; ML vocabulary hits=80","representative broad-term source hits: [{\"path\": \"hdbscan/branch_data.py\", \"line\": 9, \"text\": \"Recreates and caches internal data structures from the clustering stage.\"}, {\"path\": \"hdbscan/branch_data.py\", \"line\": 21, \"text\": \"The condensed tree produced during clustering, used to extract outliers.\"}, {\"path\": \"hdbscan/branch_data.py\", \"line\": 24, \"text\": \"The min_samples value used in clustering.\"}, {\"path\": \"hdbscan/branch_data.py\", \"line\": 33, \"text\": \"The metric used to determine distance for the clustering.\"}, {\"path\": \"hdbscan/branches.py\", \"line\": 110, \"text\": \"Has no effect when using ``leaf`` clustering (where clusters are\"}]","targeted static implementation source: share/mamba/envs/pandda2/lib/python3.9/site-packages/hdbscan/hdbscan_.py:703,932-935,1135-1145 defines density-based HDBSCAN clustering; no fitted checkpoint is evidenced.","node identity: pydist:share/mamba/envs/pandda2:hdbscan; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:idna","disposition":"internationalized domain-name codec","rationale":"Protocol utility; no ML role. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/idna-3.20.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/idna-3.20.dist-info/METADATA: installed metadata ['Name: idna', 'Version: 3.20', 'Requires-Dist: ruff >= 0.16.0 ; extra == \"all\"', 'Requires-Dist: mypy >= 1.11.2 ; extra == \"all\"', 'Requires-Dist: ty >= 0.0.37 ; extra == \"all\"', 'Requires-Dist: pytest >= 8.3.2 ; extra == \"all\"', 'Requires-Dist: hypothesis >= 6.141.1 ; extra == \"all\"', 'Requires-Dist: coverage >= 7.10.0 ; extra == \"all\"']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['idna']; RECORD rows=28; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/idna']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:imageio","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: image read/write package. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio-2.37.2.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio-2.37.2.dist-info/METADATA: Name: ImageIO","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio-2.37.2.dist-info/METADATA: Version: 2.37.2","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio-2.37.2.dist-info/METADATA: Summary: Read and write images and video across all major formats. Supports scientific and volumetric data.","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio/plugins/_tifffile.py:4070: if \"ModelPixelScaleTag\" in tags:","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio/plugins/_tifffile.py:4071: value = numpy.array(tags[\"ModelPixelScaleTag\"].value).tolist()","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio/plugins/_tifffile.py:4072: result[\"ModelPixelScale\"] = value","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio/plugins/_tifffile.py:4073: if \"ModelTiepointTag\" in tags:","share/mamba/envs/pandda2/lib/python3.9/site-packages/imageio/plugins/_tifffile.py:4074: value = tags[\"ModelTiepointTag\"].value"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:importlib-resources","disposition":"general runtime/development infrastructure","rationale":"Resource-loading compatibility package package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/importlib_resources-6.5.2.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/importlib_resources-6.5.2.dist-info/METADATA; sha256=ca0953ffb4bf3ecad241a55381929061fa26694943fa957be1fffd2ddd118e86; record exists=True","top_level.txt roots (metadata-derived): importlib_resources","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/importlib_resources']; bounded scan files=30, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:iniconfig","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/iniconfig-2.0.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/iniconfig-2.0.0.dist-info/METADATA; metadata SHA-256 2de8258cab6765f84ebd3c4ff692b10bd847512a8ab2089986d5cc42fc11227d","top_level.txt roots=[]; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/iniconfig-2.0.0.dist-info/RECORD; RECORD existing=12/16","read-only source scan: 4 Python files / 8821 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:iniconfig; environment=share/mamba/envs/pandda2; version=2.0.0"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:jinja2","disposition":"template-engine","rationale":"Installed jinja2 3.1.6 in share/mamba/envs/pandda2 is template-engine; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/jinja2-3.1.6.dist-info/METADATA; Name: Jinja2 | Version: 3.1.6 | Summary: A very fast and expressive template engine.","owner: top_level=(absent); source_roots_from_METADATA_or_RECORD=['jinja2']; RECORD_rows=57; RECORD_sample=['jinja2-3.1.6.dist-info/INSTALLER', 'jinja2-3.1.6.dist-info/METADATA', 'jinja2-3.1.6.dist-info/RECORD', 'jinja2-3.1.6.dist-info/WHEEL', 'jinja2-3.1.6.dist-info/entry_points.txt', 'jinja2-3.1.6.dist-info/licenses/LICENSE.txt', 'jinja2/__init__.py', 'jinja2/__pycache__/__init__.cpython-39.pyc']","declared dependencies: Requires-Dist: MarkupSafe>=2.0; Requires-Dist: Babel>=2.7 ; extra == \"i18n\""],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:joblib","disposition":"serialization-and-parallelism-library","rationale":"Joblib provides parallelism and pickle-backed persistence. The assigned compressed/pickle files under joblib/test/data are library fixtures, while the core ConKit assets are a separate application-level model path. No serialized object was loaded.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/joblib-1.5.3.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:jsonschema","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/jsonschema-4.25.1.dist-info/METADATA sha256=31f83c1579e46e1af62269cefa5d83534ef155f3ee21914f7881bbd544bc125c bytes=7608 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/jsonschema-4.25.1.dist-info/RECORD rows=80; sample=[\"../../../bin/jsonschema,sha256=EcJAc1DP9fvdrPZq89UDgZAkSCpKYZV6a-KWSCGpA3Q,227\", \"jsonschema-4.25.1.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"jsonschema-4.25.1.dist-info/METADATA,sha256=Mfg8FXnkbhr2ImnO-l2DU07xVfPuIZFPeIG71US8Elw,7608\", \"jsonschema-4.25.1.dist-info/RECORD,,\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=jsonschema env=share/mamba/envs/pandda2: 36 files, 345632 bytes, 2 files with broad ML/loader marker hits","representative package source share/mamba/envs/pandda2/lib/python3.9/site-packages/jsonschema/tests/test_cli.py sha256=03cf6be4b387cbea5e2cf640e580e439a3135aacd03bfc364eef16173fefa613"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:jsonschema-specifications","disposition":"JSON Schema reference metadata","rationale":"schema data only","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/jsonschema_specifications-2025.9.1.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/jsonschema_specifications-2025.9.1.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"referencing>=0.31.0\"]; ownership={\"record_file_count\": 33}","audits/ccp4-10.0.001/python.json AST group package=jsonschema_specifications root=share/mamba/envs/pandda2/lib/python3.9/site-packages files=4 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:kiwisolver","disposition":"constraint solver","rationale":"Cassowary constraint solver used by plotting/UI dependencies.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/kiwisolver-1.4.7.dist-info/METADATA; SHA-256=21c9140831e45cd51baa53d19bc9674ba662edce1f90d0316138776331c8d9bf; Name=kiwisolver; Version=1.4.7; Summary=A fast implementation of the Cassowary constraint solver","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/kiwisolver-1.4.7.dist-info/top_level.txt; top_level=[\"kiwisolver\"]; RECORD rows=11; RECORD sample=[\"kiwisolver-1.4.7.dist-info/INSTALLER\", \"kiwisolver-1.4.7.dist-info/LICENSE\", \"kiwisolver-1.4.7.dist-info/METADATA\", \"kiwisolver-1.4.7.dist-info/RECORD\", \"kiwisolver-1.4.7.dist-info/WHEEL\", \"kiwisolver-1.4.7.dist-info/top_level.txt\", \"kiwisolver/__init__.py\", \"kiwisolver/_cext.cpython-39-x86_64-linux-gnu.so\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 2 files, 2255 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:share/mamba/envs/pandda2:kiwisolver; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:lazy-loader","disposition":"lazy import utility","rationale":"Delays optional module imports; no ML role. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/lazy_loader-0.6.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/lazy_loader-0.6.dist-info/METADATA: installed metadata ['Name: lazy-loader', 'Version: 0.6', 'Requires-Dist: packaging', 'Requires-Dist: pytest>=8.0; extra == \"test\"', 'Requires-Dist: pytest-cov>=5.0; extra == \"test\"', 'Requires-Dist: coverage[toml]>=7.2; extra == \"test\"', 'Requires-Dist: pre-commit==4.3.0; extra == \"lint\"', 'Requires-Dist: changelist==0.5; extra == \"dev\"', 'Requires-Dist: spin==0.15; extra == \"dev\"']","metadata-owned top_level/RECORD roots: top_level=['lazy_loader']; RECORD roots=['lazy_loader']; RECORD rows=8; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/lazy_loader']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:lightning-utilities","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: PyTorch Lightning helper utilities; not a model trainer or checkpoint package. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities-0.15.2.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities-0.15.2.dist-info/METADATA: Name: lightning-utilities","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities-0.15.2.dist-info/METADATA: Version: 0.15.2","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities-0.15.2.dist-info/METADATA: Summary: Lightning toolbox for across the our ecosystem.","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities/docs/formatting.py:54: # /home/docs/checkouts/readthedocs.org/user_builds/pytorch_lightning/checkouts/","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities/docs/formatting.py:55: #  devel/pytorch_lightning/utilities/cls_experiment.py#L26-L176","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities/core/apply_func.py:15: # https://github.com/pytorch/pytorch/blob/v1.8.1/torch/nn/parallel/scatter_gather.py#L4-L8","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities/core/imports.py:71: >>> compare_version(\"torch\", operator.ge, \"0.1\")","share/mamba/envs/pandda2/lib/python3.9/site-packages/lightning_utilities/core/imports.py:99: >>> RequirementCache(\"torch>=0.1\")"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:llvmlite","disposition":"numerical/runtime infrastructure","rationale":"LLVM JIT binding used by Numba/numerical kernels; 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source_roots_from_METADATA_or_RECORD=['markupsafe']; RECORD_rows=14; RECORD_sample=['markupsafe-3.0.4.dist-info/INSTALLER', 'markupsafe-3.0.4.dist-info/METADATA', 'markupsafe-3.0.4.dist-info/RECORD', 'markupsafe-3.0.4.dist-info/WHEEL', 'markupsafe-3.0.4.dist-info/licenses/LICENSE.txt', 'markupsafe-3.0.4.dist-info/top_level.txt', 'markupsafe/__init__.py', 'markupsafe/__pycache__/__init__.cpython-39.pyc']"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:matplotlib","disposition":"plotting-library","rationale":"Matplotlib supplies plotting and sample datasets; package-level plotting support does not establish trained inference.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/matplotlib-3.9.4.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:mdurl","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/mdurl-0.1.2.dist-info/METADATA sha256=b53b29d48f499367053fda3c81e7ce27d2558380ebbf83e66023b02eb7ddd25d bytes=1638 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/mdurl-0.1.2.dist-info/RECORD rows=18; sample=[\"mdurl-0.1.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"mdurl-0.1.2.dist-info/LICENSE,sha256=fGBd9uKGZ6lgMRjpgnT2SknOPu0NJvzM6VNKNF4O-VU,2338\", \"mdurl-0.1.2.dist-info/METADATA,sha256=tTsp1I9Jk2cFP9o8gefOJ9JVg4Drv4PmYCOwLrfd0l0,1638\", \"mdurl-0.1.2.dist-info/RECORD,,\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=mdurl env=share/mamba/envs/pandda2: 6 files, 18437 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:msgpack","disposition":"binary serialization library","rationale":"data serialization infrastructure only","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/msgpack-1.1.2.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/msgpack-1.1.2.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"record_file_count\": 15, \"top_level.txt\": \"msgpack\\n\"}","audits/ccp4-10.0.001/python.json AST group package=msgpack root=lib/python3.11/site-packages files=4 hit_files=0 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:multidict","disposition":"container utility","rationale":"Multi-value dictionary infrastructure.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/multidict-6.7.1.dist-info/METADATA; SHA-256=4913fdaae936a309c29b89b98c2dbebd237203fb27ab9e68ae5e4ec17ba3024f; Name=multidict; Version=6.7.1; Summary=multidict implementation","declared Requires-Dist (1): [\"typing-extensions>=4.1.0; python_version < \\\"3.11\\\"\"]","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/multidict-6.7.1.dist-info/top_level.txt; top_level=[\"multidict\"]; RECORD rows=12; RECORD sample=[\"multidict-6.7.1.dist-info/INSTALLER\", \"multidict-6.7.1.dist-info/METADATA\", \"multidict-6.7.1.dist-info/RECORD\", \"multidict-6.7.1.dist-info/WHEEL\", \"multidict-6.7.1.dist-info/licenses/LICENSE\", \"multidict-6.7.1.dist-info/top_level.txt\", \"multidict/__init__.py\", \"multidict/_abc.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 4 files, 44007 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:share/mamba/envs/pandda2:multidict; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:networkx","disposition":"graph algorithms library","rationale":"Graph data structures and algorithms; clustering-like graph utilities are generic algorithms, no trained model identified. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx-3.2.1.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx-3.2.1.dist-info/METADATA: installed metadata ['Name: networkx', 'Version: 3.2.1', \"Requires-Dist: numpy >=1.22 ; extra == 'default'\", \"Requires-Dist: scipy !=1.11.0,!=1.11.1,>=1.9 ; extra == 'default'\", \"Requires-Dist: matplotlib >=3.5 ; extra == 'default'\", \"Requires-Dist: pandas >=1.4 ; extra == 'default'\", \"Requires-Dist: changelist ==0.4 ; extra == 'developer'\", \"Requires-Dist: pre-commit >=3.2 ; extra == 'developer'\", \"Requires-Dist: mypy >=1.1 ; extra == 'developer'\", \"Requires-Dist: rtoml ; extra == 'developer'\", \"Requires-Dist: sphinx >=7 ; extra == 'doc'\", \"Requires-Dist: pydata-sphinx-theme >=0.14 ; extra == 'doc'\", \"Requires-Dist: sphinx-gallery >=0.14 ; extra == 'doc'\", \"Requires-Dist: numpydoc >=1.6 ; extra == 'doc'\", \"Requires-Dist: pillow >=9.4 ; extra == 'doc'\", \"Requires-Dist: nb2plots >=0.7 ; extra == 'doc'\", \"Requires-Dist: texext >=0.6.7 ; extra == 'doc'\", \"Requires-Dist: nbconvert <7.9 ; extra == 'doc'\"]","metadata-owned top_level/RECORD roots: top_level=['networkx']; RECORD roots=['networkx']; RECORD rows=1137; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx']","Installed source scan examples: share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx/conftest.py:111 \"ignore\", category=DeprecationWarning, message=\"\\nforest_str is deprecated\"; share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx/algorithms/sparsifiers.py:75 # phase 1: forming the clusters; share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx/algorithms/sparsifiers.py:79 # clustering is a dictionary that maps nodes in a cluster to the; share/mamba/envs/pandda2/lib/python3.9/site-packages/networkx/algorithms/sparsifiers.py:80 # cluster center"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:numba","disposition":"numerical compiler/runtime","rationale":"Installed package role from metadata and static implementation review: JIT compiler for numerical Python, with CUDA tooling; not a trained-model package. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/numba-0.60.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba-0.60.0.dist-info/METADATA: Name: numba","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba-0.60.0.dist-info/METADATA: Version: 0.60.0","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba-0.60.0.dist-info/METADATA: Summary: compiling Python code using LLVM","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba/cpython/builtins.py:162: model = context.data_model_manager[toty]","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba/cpython/builtins.py:163: return model.set(builder, model.make_uninitialized(), actual)","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba/cpython/builtins.py:169: model = context.data_model_manager[fromty]","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba/cpython/builtins.py:170: val = model.get(builder, val)","share/mamba/envs/pandda2/lib/python3.9/site-packages/numba/cpython/listobj.py:66: return self._datamodel.from_data(self._builder, data_item)"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:numpy","disposition":"numerical/runtime infrastructure","rationale":"Array and linear-algebra runtime used by scientific algorithms; model words in examples/tests do not identify a shipped estimator.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/numpy-1.26.4.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/numpy-1.26.4.dist-info/METADATA; sha256=b09734a7fed44e84b4c8161934ce532dff1e779ec6822d415644d117f6381070; record exists=True","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/numpy']; bounded scan files=192, truncated=True"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:nvidia-cublas-cu11","disposition":"CUDA BLAS accelerator runtime package","rationale":"This is GPU numerical runtime support in the separate pandda2 environment, not a model package.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia_cublas_cu11-11.10.3.66.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia_cublas_cu11-11.10.3.66.dist-info/METADATA; metadata SHA-256 8c18e40e2ae47176e6a389af379e3463e59d957e525b29d502197b311ce531de","top_level.txt roots=['nvidia/cublas']; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia_cublas_cu11-11.10.3.66.dist-info/RECORD; RECORD existing=15/15","read-only source scan: 0 Python files / 0 bytes; 0 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:nvidia-cublas-cu11; environment=share/mamba/envs/pandda2; version=11.10.3.66","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia_cublas_cu11-11.10.3.66.dist-info/METADATA"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:nvidia-cuda-nvrtc-cu11","disposition":"CUDA-runtime-compiler-dependency","rationale":"The pandda2 distribution owns NVIDIA CUDA runtime/compiler files; the assigned ELF inventory separately shows Torch/cuDNN/CUDA libraries. This is compute infrastructure, not a trained model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia_cuda_nvrtc_cu11-11.7.99.dist-info/METADATA; Name: nvidia-cuda-nvrtc-cu11 | Version: 11.7.99 | Summary: NVRTC native runtime libraries","owner: top_level=['nvidia']; source_roots_from_METADATA_or_RECORD=['nvidia']; RECORD_rows=17; RECORD_sample=['nvidia/__init__.py', 'nvidia/__pycache__/__init__.cpython-39.pyc', 'nvidia/cuda_nvrtc/__init__.py', 'nvidia/cuda_nvrtc/__pycache__/__init__.cpython-39.pyc', 'nvidia/cuda_nvrtc/include/__init__.py', 'nvidia/cuda_nvrtc/include/__pycache__/__init__.cpython-39.pyc', 'nvidia/cuda_nvrtc/include/nvrtc.h', 'nvidia/cuda_nvrtc/lib/__init__.py']","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_backend.h:299     CUDNN_ATTR_OPERATION_BN_BWD_WEIGHTS_MATH_PREC        = 1620,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_backend.h:300     CUDNN_ATTR_OPERATION_BN_BWD_WEIGHTS_MEAN_DESC        = 1621,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_backend.h:301     CUDNN_ATTR_OPERATION_BN_BWD_WEIGHTS_INVSTD_DESC      = 1622,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_v8.h:50 /*   cudnn : Neural Networks Library","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_train.h:153                         size_t weightSpaceSize,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_train.h:154                         const void *weightSpace,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_train.h:161 cudnnRNNBackwardWeights(cudnnHandle_t handle,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_infer.h:306 cudnnGetRNNWeightSpaceSize(cudnnHandle_t handle, cudnnRNNDescriptor_t rnnDesc, size_t *weightSpaceSize);","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_infer.h:334                         size_t weightSpaceSize,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_infer.h:335                         const void *weightSpace,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn.h:50 /*   cudnn : Neural Networks Library","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_train_v8.h:457                                     const cudnnSpatialTransformerDescriptor_t stDesc,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_train_v8.h:463                               cudnnSpatialTransformerDescriptor_t stDesc,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_train.h:457                                     const cudnnSpatialTransformerDescriptor_t stDesc,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_train.h:463                               cudnnSpatialTransformerDescriptor_t stDesc,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_infer_v8.h:164 /* Data structures to represent Image/Filter and the Neural Network Layer */","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_infer_v8.h:170 typedef struct cudnnSpatialTransformerStruct *cudnnSpatialTransformerDescriptor_t;","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_infer_v8.h:933 /* APIs for spatial transformer network*/","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_backend_v8.h:299     CUDNN_ATTR_OPERATION_BN_BWD_WEIGHTS_MATH_PREC        = 1620,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_backend_v8.h:300     CUDNN_ATTR_OPERATION_BN_BWD_WEIGHTS_MEAN_DESC        = 1621,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_backend_v8.h:301     CUDNN_ATTR_OPERATION_BN_BWD_WEIGHTS_INVSTD_DESC      = 1622,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_infer.h:164 /* Data structures to represent Image/Filter and the Neural Network Layer */","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_infer.h:170 typedef struct cudnnSpatialTransformerStruct *cudnnSpatialTransformerDescriptor_t;","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_ops_infer.h:933 /* APIs for spatial transformer network*/","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_cnn_infer_v8.h:404     /* [per channel scale], [per channel bias], [activation], convolutionBackwardWeights */","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_infer_v8.h:306 cudnnGetRNNWeightSpaceSize(cudnnHandle_t handle, cudnnRNNDescriptor_t rnnDesc, size_t *weightSpaceSize);","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_infer_v8.h:334                         size_t weightSpaceSize,","share/mamba/envs/pandda2/lib/python3.9/site-packages/nvidia/cudnn/include/cudnn_adv_infer_v8.h:335                         const void *weightSpace,"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:nvidia-cuda-runtime-cu11","disposition":"CUDA-runtime-infrastructure","rationale":"This distribution owns CUDA runtime headers/libraries in the pandda2 environment; it is execution infrastructure, not trained model 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features.","Installed metadata exact Requires-Dist=[]; ownership={\"record_file_count\": 54}","audits/ccp4-10.0.001/python.json AST group package=packaging root=lib/python3.11/site-packages files=16 hit_files=2 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:pandas","disposition":"dataframe and statistics library","rationale":"Data frame/statistics infrastructure; source-hit scan found no model loader or trained asset. Broad source terms such as regression/classifier are documentation or API vocabulary, not evidence of a trained model.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/pandas-2.3.3.dist-info/METADATA; SHA-256=40ee953dc7ca155840b639a1881ff84578075187fce0ac20eeda55a7fa0d9a90; Name=pandas; Version=2.3.3; Summary=Powerful data structures for data analysis, time series, and statistics","declared Requires-Dist (85): [\"numpy>=1.22.4; python_version < \\\"3.11\\\"\",\"numpy>=1.23.2; python_version == \\\"3.11\\\"\",\"numpy>=1.26.0; python_version >= \\\"3.12\\\"\",\"python-dateutil>=2.8.2\",\"pytz>=2020.1\",\"tzdata>=2022.7\",\"hypothesis>=6.46.1; extra == \\\"test\\\"\",\"pytest>=7.3.2; extra == \\\"test\\\"\",\"pytest-xdist>=2.2.0; extra == \\\"test\\\"\",\"pyarrow>=10.0.1; extra == \\\"pyarrow\\\"\",\"bottleneck>=1.3.6; extra == \\\"performance\\\"\",\"numba>=0.56.4; extra == \\\"performance\\\"\",\"numexpr>=2.8.4; extra == \\\"performance\\\"\",\"scipy>=1.10.0; 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environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:pandda-2-gemmi","disposition":"scientific workflow package with shipped learned event-scoring models","rationale":"Source implements density clustering and 3D ResNet event/build scoring; its default scoring loader opens `model_event.ckpt` (and `model_build.ckpt`) with `torch.load`. The event checkpoint is an assigned shipped asset. A separate RDKit natural-product score model is also shipped in this environment, but no CCP4 application path to it was verified. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_2_gemmi-0.0.1.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_2_gemmi-0.0.1.dist-info/METADATA: installed metadata ['Name: pandda_2_gemmi', 'Version: 0.0.1', 'Requires-Dist: numpy<2.0', 'Requires-Dist: scipy', 'Requires-Dist: joblib', 'Requires-Dist: scikit-learn', 'Requires-Dist: umap-learn', 'Requires-Dist: hdbscan', 'Requires-Dist: matplotlib', 'Requires-Dist: rich', 'Requires-Dist: seaborn', 'Requires-Dist: rdkit', 'Requires-Dist: ray', 'Requires-Dist: fire', 'Requires-Dist: bokeh', 'Requires-Dist: gdown', 'Requires-Dist: typing_extensions>=4.13.0', 'Requires-Dist: torch==1.13.1']","metadata-owned top_level/RECORD roots: top_level=['pandda_gemmi']; RECORD roots=['pandda_2_gemmi-0.0.1.data', 'pandda_gemmi']; RECORD rows=210; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi']","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_2_gemmi-0.0.1.dist-info/METADATA:L2; Requires-Dist includes torch==1.13.1, scikit-learn, hdbscan, umap-learn, rdkit and scikit-image","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/pandda/get_scoring_models.py:80-125 (conditional event/build checkpoint loaders)","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/base.py:97-108 (torch.load(..., map_location=\"cpu\"))","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/args/args.py:14 (use_ligand_data defaults true)","share/mamba/envs/pandda2/lib/python3.9/site-packages/rdkit/Contrib/NP_Score/npscorer.py:27-33,36-74 (gzip pickle model loader and Morgan-fingerprint NP-likeness scoring); publicnp.model.gz is outside the assigned asset list, so surfaced as a lead only"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:pillow","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: image codec and image I/O library. 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Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pip-25.2.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/pip-25.2.dist-info/METADATA; sha256=97a3ad14d71fd8914a38f24af5b31a1f9faeb05aea66a4af40d979d6d7ad229f; record exists=True","top_level.txt roots (metadata-derived): pip","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/pip']; bounded scan files=51, truncated=True"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:pluggy","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pluggy-1.6.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/pluggy-1.6.0.dist-info/METADATA; 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source_roots_from_METADATA_or_RECORD=['propcache']; RECORD_rows=18; RECORD_sample=['propcache-0.4.1.dist-info/INSTALLER', 'propcache-0.4.1.dist-info/METADATA', 'propcache-0.4.1.dist-info/RECORD', 'propcache-0.4.1.dist-info/WHEEL', 'propcache-0.4.1.dist-info/licenses/LICENSE', 'propcache-0.4.1.dist-info/licenses/NOTICE', 'propcache-0.4.1.dist-info/top_level.txt', 'propcache/__init__.py']"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:protobuf","disposition":"serialization-protocol-library","rationale":"Protobuf is a general serialization protocol implementation; no model use is established by the package row.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/protobuf-6.33.6.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:pygments","disposition":"general_utility_or_developer_infrastructure","rationale":"Installed utility/developer/network/validation package; metadata, ownership and bounded package source audit do not establish a model, trained weights, or CCP4 ML inference path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/pygments-2.19.2.dist-info/METADATA sha256=7ae100d67d67006c6479803dd835fcf47a9b59fac794441ea8e66aa7f5984d82 bytes=2512 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/pygments-2.19.2.dist-info/RECORD rows=686; sample=[\"../../../bin/pygmentize,sha256=gYckdOtZjdzJhPEr5We9-fW9VWBfCj6Y6f1T-yBrF6k,498\", \"pygments-2.19.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"pygments-2.19.2.dist-info/METADATA,sha256=euEA1n1nAGxkeYA92DX89HqbWfrHlEQeqOZqp_WYTYI,2512\", \"pygments-2.19.2.dist-info/RECORD,,\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=pygments env=share/mamba/envs/pandda2: 338 files, 4452013 bytes, 7 files with broad ML/loader marker hits","representative package source share/mamba/envs/pandda2/lib/python3.9/site-packages/pygments/sphinxext.py sha256=5447bfa073602e810630773644e7db79eda61763cf44417213afe6fc937916f4"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:pynndescent","disposition":"approximate-nearest-neighbor and graph-construction utility","rationale":"pynndescent is an algorithmic neighbor-search package; no trained checkpoint or CCP4 application call path was found","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pynndescent-0.6.0.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/pynndescent-0.6.0.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"scikit-learn>=0.18\", \"scipy>=1.0\", \"numba>=0.55.0\", \"llvmlite>=0.38\", \"joblib>=0.11\", \"pytest; extra == \\\"testing\\\"\"]; ownership={\"record_file_count\": 26, \"top_level.txt\": \"pynndescent\\n\"}","audits/ccp4-10.0.001/python.json AST group package=pynndescent root=share/mamba/envs/pandda2/lib/python3.9/site-packages files=10 hit_files=3 imports={\"sklearn\": 3}","share/mamba/envs/pandda2/lib/python3.9/site-packages/pynndescent implementation and installed metadata Requires-Dist (scikit-learn/scipy/numba/llvmlite/joblib)"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:pyparsing","disposition":"grammar parser","rationale":"Parser/grammar construction library.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/pyparsing-3.3.3.dist-info/METADATA; 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environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:pysocks","disposition":"SOCKS proxy transport support","rationale":"Network transport helper; optional requests extra selects use. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/PySocks-1.7.1.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/PySocks-1.7.1.dist-info/METADATA: installed metadata ['Name: PySocks', 'Version: 1.7.1']","metadata-owned top_level/RECORD roots: top_level=['socks', 'sockshandler']; RECORD roots=['__pycache__', 'socks.py', 'sockshandler.py']; RECORD rows=10; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/socks.py', 'share/mamba/envs/pandda2/lib/python3.9/site-packages/sockshandler.py']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:pytest","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: test runner. 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This confirms a framework runtime paired with a custom 3D ResNet/checkpoint.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pytorch_lightning-2.2.5.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/pytorch_lightning-2.2.5.dist-info/METADATA; metadata SHA-256 825e67d39879cb26ad2378eef5f947053d5ebeb381ed1f12e98f7ebd2e6ee06f","top_level.txt roots=['lightning_fabric', 'pytorch_lightning']; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/pytorch_lightning-2.2.5.dist-info/RECORD; RECORD existing=275/537","read-only source scan: 262 Python files / 2142793 bytes; 233 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:pytorch-lightning; environment=share/mamba/envs/pandda2; version=2.2.5","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/build.py:6","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/event.py:10","package tree: 262 Python files / 2,142,793 bytes read; 233 term-hit files"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:pytz","disposition":"time-zone-database","rationale":"Installed pytz 2026.5 in share/mamba/envs/pandda2 is time-zone-database; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pytz-2026.5.dist-info/METADATA; Name: pytz | Version: 2026.5 | Summary: World timezone definitions, modern and historical","owner: top_level=['pytz']; source_roots_from_METADATA_or_RECORD=['pytz']; RECORD_rows=623; RECORD_sample=['pytz-2026.5.dist-info/INSTALLER', 'pytz-2026.5.dist-info/LICENSE.txt', 'pytz-2026.5.dist-info/METADATA', 'pytz-2026.5.dist-info/RECORD', 'pytz-2026.5.dist-info/WHEEL', 'pytz-2026.5.dist-info/top_level.txt', 'pytz-2026.5.dist-info/zip-safe', 'pytz/__init__.py']"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:pyyaml","disposition":"configuration-parser","rationale":"PyYAML parses configuration; not a model consumer.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/pyyaml-6.0.3.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:ray","disposition":"distributed_task_runtime_with_optional_ml_integrations","rationale":"Ray is installed in PanDDA2 and the shipped PanDDA application adapter uses it to initialize local CPU workers and dispatch generic callables. Ray source contains broad ML integrations, but their optional framework imports do not prove this CCP4 path performs ML.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/ray-2.51.2.dist-info/METADATA sha256=7a1523d1f6c9acc6cd9273630ac077881abc3c6711114f61734e3099f172733a bytes=21502 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/ray-2.51.2.dist-info/RECORD rows=4831; sample=[\"../../../bin/ray,sha256=Q3m5oN-YN_p0vImgNPJ6n4y7MZRQLpLDeepPNabZS4I,232\", \"../../../bin/serve,sha256=XE1qKp9-tL9EqhmvX9ONAyQe1_OJOjBQwPOoRKxUuzo,228\", \"../../../bin/tune,sha256=2daTPDmkYZ8FkQNGa_J59hMwVhz_iP_uxaI_frnX70A,231\", \"ray-2.51.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\"]","top_level share/mamba/envs/pandda2/lib/python3.9/site-packages/ray-2.51.2.dist-info/top_level.txt=[\"ray\"]","static Python audit group package=ray env=share/mamba/envs/pandda2: 2292 files, 22428106 bytes, 536 files with broad ML/loader marker hits","representative package source share/mamba/envs/pandda2/lib/python3.9/site-packages/ray/actor.py sha256=c517b4d9357d54920b518b5b9599c49de9b355e84f849ec3a7b536cfab692eb9","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/processor/processor_ray.py:3,8-23,26-43 initializes Ray and dispatches generic functions","python.json Ray group includes optional/dynamic integration imports for torch, tensorflow, sklearn, transformers, xgboost, lightgbm, optuna, jax and other frameworks; no installed app model path is established"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:rdkit","disposition":"chemical informatics package with optional classical ML contributions and an NP_Score model archive","rationale":"RDKit Contrib/FreeWilson/freewilson.py:144-145 uses Ridge/r2_score and Contrib/pzc/p_con.py:19-22 imports RandomForestClassifier; these are contribution/workflow code, while the separate publicnp.model.gz archive has its own scoring loader","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/rdkit-2025.9.2.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/rdkit-2025.9.2.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"numpy\", \"Pillow\"]; ownership={\"record_file_count\": 1282, \"top_level.txt\": \"rdkit\\n\"}","audits/ccp4-10.0.001/python.json AST group package=rdkit root=lib/python3.11/site-packages files=249 hit_files=6 imports={}","share/mamba/envs/pandda2/lib/python3.9/site-packages/rdkit/Contrib/FreeWilson/freewilson.py:144-145; rdkit/Contrib/pzc/p_con.py:19-22","share/RDKit/Contrib/NP_Score/publicnp.model.gz is reviewed in assigned archives; npscorer.py:2-11,27-33,36-74,95-100"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:referencing","disposition":"JSON reference resolver","rationale":"JSON Schema reference-resolution utility.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/referencing-0.36.2.dist-info/METADATA; SHA-256=f1ec8cf77a53d149e03e4370d19c5281753c77f24abc3468d27c614b05bd7206; Name=referencing; Version=0.36.2; Summary=JSON Referencing + Python","declared Requires-Dist (3): [\"attrs>=22.2.0\",\"rpds-py>=0.7.0\",\"typing-extensions>=4.4.0; python_version < '3.13'\"]","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/referencing-0.36.2.dist-info/top_level.txt; top_level=[]; RECORD rows=20; RECORD sample=[\"referencing-0.36.2.dist-info/INSTALLER\", \"referencing-0.36.2.dist-info/METADATA\", \"referencing-0.36.2.dist-info/RECORD\", \"referencing-0.36.2.dist-info/WHEEL\", \"referencing-0.36.2.dist-info/licenses/COPYING\", \"referencing/__init__.py\", \"referencing/_attrs.py\", \"referencing/_attrs.pyi\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 13 files, 109303 bytes, 0 skipped/overflow; ML vocabulary hits=4","representative broad-term source hits: [{\"path\": \"referencing/_core.py\", \"line\": 304, \"text\": \"database, a separate set of files, over the network, etc.).\"}, {\"path\": \"referencing/_core.py\", \"line\": 315, \"text\": \"dynamically, either over the network, from a database, or the like.\"}, {\"path\": \"referencing/retrieval.py\", \"line\": 41, \"text\": \"network) might otherwise be called repeatedly.\"}, {\"path\": \"referencing/retrieval.py\", \"line\": 57, \"text\": \"# Normally, go get some expensive JSON from the network, a file ...\"}]","node identity: pydist:share/mamba/envs/pandda2:referencing; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:requests","disposition":"HTTP client","rationale":"Network/API transport; 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The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/rich-15.0.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/rich-15.0.0.dist-info/METADATA: Name: rich","share/mamba/envs/pandda2/lib/python3.9/site-packages/rich-15.0.0.dist-info/METADATA: Version: 15.0.0","share/mamba/envs/pandda2/lib/python3.9/site-packages/rich-15.0.0.dist-info/METADATA: Summary: Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:rpds-py","disposition":"general runtime/development infrastructure","rationale":"Persistent data structures package. Its installed metadata/source-root evidence does not establish an ML application role or trained model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/rpds_py-0.27.1.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/rpds_py-0.27.1.dist-info/METADATA; sha256=b76fe460f93be155403bdb6a74d01661c967c3e2ae522fe9963c297c7a1faea9; record exists=True","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/rpds']; bounded scan files=1, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:scikit-image","disposition":"image processing package with generic trainable-segmentation capability","rationale":"Its generic TrainableSegmenter defaults to sklearn RandomForestClassifier and has fit/predict methods. PanDDA2 imports only skimage.segmentation.expand_labels in the located caller search, so the generic classifier capability is not evidence that PanDDA uses this estimator.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/scikit_image-0.24.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/scikit_image-0.24.0.dist-info/METADATA; metadata SHA-256 69c81fe75254bbe9375d1f2910b7788cc65668210cec4eb580e40da665f4729d","top_level.txt roots=[]; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/scikit_image-0.24.0.dist-info/RECORD; RECORD existing=477/834","read-only source scan: 357 Python files / 3149207 bytes; 33 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:scikit-image; environment=share/mamba/envs/pandda2; version=0.24.0","share/mamba/envs/pandda2/lib/python3.9/site-packages/skimage/future/trainable_segmentation.py:4-9,37-56","share/mamba/envs/pandda2/lib/python3.9/site-packages/pandda_gemmi/cnn/event.py:4","package tree: 357 Python files / 3,149,207 bytes read; 33 term-hit files"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:scikit-learn","disposition":"machine-learning-framework","rationale":"The installed distribution is the complete scikit-learn ML framework (METADATA summary and 1,465 owned RECORD entries under sklearn/). Runtime dependencies on NumPy, SciPy, joblib and threadpoolctl are installed in pandda2; the package itself does not prove a CCP4 application path.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/scikit_learn-1.6.1.dist-info/METADATA; Name: scikit-learn | Version: 1.6.1 | Summary: A set of python modules for machine learning and data mining","owner: top_level=(absent); source_roots_from_METADATA_or_RECORD=['sklearn']; RECORD_rows=1465; RECORD_sample=['scikit_learn-1.6.1.dist-info/COPYING', 'scikit_learn-1.6.1.dist-info/INSTALLER', 'scikit_learn-1.6.1.dist-info/METADATA', 'scikit_learn-1.6.1.dist-info/RECORD', 'scikit_learn-1.6.1.dist-info/WHEEL', 'scikit_learn.libs/libgomp-a34b3233.so.1.0.0', 'sklearn/__check_build/__init__.py', 'sklearn/__check_build/__pycache__/__init__.cpython-39.pyc']","declared dependencies: Requires-Dist: numpy>=1.19.5; Requires-Dist: scipy>=1.6.0; Requires-Dist: joblib>=1.2.0; Requires-Dist: threadpoolctl>=3.1.0; Requires-Dist: numpy>=1.19.5; extra == \"build\"; Requires-Dist: scipy>=1.6.0; extra == \"build\"; Requires-Dist: cython>=3.0.10; extra == \"build\"; Requires-Dist: meson-python>=0.16.0; extra == \"build\"; Requires-Dist: numpy>=1.19.5; extra == \"install\"; Requires-Dist: scipy>=1.6.0; extra == \"install\"; Requires-Dist: joblib>=1.2.0; extra == \"install\"; Requires-Dist: threadpoolctl>=3.1.0; extra == \"install\"","RECORD ownership includes sklearn/__check_build/* and compiled sklearn algorithm subpackages; native audit records sklearn extension ELF hashes/DT_NEEDED."],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:scipy","disposition":"numerical-and-statistical-library","rationale":"SciPy supplies numerical methods including general k-means and scientific routines; this is algorithm capability, not an application-level learned model.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/scipy-1.13.1.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:seaborn","disposition":"statistical_visualization_library","rationale":"Seaborn supplies statistical plots and estimators (including regression/KDE plotting APIs), but the installed source scan found no trained model assets or CCP4 application model-loading path.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/seaborn-0.13.2.dist-info/METADATA sha256=98cfe2b7a5004466cdd5c7c8ccf016ebdcfa0337fc177ea7aad27f527c53fc96 bytes=5381 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/seaborn-0.13.2.dist-info/RECORD rows=113; sample=[\"seaborn-0.13.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"seaborn-0.13.2.dist-info/LICENSE.md,sha256=NXrSduCG-rUBFj1OmgrhPC_QZH6wjSMF-8DKOBOJJgE,1491\", \"seaborn-0.13.2.dist-info/METADATA,sha256=mM_it6UARGbN1cfIzPAW69z6Azf8F36nqtJ_UnxT_JY,5381\", \"seaborn-0.13.2.dist-info/RECORD,,\"]","No top_level.txt in this dist-info; RECORD file list inspected for ownership.","static Python audit group package=seaborn env=share/mamba/envs/pandda2: 54 files, 1031041 bytes, 0 files with broad ML/loader marker hits"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:setuptools","disposition":"Python package installation/build tooling in the ABCFold environment","rationale":"installer/build metadata only; recorded egg-info is under the Python 3.11 environment path despite the py3.10 egg-info suffix","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/setuptools-79.0.1-py3.9.egg-info/PKG-INFO:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/setuptools-79.0.1-py3.9.egg-info/PKG-INFO:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[\"pytest!=8.1.*,>=6; extra == \\\"test\\\"\", \"virtualenv>=13.0.0; extra == \\\"test\\\"\", \"wheel>=0.44.0; extra == \\\"test\\\"\", \"pip>=19.1; extra == \\\"test\\\"\", \"packaging>=24.2; extra == \\\"test\\\"\", \"jaraco.envs>=2.2; extra == \\\"test\\\"\", \"pytest-xdist>=3; extra == \\\"test\\\"\", \"jaraco.path>=3.7.2; extra == \\\"test\\\"\", \"build[virtualenv]>=1.0.3; extra == \\\"test\\\"\", \"filelock>=3.4.0; extra == \\\"test\\\"\", \"ini2toml[lite]>=0.14; extra == \\\"test\\\"\", \"tomli-w>=1.0.0; extra == \\\"test\\\"\", \"pytest-timeout; extra == \\\"test\\\"\", \"pytest-perf; sys_platform != \\\"cygwin\\\" and extra == \\\"test\\\"\", \"jaraco.develop>=7.21; (python_version >= \\\"3.9\\\" and sys_platform != \\\"cygwin\\\") and extra == \\\"test\\\"\", \"pytest-home>=0.5; extra == \\\"test\\\"\", \"pytest-subprocess; extra == \\\"test\\\"\", \"pyproject-hooks!=1.1; extra == \\\"test\\\"\", \"jaraco.test>=5.5; extra == \\\"test\\\"\", \"sphinx>=3.5; extra == \\\"doc\\\"\", \"jaraco.packaging>=9.3; extra == \\\"doc\\\"\", \"rst.linker>=1.9; extra == \\\"doc\\\"\", \"furo; extra == \\\"doc\\\"\", \"sphinx-lint; extra == \\\"doc\\\"\", \"jaraco.tidelift>=1.4; extra == \\\"doc\\\"\", \"pygments-github-lexers==0.0.5; extra == \\\"doc\\\"\", \"sphinx-favicon; extra == \\\"doc\\\"\", \"sphinx-inline-tabs; extra == \\\"doc\\\"\", \"sphinx-reredirects; extra == \\\"doc\\\"\", \"sphinxcontrib-towncrier; extra == \\\"doc\\\"\", \"sphinx-notfound-page<2,>=1; extra == \\\"doc\\\"\", \"pyproject-hooks!=1.1; extra == \\\"doc\\\"\", \"towncrier<24.7; extra == \\\"doc\\\"\", \"packaging>=24.2; extra == \\\"core\\\"\", \"more_itertools>=8.8; extra == \\\"core\\\"\", \"jaraco.text>=3.7; extra == \\\"core\\\"\", \"importlib_metadata>=6; python_version < \\\"3.10\\\" and extra == \\\"core\\\"\", \"tomli>=2.0.1; python_version < \\\"3.11\\\" and extra == \\\"core\\\"\", \"wheel>=0.43.0; extra == \\\"core\\\"\", \"platformdirs>=4.2.2; extra == \\\"core\\\"\", \"jaraco.functools>=4; extra == \\\"core\\\"\", \"more_itertools; extra == \\\"core\\\"\", \"pytest-checkdocs>=2.4; extra == \\\"check\\\"\", \"pytest-ruff>=0.2.1; sys_platform != \\\"cygwin\\\" and extra == \\\"check\\\"\", \"ruff>=0.8.0; sys_platform != \\\"cygwin\\\" and extra == \\\"check\\\"\", \"pytest-cov; extra == \\\"cover\\\"\", \"pytest-enabler>=2.2; extra == \\\"enabler\\\"\", \"pytest-mypy; extra == \\\"type\\\"\", \"mypy==1.14.*; extra == \\\"type\\\"\", \"importlib_metadata>=7.0.2; python_version < \\\"3.10\\\" and extra == \\\"type\\\"\", \"jaraco.develop>=7.21; sys_platform != \\\"cygwin\\\" and extra == \\\"type\\\"\"]; ownership={\"SOURCES.txt\": \"LICENSE\\nMANIFEST.in\\nNEWS.rst\\nREADME.rst\\nconftest.py\\nexercises.py\\nlauncher.c\\nmypy.ini\\npyproject.toml\\npytest.ini\\nsetup.cfg\\nsetup.py\\ntox.ini\\n_distutils_hack/__init__.py\\n_distutils_hack/override.py\\ndocs/artwork.rst\\ndocs/build_meta.rst\\ndocs/conf.py\\ndocs/history.rst\\ndocs/index.rst\\ndocs/pkg_resources.rst\\ndocs/python 2 sunset.rst\\ndocs/roadmap.rst\\ndocs/setuptools.rst\\ndocs/deprecated/changed_keywords.rst\\ndocs/deprecated/commands.rst\\ndocs/deprecated/dependency_links.rst\\ndocs/deprecated/distutils-legacy.rst\\ndocs/deprecated/easy_install.rst\\ndocs/deprecated/functionalities.rst\\ndocs/deprecated/index.rst\\ndocs/deprecated/python_eggs.rst\\ndocs/deprecated/resource_extraction.rst\\ndocs/deprecated/zip_safe.rst\\ndocs/deprecated/distutils/_setuptools_disclaimer.rst\\ndocs/deprecated/distutils/apiref.rst\\ndocs/deprecated/distutils/builtdist.rst\\ndocs/deprecated/distutils/commandref.rst\\ndocs/deprecated/distutils/configfile.rst\\ndocs/deprecated/distutils/examples.rst\\ndocs/deprecated/distutils/extending.rst\\ndocs/deprecated/distutils/index.rst\\ndocs/deprecated/distutils/introduction.rst\\ndocs/deprecated/distutils/packageindex.rst\\ndocs/deprecated/distutils/setupscript.rst\\ndocs/deprecated/distutils/sourcedist.rst\\ndocs/deprecated/distutils/uploading.rst\\ndocs/development/developer-guide.rst\\ndocs/development/index.rst\\ndocs/development/releases.rst\\ndocs/references/keywords.rst\\ndocs/userguide/datafiles.rst\\ndocs/userguide/declarative_config.rst\\ndocs/userguide/dependency_management.rst\\ndocs/userguide/development_mode.rst\\n\", \"entry_points.txt\": \"[distutils.commands]\\nalias = setuptools.command.alias:alias\\nbdist_egg = setuptools.command.bdist_egg:bdist_egg\\nbdist_rpm = setuptools.command.bdist_rpm:bdist_rpm\\nbdist_wheel = setuptools.command.bdist_wheel:bdist_wheel\\nbuild = setuptools.command.build:build\\nbuild_clib = setuptools.command.build_clib:build_clib\\nbuild_ext = setuptools.command.build_ext:build_ext\\nbuild_py = setuptools.command.build_py:build_py\\ndevelop = setuptools.command.develop:develop\\ndist_info = setuptools.command.dist_info:dist_info\\neasy_install = setuptools.command.easy_install:easy_install\\neditable_wheel = setuptools.command.editable_wheel:editable_wheel\\negg_info = setuptools.command.egg_info:egg_info\\ninstall = setuptools.command.install:install\\ninstall_egg_info = setuptools.command.install_egg_info:install_egg_info\\ninstall_lib = setuptools.command.install_lib:install_lib\\ninstall_scripts = setuptools.command.install_scripts:install_scripts\\nrotate = setuptools.command.rotate:rotate\\nsaveopts = setuptools.command.saveopts:saveopts\\nsdist = setuptools.command.sdist:sdist\\nsetopt = setuptools.command.setopt:setopt\\n\\n[distutils.setup_keywords]\\ndependency_links = setuptools.dist:assert_string_list\\neager_resources = setuptools.dist:assert_string_list\\nentry_points = setuptools.dist:check_entry_points\\nexclude_package_data = setuptools.dist:check_package_data\\nextras_require = setuptools.dist:check_extras\\ninclude_package_data = setuptools.dist:assert_bool\\ninstall_requires = setuptools.dist:check_requirements\\nnamespace_p\", \"top_level.txt\": \"_distutils_hack\\npkg_resources\\nsetuptools\\n\"}","audits/ccp4-10.0.001/python.json AST group package=setuptools root=lib/python3.11/site-packages files=346 hit_files=44 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:six","disposition":"compatibility utility","rationale":"Python compatibility utility.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/six-1.17.0.dist-info/METADATA; SHA-256=562042078c2752549f6d8a7c86dbc5dd708088a7be6d80672ec7b07100b72468; Name=six; Version=1.17.0; Summary=Python 2 and 3 compatibility utilities","declared Requires-Dist (0): []","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/six-1.17.0.dist-info/top_level.txt; top_level=[\"six\"]; RECORD rows=7; RECORD sample=[\"six-1.17.0.dist-info/INSTALLER\", \"six-1.17.0.dist-info/LICENSE\", \"six-1.17.0.dist-info/METADATA\", \"six-1.17.0.dist-info/RECORD\", \"six-1.17.0.dist-info/WHEEL\", \"six-1.17.0.dist-info/top_level.txt\", \"six.py\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 1 files, 34703 bytes, 0 skipped/overflow; ML vocabulary hits=0","node identity: pydist:share/mamba/envs/pandda2:six; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:soupsieve","disposition":"HTML selector engine","rationale":"Markup query utility; no ML role. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/soupsieve-2.8.4.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/soupsieve-2.8.4.dist-info/METADATA: installed metadata ['Name: soupsieve', 'Version: 2.8.4']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['soupsieve']; RECORD rows=20; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/soupsieve']"],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:termcolor","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: terminal color formatting. The expanded source scan did not establish a trained model or neural inference path for this package; where it contains statistical helpers, those remain distinct from neural model artifacts.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/termcolor-3.1.0.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/termcolor-3.1.0.dist-info/METADATA: Name: termcolor","share/mamba/envs/pandda2/lib/python3.9/site-packages/termcolor-3.1.0.dist-info/METADATA: Version: 3.1.0","share/mamba/envs/pandda2/lib/python3.9/site-packages/termcolor-3.1.0.dist-info/METADATA: Summary: ANSI color formatting for output in terminal"],"review_file":"audits/ccp4-10.0.001/full-review/part-02.json"},{"identity":"pydist:share/mamba/envs/pandda2:threadpoolctl","disposition":"numerical/runtime infrastructure","rationale":"Native BLAS/OpenMP thread-pool control; no model asset.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/threadpoolctl-3.7.0.dist-info/METADATA:L2","cpu64 installed record share/mamba/envs/pandda2/lib/python3.9/site-packages/threadpoolctl-3.7.0.dist-info/METADATA; sha256=09b19e721560cd12246402d44e53c1ede5194b8398ef60822f02cab86ccf8d1f; record exists=True","metadata-derived source roots ['share/mamba/envs/pandda2/lib/python3.9/site-packages/threadpoolctl.py']; bounded scan files=1, truncated=False"],"review_file":"audits/ccp4-10.0.001/full-review/part-03.json"},{"identity":"pydist:share/mamba/envs/pandda2:tifffile","disposition":"general-purpose parser, ordering, test, or transport support","rationale":"Package metadata, top-level ownership and the static source scan identify general support functionality; no model implementation or serialized model loader was located.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/tifffile-2024.8.30.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/tifffile-2024.8.30.dist-info/METADATA; metadata SHA-256 3211d63f6e5519c553ce1ba6c21c9bce6fa19e7bae04c0656b4ec139c7bdcd60","top_level.txt roots=['tifffile']; RECORD=share/mamba/envs/pandda2/lib/python3.9/site-packages/tifffile-2024.8.30.dist-info/RECORD; RECORD existing=21/30","read-only source scan: 9 Python files / 987413 bytes; 1 files matched broad ML term inventory; package source was not imported","installed distribution identity: pydist:share/mamba/envs/pandda2:tifffile; environment=share/mamba/envs/pandda2; version=2024.8.30","bounded hit review: 1 hit files were parser/build/test/support contexts; no scientific model consumer identified"],"review_file":"audits/ccp4-10.0.001/full-review/part-04.json"},{"identity":"pydist:share/mamba/envs/pandda2:tomli","disposition":"TOML-parser","rationale":"Installed tomli 2.2.1 in share/mamba/envs/pandda2 is TOML-parser; metadata and import ownership were inspected to distinguish support infrastructure from model/application packages.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/tomli-2.2.1.dist-info/METADATA; Name: tomli | Version: 2.2.1 | Summary: A lil' TOML parser","owner: top_level=(absent); source_roots_from_METADATA_or_RECORD=['tomli']; RECORD_rows=16; RECORD_sample=['tomli-2.2.1.dist-info/INSTALLER', 'tomli-2.2.1.dist-info/METADATA', 'tomli-2.2.1.dist-info/RECORD', 'tomli-2.2.1.dist-info/REQUESTED', 'tomli-2.2.1.dist-info/WHEEL', 'tomli-2.2.1.dist-info/direct_url.json', 'tomli-2.2.1.dist-info/licenses/LICENSE', 'tomli/__init__.py']"],"review_file":"audits/ccp4-10.0.001/full-review/part-05.json"},{"identity":"pydist:share/mamba/envs/pandda2:torch","disposition":"deep-learning-runtime-framework","rationale":"PyTorch 1.13.1 and LibTorch/CUDA native libraries are installed in the isolated pandda2 environment. Framework/native presence alone does not identify an application call or specific weights; the assigned TorchMetrics AlexNet payload is a separate third-party metric asset.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/torch-1.13.1.dist-info/METADATA:L2"],"review_file":"audits/ccp4-10.0.001/full-review/part-06.json"},{"identity":"pydist:share/mamba/envs/pandda2:torchmetrics","disposition":"machine_learning_metrics_library_with_packaged_lpips_weights","rationale":"TorchMetrics is an ML metric library. Its installed LPIPS source optionally imports torchvision and loads per-network .pth calibration weights on CPU; no CCP4 application caller to this API was identified.","evidence":["installed metadata share/mamba/envs/pandda2/lib/python3.9/site-packages/torchmetrics-1.5.2.dist-info/METADATA sha256=ba54ecadb8ed1509c8c4850748531998019950fa23e419b607e0a53a37f13795 bytes=20635 (manifest metadata hash matches)","ownership file share/mamba/envs/pandda2/lib/python3.9/site-packages/torchmetrics-1.5.2.dist-info/RECORD rows=654; sample=[\"torchmetrics-1.5.2.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4\", \"torchmetrics-1.5.2.dist-info/LICENSE,sha256=-jH0M_W0vB-3MPucZ4-QGC2Tv3a22Yuk0A9ARUrIuDI,11352\", \"torchmetrics-1.5.2.dist-info/METADATA,sha256=ulTsrbjtFQnIxIUHSFMZmAGZUPoj5Bm2B-ClOjfxN5U,20635\", \"torchmetrics-1.5.2.dist-info/RECORD,,\"]","top_level share/mamba/envs/pandda2/lib/python3.9/site-packages/torchmetrics-1.5.2.dist-info/top_level.txt=[\"torchmetrics\"]","static Python audit group package=torchmetrics env=share/mamba/envs/pandda2: 322 files, 3167450 bytes, 322 files with broad ML/loader marker hits","representative package source share/mamba/envs/pandda2/lib/python3.9/site-packages/torchmetrics/metric.py sha256=200034a81d530c27b071eeccf09b5690de6f28bc4881a9931288636f0cccb895","share/mamba/envs/pandda2/lib/python3.9/site-packages/torchmetrics/functional/image/lpips.py:45-62,319-325","torchmetrics owns per-model lpips_models assets through installed RECORD; only the squeeze.pth candidate is in this shard"],"review_file":"audits/ccp4-10.0.001/full-review/part-07.json"},{"identity":"pydist:share/mamba/envs/pandda2:tornado","disposition":"asynchronous networking/web support in the PanDDA2 environment","rationale":"server/event-loop support only","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/tornado-6.5.10.dist-info/METADATA:L2","Installed distribution identity confirmed from share/mamba/envs/pandda2/lib/python3.9/site-packages/tornado-6.5.10.dist-info/METADATA:L2; Python audit groups and package-owned source were used to distinguish runtime code, examples/tests and optional features.","Installed metadata exact Requires-Dist=[]; ownership={\"record_file_count\": 171, \"top_level.txt\": \"tornado\\n\"}","audits/ccp4-10.0.001/python.json AST group package=tornado root=lib/python3.11/site-packages files=72 hit_files=9 imports={}"],"review_file":"audits/ccp4-10.0.001/full-review/part-08.json"},{"identity":"pydist:share/mamba/envs/pandda2:tqdm","disposition":"progress reporting utility","rationale":"Progress reporting; its Keras adapter is UI integration only and source scan does not establish inference. `tqdm/keras.py` imports TensorFlow Keras for progress callbacks; that adapter is not evidence of model inference.","evidence":["installed metadata: share/mamba/envs/pandda2/lib/python3.9/site-packages/tqdm-4.70.1.dist-info/METADATA; SHA-256=a5da70b966afea3a759716041bad7187f2ece02c22348cf9e7c0a512bbf15f57; Name=tqdm; Version=4.70.1; Summary=Fast, Extensible Progress Meter","declared Requires-Dist (8): [\"colorama; platform_system == \\\"Windows\\\"\",\"requests; extra == \\\"discord\\\"\",\"envwrap; extra == \\\"discord\\\"\",\"slack-sdk; extra == \\\"slack\\\"\",\"envwrap; extra == \\\"slack\\\"\",\"requests; extra == \\\"telegram\\\"\",\"envwrap; extra == \\\"telegram\\\"\",\"ipywidgets>=6; extra == \\\"notebook\\\"\"]","ownership: top_level metadata path candidate=share/mamba/envs/pandda2/lib/python3.9/site-packages/tqdm-4.70.1.dist-info/top_level.txt; top_level=[\"tqdm\"]; RECORD rows=41; RECORD sample=[\"../../../bin/tqdm\", \"tqdm-4.70.1.dist-info/INSTALLER\", \"tqdm-4.70.1.dist-info/METADATA\", \"tqdm-4.70.1.dist-info/RECORD\", \"tqdm-4.70.1.dist-info/WHEEL\", \"tqdm-4.70.1.dist-info/entry_points.txt\", \"tqdm-4.70.1.dist-info/licenses/LICENCE\", \"tqdm-4.70.1.dist-info/top_level.txt\"]; empty top_level list means no import-root claim from that metadata file","static source scan: 31 files, 162597 bytes, 0 skipped/overflow; ML vocabulary hits=2","representative broad-term source hits: [{\"path\": \"tqdm/keras.py\", \"line\": 10, \"text\": \"from tensorflow import keras\"}, {\"path\": \"tqdm/std.py\", \"line\": 291, \"text\": \"(network, skipping items, etc) you should set miniters=1.\"}]","node identity: pydist:share/mamba/envs/pandda2:tqdm; environment=share/mamba/envs/pandda2; shipped=y; node SHA field=not recorded for distribution metadata"],"review_file":"audits/ccp4-10.0.001/full-review/part-09.json"},{"identity":"pydist:share/mamba/envs/pandda2:typing-extensions","disposition":"Python typing compatibility","rationale":"Typing API backports; no ML role. This is a distinct installed record in the share/mamba/envs/pandda2 environment; no identity was borrowed from another environment.","evidence":["share/mamba/envs/pandda2/lib/python3.9/site-packages/typing_extensions-4.14.1.dist-info/METADATA:L2","share/mamba/envs/pandda2/lib/python3.9/site-packages/typing_extensions-4.14.1.dist-info/METADATA: installed metadata ['Name: typing_extensions', 'Version: 4.14.1']","metadata-owned top_level/RECORD roots: top_level=None; RECORD roots=['__pycache__', 'typing_extensions.py']; RECORD rows=9; resolved roots=['share/mamba/envs/pandda2/lib/python3.9/site-packages/typing_extensions.py']","Installed source scan examples: share/mamba/envs/pandda2/lib/python3.9/site-packages/typing_extensions.py:597 \"\"\"Allow instance and class checks for special stdlib modules.; share/mamba/envs/pandda2/lib/python3.9/site-packages/typing_extensions.py:3423 # As a courtesy, register the most common stdlib buffer classes."],"review_file":"audits/ccp4-10.0.001/full-review/part-01.json"},{"identity":"pydist:share/mamba/envs/pandda2:tzdata","disposition":"non-model support package","rationale":"Installed package role from metadata and static implementation review: IANA time-zone database. 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