Coverage report: 88%

Files Functions Classes

coverage.py v7.9.1, created at 2025-07-22 12:22 +0200

File function statements missing excluded branches partial coverage
MPP/MPP.py Lumping.__init__ 30 1 0 2 1 94%
MPP/MPP.py Lumping._add_feature 10 2 0 6 2 75%
MPP/MPP.py Lumping.run_mpp 12 2 0 4 1 81%
MPP/MPP.py Lumping.assign_macrostates 21 2 0 4 1 88%
MPP/MPP.py Lumping.gpcca 50 1 0 14 1 97%
MPP/MPP.py Lumping.save_macrostate_trajectory 5 5 0 2 0 0%
MPP/MPP.py Lumping.save_Z 9 6 0 8 2 29%
MPP/MPP.py Lumping.load_Z 14 2 0 4 2 78%
MPP/MPP.py Lumping.save_rmsd 1 0 0 0 0 100%
MPP/MPP.py Lumping.load_rmsd 1 0 0 0 0 100%
MPP/MPP.py Lumping.draw_random_frames_indices 11 0 0 8 0 100%
MPP/MPP.py Lumping.draw_random_frames 6 0 0 4 0 100%
MPP/MPP.py Lumping.get_best_defined_contacts 4 0 0 2 0 100%
MPP/MPP.py Lumping.get_least_moving_residues 6 0 0 2 0 100%
MPP/MPP.py Lumping.write_least_moving_residues 7 2 0 4 1 73%
MPP/MPP.py Lumping.__add__ 8 3 0 4 2 58%
MPP/MPP.py Lumping.reference 5 0 0 2 1 86%
MPP/MPP.py Lumping.n_i 5 1 0 4 1 78%
MPP/MPP.py Lumping.n_i 3 3 0 2 0 0%
MPP/MPP.py Lumping.timescales 3 0 0 2 1 80%
MPP/MPP.py Lumping.calc_timescales 3 0 0 2 0 100%
MPP/MPP.py Lumping.linkage 3 3 0 2 0 0%
MPP/MPP.py Lumping.macrostate_population 7 0 0 6 0 100%
MPP/MPP.py Lumping.rmsd 3 0 0 2 0 100%
MPP/MPP.py Lumping.rmsd_sharpness 1 0 0 0 0 100%
MPP/MPP.py Lumping.shannon_entropy 5 0 0 4 1 89%
MPP/MPP.py Lumping.davies_bouldin_index 5 0 0 4 1 89%
MPP/MPP.py Lumping.gmrq 3 0 0 2 1 80%
MPP/MPP.py Lumping.macro_micro_feature 6 0 0 6 1 92%
MPP/MPP.py Lumping.tree 5 0 0 4 0 100%
MPP/MPP.py Lumping.build_tree 15 0 0 8 0 100%
MPP/MPP.py Lumping.trajectory 1 0 0 0 0 100%
MPP/MPP.py Lumping.trajectory 11 3 0 8 3 68%
MPP/MPP.py Lumping.topology_file 3 1 0 2 1 60%
MPP/MPP.py Lumping.topology_file 3 1 0 2 1 60%
MPP/MPP.py Lumping.xtc_trajectory_file 3 1 0 2 1 60%
MPP/MPP.py Lumping.xtc_trajectory_file 3 1 0 2 1 60%
MPP/MPP.py Lumping.frame_length 1 0 0 0 0 100%
MPP/MPP.py Lumping.frame_length 1 0 0 0 0 100%
MPP/MPP.py Plotter.__init__ 1 0 0 0 0 100%
MPP/MPP.py Plotter.dendrogram 1 0 0 0 0 100%
MPP/MPP.py Plotter.implied_timescales 6 1 0 2 1 75%
MPP/MPP.py Plotter.macro_feature 1 0 0 0 0 100%
MPP/MPP.py Plotter.rmsd 1 0 0 0 0 100%
MPP/MPP.py Plotter.delta_rmsd 1 0 0 0 0 100%
MPP/MPP.py Plotter.contact_rep 1 0 0 0 0 100%
MPP/MPP.py Plotter.relative_implied_timescales 1 0 0 0 0 100%
MPP/MPP.py Plotter.ck_test 1 0 0 0 0 100%
MPP/MPP.py Plotter.state_network 1 0 0 0 0 100%
MPP/MPP.py Plotter.stochastic_state_similarity 1 0 0 0 0 100%
MPP/MPP.py Plotter.transition_matrix 1 0 0 0 0 100%
MPP/MPP.py Plotter.transition_time 1 0 0 0 0 100%
MPP/MPP.py Plotter.graph 1 1 0 0 0 0%
MPP/MPP.py Plotter.sankey 1 0 0 0 0 100%
MPP/MPP.py Plotter.macrostate_trajectory 1 0 0 0 0 100%
MPP/MPP.py (no function) 122 0 0 0 0 100%
MPP/__init__.py (no function) 6 0 0 0 0 100%
MPP/core.py BinaryTreeNode.__init__ 24 0 0 0 0 100%
MPP/core.py BinaryTreeNode.population 3 0 0 2 0 100%
MPP/core.py BinaryTreeNode.population 3 1 0 2 1 60%
MPP/core.py BinaryTreeNode.q 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.q 3 1 0 2 1 60%
MPP/core.py BinaryTreeNode.feature 3 0 0 2 0 100%
MPP/core.py BinaryTreeNode.feature 3 1 0 2 1 60%
MPP/core.py BinaryTreeNode.left 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.left 7 2 0 6 2 69%
MPP/core.py BinaryTreeNode.right 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.right 7 2 0 6 2 69%
MPP/core.py BinaryTreeNode.children 6 0 0 4 0 100%
MPP/core.py BinaryTreeNode.is_leaf 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.is_macrostate 8 0 0 6 0 100%
MPP/core.py BinaryTreeNode.is_macrostate 3 1 0 2 1 60%
MPP/core.py BinaryTreeNode.macrostates 7 0 0 6 0 100%
MPP/core.py BinaryTreeNode.all_macrostates 3 0 0 2 0 100%
MPP/core.py BinaryTreeNode.parent_macrostate 6 0 0 4 0 100%
MPP/core.py BinaryTreeNode.assigned_macrostate 21 1 0 10 1 94%
MPP/core.py BinaryTreeNode.bins 8 1 0 4 1 83%
MPP/core.py BinaryTreeNode.feature_norm 5 0 0 4 0 100%
MPP/core.py BinaryTreeNode.colors 6 0 0 4 0 100%
MPP/core.py BinaryTreeNode.color 4 1 0 4 1 75%
MPP/core.py BinaryTreeNode.edge_width 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.macrostate 6 6 0 4 0 0%
MPP/core.py BinaryTreeNode.x 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.x_origin 4 0 0 4 0 100%
MPP/core.py BinaryTreeNode.x_origin 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.x_target 5 1 0 4 1 78%
MPP/core.py BinaryTreeNode.x_target 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.y 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.y_origin 5 0 0 4 1 89%
MPP/core.py BinaryTreeNode.y_origin 1 0 0 0 0 100%
MPP/core.py BinaryTreeNode.y_target 3 1 0 2 1 60%
MPP/core.py BinaryTreeNode.plot 5 0 0 4 0 100%
MPP/core.py BinaryTreeNode.plot_tree 3 0 0 2 0 100%
MPP/core.py cluster 32 2 0 10 2 90%
MPP/core.py (no function) 83 0 0 0 0 100%
MPP/graph/__init__.py (no function) 1 0 0 0 0 100%
MPP/graph/curved_edges.py curved_edges 29 1 0 4 1 94%
MPP/graph/curved_edges.py (no function) 4 0 0 0 0 100%
MPP/graph/kinetic_network.py assign_color 6 0 0 0 0 100%
MPP/graph/kinetic_network.py _color 2 0 0 0 0 100%
MPP/graph/kinetic_network.py _bin 5 1 0 4 1 78%
MPP/graph/kinetic_network.py get_luminance 5 0 0 0 0 100%
MPP/graph/kinetic_network.py draw_knetwork 55 8 0 16 5 82%
MPP/graph/kinetic_network.py (no function) 20 0 0 0 0 100%
MPP/kernel.py LumpingKernel.__init__ 3 0 0 0 0 100%
MPP/kernel.py LumpingKernel.__call__ 40 3 0 20 3 90%
MPP/kernel.py LumpingKernel.__repr__ 1 1 0 0 0 0%
MPP/kernel.py FeatureKernel.__init__ 4 1 0 2 1 67%
MPP/kernel.py FeatureKernel.__repr__ 1 1 0 0 0 0%
MPP/kernel.py FeatureKernel._init_feature 7 0 0 2 0 100%
MPP/kernel.py FeatureKernel.reset 2 0 0 0 0 100%
MPP/kernel.py FeatureKernel.apply 5 0 0 2 0 100%
MPP/kernel.py FeatureKernel.update 2 0 0 0 0 100%
MPP/kernel.py FeatureKernel.js 8 1 0 4 2 75%
MPP/kernel.py FeatureKernel.full_feature_from_Z 11 1 0 6 1 88%
MPP/kernel.py (no function) 17 0 0 0 0 100%
MPP/plot.py plot_tree 42 0 0 6 0 100%
MPP/plot.py stochastic_state_similarity 18 0 0 2 0 100%
MPP/plot.py implied_timescales 61 12 0 36 11 68%
MPP/plot.py _plot_impl_times 13 1 0 6 1 89%
MPP/plot.py relative_implied_timescales 23 0 0 2 0 100%
MPP/plot.py plot_heatmap 12 12 0 2 0 0%
MPP/plot.py transition_matrix 48 0 0 12 1 98%
MPP/plot.py transition_time 55 0 0 16 1 99%
MPP/plot.py macro_feature 19 0 0 2 1 95%
MPP/plot.py add_ref 12 0 0 6 0 100%
MPP/plot.py contact_rep 43 3 0 12 2 91%
MPP/plot.py sankey_diagram 13 0 0 8 2 90%
MPP/plot.py rmsd 77 4 0 16 5 90%
MPP/plot.py delta_rmsd 84 4 0 16 5 91%
MPP/plot.py state_trajectory 40 2 0 12 2 92%
MPP/plot.py chapman_kolmogorov 10 0 0 6 0 100%
MPP/plot.py plot_ck_test 35 2 0 12 2 91%
MPP/plot.py state_network 1 0 0 0 0 100%
MPP/plot.py (no function) 35 0 0 0 0 100%
MPP/run.py Data.__init__ 28 2 0 6 2 88%
MPP/run.py Data.prepare_mpp 12 1 0 8 1 90%
MPP/run.py Data.setup_mpp 9 0 0 6 2 87%
MPP/run.py Data.perform_mpp 6 0 0 2 0 100%
MPP/run.py Data.perform_gpcca 9 0 0 6 2 87%
MPP/run.py Data.get_rmsd 5 2 0 4 2 56%
MPP/run.py plot 38 2 0 32 2 94%
MPP/run.py draw_random_frames 7 7 0 2 0 0%
MPP/run.py write_random_frames_indices 1 0 0 0 0 100%
MPP/run.py parse_args 12 0 0 0 0 100%
MPP/run.py main 14 2 0 10 2 83%
MPP/run.py (no function) 20 1 0 2 1 91%
MPP/sankey_gap.py check_data_matches_labels 14 7 0 14 5 43%
MPP/sankey_gap.py sankey 113 32 0 70 21 70%
MPP/sankey_gap.py _get_positions_and_total_widths 16 0 0 4 0 100%
MPP/sankey_gap.py _draw_label 1 0 0 0 0 100%
MPP/sankey_gap.py (no function) 17 0 0 0 0 100%
MPP/utils.py translate_trajectory 10 3 0 6 1 62%
MPP/utils.py macrostate_tmat 6 0 0 4 0 100%
MPP/utils.py get_grid_format 8 0 0 4 0 100%
MPP/utils.py gmrq 5 0 0 2 0 100%
MPP/utils.py Z_to_linkage 6 0 0 2 0 100%
MPP/utils.py linkage_to_Z 15 0 0 2 0 100%
MPP/utils.py merge_states 7 0 0 2 0 100%
MPP/utils.py calc_full_tmat 13 1 0 6 1 89%
MPP/utils.py Z_to_mask 9 0 0 2 0 100%
MPP/utils.py get_macrostate_assignment_from_tree 10 0 0 0 0 100%
MPP/utils.py similarity 12 0 0 6 0 100%
MPP/utils.py shannon_entropy 2 0 0 0 0 100%
MPP/utils.py weighting_function 4 0 0 2 0 100%
MPP/utils.py load_trajectory 5 1 0 2 1 71%
MPP/utils.py load_mean_frames 4 4 0 0 0 0%
MPP/utils.py find_mean_frame 3 0 0 0 0 100%
MPP/utils.py estimate_rmsd 2 0 0 0 0 100%
MPP/utils.py align_trajectory_to_reference 17 2 0 4 1 86%
MPP/utils.py calc_var 3 0 0 0 0 100%
MPP/utils.py opt_num_batches 1 0 0 0 0 100%
MPP/utils.py calc_rmsd 15 1 0 6 1 90%
MPP/utils.py find_state_lengths 14 0 0 4 0 100%
MPP/utils.py get_multi_state_trajectory 8 0 0 4 0 100%
MPP/utils.py (no function) 27 0 0 0 0 100%
tests/__init__.py (no function) 0 0 0 0 0 100%
tests/test_plots.py _run_main_with_args 10 2 0 0 0 80%
tests/test_plots.py TestPlotting.setUp 3 0 0 0 0 100%
tests/test_plots.py TestPlotting._run_plot 3 0 0 0 0 100%
tests/test_plots.py TestPlotting._get_key 4 1 0 4 1 75%
tests/test_plots.py TestPlotting.run_single_plot_test 16 4 0 4 2 70%
tests/test_plots.py TestPlotting.test_manual_dendrogram 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_timescales 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_sankey 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_contacts 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_macrotraj_ref 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_macrotraj_PDZ3 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_ck_test 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_state_network 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_macro_feature 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_rmsd 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_delta_rmsd 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_stochastic_state_similarity 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_relative_implied_timescales 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_transition_matrix 4 0 0 0 0 100%
tests/test_plots.py TestPlotting.test_manual_transition_time 4 0 0 0 0 100%
tests/test_plots.py file_hash 5 5 0 2 0 0%
tests/test_plots.py (no function) 36 1 0 2 1 95%
tests/test_properties.py get_d 8 2 0 4 2 67%
tests/test_properties.py TestProperties.setUp 2 0 0 0 0 100%
tests/test_properties.py TestProperties.test_shannon_entropy 1 0 0 0 0 100%
tests/test_properties.py TestProperties.test_gmrq 1 0 0 0 0 100%
tests/test_properties.py TestProperties.test_davies_bouldin_index 1 0 0 0 0 100%
tests/test_properties.py (no function) 16 0 0 0 0 100%
tests/test_rmsd.py get_d 8 2 0 4 2 67%
tests/test_rmsd.py TestRMSD_HP35.setUp 2 0 0 0 0 100%
tests/test_rmsd.py TestRMSD_HP35.compare_text_files 4 4 0 0 0 0%
tests/test_rmsd.py TestRMSD_HP35.test_draw_random_indices 10 0 0 2 0 100%
tests/test_rmsd.py TestRMSD_HP35.test_draw_random_frames 8 0 0 2 0 100%
tests/test_rmsd.py TestRMSD_aSyn.setUp 2 0 0 0 0 100%
tests/test_rmsd.py TestRMSD_aSyn.compare_text_files 4 0 0 0 0 100%
tests/test_rmsd.py TestRMSD_aSyn.test_write_least_moving_residues 5 0 0 0 0 100%
tests/test_rmsd.py TestRMSD_PDZ3.setUp 2 0 0 0 0 100%
tests/test_rmsd.py TestRMSD_PDZ3.test_rmsd_property 6 0 0 0 0 100%
tests/test_rmsd.py TestRMSD_PDZ3.test_rmsd_sharpness 3 0 0 0 0 100%
tests/test_rmsd.py (no function) 27 0 0 0 0 100%
tests/test_run.py _run_main_with_args 10 2 0 0 0 80%
tests/test_run.py TestRunScript.setUp 3 0 0 0 0 100%
tests/test_run.py TestRunScript._run_command 8 0 0 4 0 100%
tests/test_run.py TestRunScript._get_key 4 1 0 4 1 75%
tests/test_run.py TestRunScript.run_and_validate_output 17 0 0 2 0 100%
tests/test_run.py TestRunScript.test_HP35_t_ref 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_HP35_t_stoch 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_HP35_kl 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_HP35_t_js 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_HP35_js 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_HP35_gpcca 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_PDZ3_kl 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_aSyn_t 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_aSyn_kl_js 1 0 0 0 0 100%
tests/test_run.py TestRunScript.test_aSyn_t_stoch 1 0 0 0 0 100%
tests/test_run.py TestRunScript.assert_same_file_count 3 0 0 0 0 100%
tests/test_run.py TestRunScript._run_random_frames_indices 11 0 0 0 0 100%
tests/test_run.py TestRunScript.test_random_frames_indices_aSyn_t_ref 1 0 0 0 0 100%
tests/test_run.py (no function) 30 0 0 0 0 100%
tests/test_utils.py get_d 8 2 0 4 2 67%
tests/test_utils.py TestProperties.setUp 2 0 0 0 0 100%
tests/test_utils.py TestProperties.test_Z_to_linkage 3 0 0 0 0 100%
tests/test_utils.py TestProperties.test_linkage_to_Z 4 0 0 0 0 100%
tests/test_utils.py TestProperties.test_calc_full_tmat 5 0 0 0 0 100%
tests/test_utils.py TestProperties.test_Z_to_mask 3 0 0 0 0 100%
tests/test_utils.py TestFullFeature.setUp 1 0 0 0 0 100%
tests/test_utils.py TestFullFeature.test_full_feature_from_Z 3 0 0 0 0 100%
tests/test_utils.py (no function) 22 0 0 0 0 100%
Total   2520 215 0 736 147 88%

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