Coverage report: 94%

Files Functions Classes

coverage.py v7.15.4, created at 2026-08-26 00:09 +0000

File function   statements missing excluded   coverage
cosmolayer/__init__.py __getattr__   10 3 0   70%
cosmolayer/__init__.py __dir__   1 0 0   100%
cosmolayer/__init__.py (no function)   9 0 6   100%
cosmolayer/cosmodata.py (no function)   2 0 0   100%
cosmolayer/cosmolayer/__init__.py (no function)   5 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureDatapoint.__post_init__   12 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureDatapoint.shape   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureDatapoint.get_inputs   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureDatapoint.get_targets   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureInferenceDataset.__init__   7 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureInferenceDataset.__len__   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureInferenceDataset.__getitem__   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureTrainingDataset.__init__   7 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureTrainingDataset.__len__   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureTrainingDataset.__getitem__   2 0 0   100%
cosmolayer/cosmolayer/cosmodata.py MixtureTrainingDataset.to_inference_dataset   1 0 0   100%
cosmolayer/cosmolayer/cosmodata.py (no function)   37 0 4   100%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.__init__   30 7 0   77%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule._build_initial_matrices   13 10 0   23%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule._infer_batch_size   5 2 0   60%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule._compute_target_statistics   37 3 0   92%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.forward   3 0 0   100%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.predict_from_log_gamma   1 0 0   100%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.configure_optimizers   1 0 0   100%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.on_fit_start   2 2 0   0%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.training_step   11 4 0   64%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.validation_step   11 4 0   64%
cosmolayer/cosmolayer/cosmolightning.py LogGammaLightningModule.test_step   16 0 0   100%
cosmolayer/cosmolayer/cosmolightning.py (no function)   28 0 0   100%
cosmolayer/cosmolayer/cosmosolver.py CosmoSolver.logspace_newton_solver   20 0 0   100%
cosmolayer/cosmolayer/cosmosolver.py CosmoSolver.forward   12 2 0   83%
cosmolayer/cosmolayer/cosmosolver.py CosmoSolver.backward   20 1 0   95%
cosmolayer/cosmolayer/cosmosolver.py (no function)   14 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.__init__   29 3 0   90%
cosmolayer/cosmolayer/layer.py CosmoLayer._check_convergence   2 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.extra_repr   1 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.log_combinatorial_activity_coefficients   5 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.mixture_probabilities   3 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.scaled_interactions   3 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.log_pure_segment_activity_coefficients   7 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.log_mixture_segment_activity_coefficients   7 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.log_residual_activity_coefficients   6 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.log_activity_coefficients   3 0 0   100%
cosmolayer/cosmolayer/layer.py CosmoLayer.forward   1 0 0   100%
cosmolayer/cosmolayer/layer.py (no function)   21 0 0   100%
cosmolayer/cosmolayer/utils.py log_matmul_exp   3 1 0   67%
cosmolayer/cosmolayer/utils.py is_loss_function   10 3 0   70%
cosmolayer/cosmolayer/utils.py (no function)   7 0 0   100%
cosmolayer/cosmolightning.py (no function)   2 0 0   100%
cosmolayer/cosmosac/__init__.py __getattr__   6 0 0   100%
cosmolayer/cosmosac/__init__.py __dir__   1 0 0   100%
cosmolayer/cosmosac/__init__.py (no function)   6 0 5   100%
cosmolayer/cosmosac/component.py Component.__init__   16 1 0   94%
cosmolayer/cosmosac/component.py Component.__repr__   3 3 0   0%
cosmolayer/cosmosac/component.py Component._get_covalent_radius   4 1 0   75%
cosmolayer/cosmosac/component.py Component._detect_bonds   7 0 0   100%
cosmolayer/cosmosac/component.py Component._get_hydrogen_bonding_classes   7 0 0   100%
cosmolayer/cosmosac/component.py Component._average_sigmas   9 0 0   100%
cosmolayer/cosmosac/component.py Component._compute_sigma_profile   9 0 0   100%
cosmolayer/cosmosac/component.py Component._compute_sigma_profiles   15 0 0   100%
cosmolayer/cosmosac/component.py Component.from_text_reader   1 0 0   100%
cosmolayer/cosmosac/component.py Component.from_file   5 2 0   60%
cosmolayer/cosmosac/component.py Component.area   1 0 0   100%
cosmolayer/cosmosac/component.py Component.volume   1 0 0   100%
cosmolayer/cosmosac/component.py Component.cosmo_format   1 0 0   100%
cosmolayer/cosmosac/component.py Component.atom_data   1 0 1   100%
cosmolayer/cosmosac/component.py Component.segment_data   1 0 1   100%
cosmolayer/cosmosac/component.py Component.bonds   1 0 0   100%
cosmolayer/cosmosac/component.py Component.sigma_grid   1 0 0   100%
cosmolayer/cosmosac/component.py Component.merge_profiles   1 1 0   0%
cosmolayer/cosmosac/component.py Component.sigma_profile   4 0 0   100%
cosmolayer/cosmosac/component.py Component.probabilities   3 0 0   100%
cosmolayer/cosmosac/component.py (no function)   48 1 0   98%
cosmolayer/cosmosac/constants.py (no function)   11 0 0   100%
cosmolayer/cosmosac/datapoint.py _get_component_data   5 0 0   100%
cosmolayer/cosmosac/datapoint.py CosmoSacMixtureDatapoint.__init__   4 0 0   100%
cosmolayer/cosmosac/datapoint.py CosmoSacMixtureDatapoint.from_series   1 0 0   100%
cosmolayer/cosmosac/datapoint.py (no function)   14 0 0   100%
cosmolayer/cosmosac/interaction_matrices.py create_cosmo_sac_2002_matrix   7 0 0   100%
cosmolayer/cosmosac/interaction_matrices.py create_cosmo_sac_2010_matrices   13 0 0   100%
cosmolayer/cosmosac/interaction_matrices.py (no function)   6 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.__init__   15 1 0   93%
cosmolayer/cosmosac/mixture.py Mixture.__len__   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.__getitem__   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture._create_component   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.add_component   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.remove_component   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.replace_component   12 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.area_per_segment   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.merge_profiles   1 1 0   0%
cosmolayer/cosmosac/mixture.py Mixture.component_names   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.areas   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.volumes   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.probabilities   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.sigma_profiles   1 1 0   0%
cosmolayer/cosmosac/mixture.py Mixture.interaction_matrices   1 0 0   100%
cosmolayer/cosmosac/mixture.py Mixture.temperature_exponents   1 0 0   100%
cosmolayer/cosmosac/mixture.py (no function)   32 0 0   100%
cosmolayer/cosmosac/model.py Model.create_interaction_matrices   1 0 0   100%
cosmolayer/cosmosac/model.py Model.create_component   1 0 0   100%
cosmolayer/cosmosac/model.py Model.create_mixture   1 0 0   100%
cosmolayer/cosmosac/model.py Model.num_segment_types   3 1 0   67%
cosmolayer/cosmosac/model.py (no function)   27 0 0   100%
cosmolayer/cosmosac/segment_groups.py (no function)   6 0 0   100%
cosmolayer/cosmosac/visualize.py estimate_vdw_radius   4 1 0   75%
cosmolayer/cosmosac/visualize.py create_atom_spheres   12 0 0   100%
cosmolayer/cosmosac/visualize.py compute_rotation_matrix   16 8 0   50%
cosmolayer/cosmosac/visualize.py create_bond_sticks   23 1 0   96%
cosmolayer/cosmosac/visualize.py ball_pivoting_algorithm   17 0 0   100%
cosmolayer/cosmosac/visualize.py find_loops   17 0 0   100%
cosmolayer/cosmosac/visualize.py geodesic_centroid   7 0 0   100%
cosmolayer/cosmosac/visualize.py surface_tessellation   41 1 0   98%
cosmolayer/cosmosac/visualize.py surface_tessellation.add_vertex   4 0 0   100%
cosmolayer/cosmosac/visualize.py surface_tessellation.midpoint_vertices   8 0 0   100%
cosmolayer/cosmosac/visualize.py generate_geometries   7 0 0   100%
cosmolayer/cosmosac/visualize.py get_parser   7 7 0   0%
cosmolayer/cosmosac/visualize.py main   4 4 0   0%
cosmolayer/cosmosac/visualize.py (no function)   28 1 0   96%
cosmolayer/cosmosolver.py (no function)   2 0 0   100%
cosmolayer/data/__init__.py (no function)   0 0 0   100%
cosmolayer/parser/__init__.py (no function)   2 0 0   100%
cosmolayer/parser/chaos.py _has_required_fields   10 0 0   100%
cosmolayer/parser/chaos.py is_chaos_json   5 0 0   100%
cosmolayer/parser/chaos.py parse_record   5 0 0   100%
cosmolayer/parser/chaos.py get_atom_dataframe   6 0 0   100%
cosmolayer/parser/chaos.py get_segment_dataframe   5 0 0   100%
cosmolayer/parser/chaos.py get_volume   4 0 0   100%
cosmolayer/parser/chaos.py (no function)   14 0 0   100%
cosmolayer/parser/common.py (no function)   9 0 0   100%
cosmolayer/parser/dmol3.py is_dmol3_format   1 0 0   100%
cosmolayer/parser/dmol3.py (no function)   9 0 0   100%
cosmolayer/parser/parser.py get_atom_dataframe   4 0 0   100%
cosmolayer/parser/parser.py get_segment_dataframe   5 0 0   100%
cosmolayer/parser/parser.py get_volume   1 0 0   100%
cosmolayer/parser/parser.py parse_cosmo_file   17 0 0   100%
cosmolayer/parser/parser.py (no function)   8 0 0   100%
cosmolayer/parser/turbomole.py is_turbomole_format   1 0 0   100%
cosmolayer/parser/turbomole.py (no function)   7 0 0   100%
cosmolayer/parser/utils.py parse_table   5 1 0   80%
cosmolayer/parser/utils.py parse_value   4 1 0   75%
cosmolayer/parser/utils.py (no function)   4 0 0   100%
cosmolayer/store/__init__.py (no function)   6 0 0   100%
cosmolayer/store/__main__.py get_parser   9 0 0   100%
cosmolayer/store/__main__.py _ensure_store_built   10 1 0   90%
cosmolayer/store/__main__.py _compute_atom_data   6 0 0   100%
cosmolayer/store/__main__.py _compute_molecule_data   5 0 0   100%
cosmolayer/store/__main__.py _print_atom_stats   7 0 0   100%
cosmolayer/store/__main__.py _print_molecule_stats   4 0 0   100%
cosmolayer/store/__main__.py main   13 1 0   92%
cosmolayer/store/__main__.py (no function)   20 1 0   95%
cosmolayer/store/_chalcedon/__init__.py (no function)   0 0 0   100%
cosmolayer/store/_chalcedon/butina_cluster.py butina_cluster   47 4 0   91%
cosmolayer/store/_chalcedon/butina_cluster.py butina_cluster.count_block   7 1 0   86%
cosmolayer/store/_chalcedon/butina_cluster.py butina_cluster.count_diagonal   6 4 0   33%
cosmolayer/store/_chalcedon/butina_cluster.py (no function)   9 0 2   100%
cosmolayer/store/_chalcedon/greedy_cluster_split.py greedy_cluster_split   25 2 0   92%
cosmolayer/store/_chalcedon/greedy_cluster_split.py (no function)   4 0 2   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py pairwise_tanimoto   10 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity.__post_init__   3 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity.fingerprint_count   1 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity.precision   1 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity.row   6 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity.chunk   5 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity._fill_dot_products_and_unions   3 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity._rows_neighbors_against   5 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py TanimotoSimilarity._block_neighbors   7 0 0   100%
cosmolayer/store/_chalcedon/tanimoto_similarity.py (no function)   23 0 2   100%
cosmolayer/store/averaging.py average_sigmas   16 0 0   100%
cosmolayer/store/averaging.py average_sigmas_by_molecule   7 0 0   100%
cosmolayer/store/averaging.py average_sigmas_by_molecule.process_range   6 0 0   100%
cosmolayer/store/averaging.py (no function)   19 0 0   100%
cosmolayer/store/binning.py row_indices_from_offsets   1 0 0   100%
cosmolayer/store/binning.py compute_per_atom_properties   3 0 0   100%
cosmolayer/store/binning.py compute_per_molecule_properties   1 0 0   100%
cosmolayer/store/binning.py accumulate_atom_profiles   15 0 0   100%
cosmolayer/store/binning.py accumulate_translated_profiles   13 0 0   100%
cosmolayer/store/binning.py (no function)   22 0 0   100%
cosmolayer/store/clustering.py FingerprintGenerator.__init__   2 0 0   100%
cosmolayer/store/clustering.py FingerprintGenerator.generate   3 0 0   100%
cosmolayer/store/clustering.py butina_cluster   7 0 0   100%
cosmolayer/store/clustering.py cluster_medoid_distances   29 0 0   100%
cosmolayer/store/clustering.py (no function)   21 0 0   100%
cosmolayer/store/coarse_graining.py compute_atom_remap   33 3 0   91%
cosmolayer/store/coarse_graining.py (no function)   2 0 0   100%
cosmolayer/store/grid.py SigmaGrid.bin_width   1 0 0   100%
cosmolayer/store/grid.py SigmaGrid.values   1 0 0   100%
cosmolayer/store/grid.py SigmaGrid.from_values   1 0 0   100%
cosmolayer/store/grid.py SigmaGrid.__len__   1 0 0   100%
cosmolayer/store/grid.py (no function)   19 0 0   100%
cosmolayer/store/parallel.py resolve_num_threads   3 1 0   67%
cosmolayer/store/parallel.py molecule_chunks   5 1 0   80%
cosmolayer/store/parallel.py run_in_threads   6 0 0   100%
cosmolayer/store/parallel.py (no function)   8 0 0   100%
cosmolayer/store/profiles.py SigmaProfileTable.level   1 0 0   100%
cosmolayer/store/profiles.py SigmaProfileTable.sigma_values   1 0 0   100%
cosmolayer/store/profiles.py SigmaProfileTable.from_segments   25 1 0   96%
cosmolayer/store/profiles.py SigmaProfileTable.from_segments.process_range   4 0 0   100%
cosmolayer/store/profiles.py SigmaProfileTable.aggregate   23 0 0   100%
cosmolayer/store/profiles.py SigmaProfileTable.aggregate.process_range   5 0 0   100%
cosmolayer/store/profiles.py (no function)   24 0 0   100%
cosmolayer/store/reporting.py print_stats   13 1 0   92%
cosmolayer/store/reporting.py (no function)   4 0 0   100%
cosmolayer/store/segments.py StoreMetadata.to_dict   1 0 0   100%
cosmolayer/store/segments.py StoreMetadata.from_dict   2 0 0   100%
cosmolayer/store/segments.py SegmentStore.__init__   10 0 0   100%
cosmolayer/store/segments.py SegmentStore._reorder_molecule   6 0 0   100%
cosmolayer/store/segments.py SegmentStore._parse_molecule   14 1 0   93%
cosmolayer/store/segments.py SegmentStore._build_molecules_df   1 0 0   100%
cosmolayer/store/segments.py SegmentStore.compute_averaged_sigmas   8 1 0   88%
cosmolayer/store/segments.py SegmentStore.assign_splits   4 0 0   100%
cosmolayer/store/segments.py SegmentStore.subsample   17 0 0   100%
cosmolayer/store/segments.py SegmentStore.coarse_grain   35 0 0   100%
cosmolayer/store/segments.py SegmentStore.save   16 3 0   81%
cosmolayer/store/segments.py SegmentStore.exists   10 2 0   80%
cosmolayer/store/segments.py SegmentStore.load   11 0 0   100%
cosmolayer/store/segments.py SegmentStore.from_cosmo_files   57 0 0   100%
cosmolayer/store/segments.py SegmentStore.sigmas   7 0 0   100%
cosmolayer/store/segments.py SegmentStore.compute_atom_sigma_profiles   4 0 0   100%
cosmolayer/store/segments.py SegmentStore.compute_molecule_sigma_profiles   3 0 0   100%
cosmolayer/store/segments.py (no function)   60 0 0   100%
cosmolayer/store/splitting.py greedy_cluster_split   5 0 0   100%
cosmolayer/store/splitting.py (no function)   5 0 0   100%
cosmolayer/store/subsampling.py apportion_counts   16 0 0   100%
cosmolayer/store/subsampling.py restrict_to_molecules   27 0 0   100%
cosmolayer/store/subsampling.py (no function)   6 0 2   100%
Total     1993 111 25   94%

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