EncoderMap Unittest Report from 2023-02-07T11:00:08+00:00

Start Time: 2023-02-07 11:00:08

Duration: 330.38 s

Summary: Total: 109, Pass: 107, Skip: 2

tests.test_losses.TestLossesPeriodic Status
test_losses_periodic Pass
Total: 1, Pass: 1 -- Duration: 748 ms
tests.test_losses.TestLossesNonPeriodic Status
test_losses_not_periodic Pass
Total: 1, Pass: 1 -- Duration: 571 ms
tests.test_losses.TestLossesADCAutoencoder Status
test_losses_ADC Pass

using backbone angles

Total: 1, Pass: 1 -- Duration: 13.71 s
tests.test_losses.TestDistanceLossScipy Status
test_non_periodic Pass
test_periodic Pass
Total: 2, Pass: 2 -- Duration: 4.38 s
encodermap.loss_functions.loss_functions Status
loss_combinator Pass
reconstruction_loss Pass
Total: 2, Pass: 2 -- Duration: 2.25 s
tests.test_angles.TestAngles Status
test_ala10_angles Pass

/home/runner/work/encodermap/encodermap Loading Cartesians... Calculating dihedrals... Calculating sidedihedrals... Calculating angles... Calculating lengths...

test_chain_in_plane Pass
Total: 2, Pass: 2 -- Duration: 248 ms
encodermap.autoencoder.autoencoder Status
AngleDihedralCartesianEncoderMap Pass
Autoencoder Pass
Total: 2, Pass: 2 -- Duration: 96.93 s
encodermap.autoencoder.autoencoder.DihedralEncoderMap Status
generate Pass
Total: 1, Pass: 1 -- Duration: 4.58 s
tests.test_backmapping_em1_em2.TestBackmappingEm1Em2 Status
test_backmapping_wo_angles Pass

ADCParameters class with Main path at /home/runner/work/encodermap/encodermap. Non-standard value of l2_reg_constant: 0 Non-standard value of use_backbone_angles: True using backbone angles main_inputs: (256, 943) encoded: (256, 2) tf.Tensor(True, shape=(), dtype=bool) decoded: (256, 943)

Total: 1, Pass: 1 -- Duration: 11.17 s
tests.test_backmapping_em1_em2.TestCompareSplits Status
test_random_shapes Pass
Total: 1, Pass: 1 -- Duration: 233 ms
encodermap.misc.backmapping Status
split_and_reverse_cartesians Pass
split_and_reverse_dihedrals Pass
Total: 2, Pass: 2 -- Duration: 3 ms
tests.test_dihedral_to_cartesian.TestDihedralToCartesianTf Status
test_straight_tetrahedral_chain_with_bond_lenght Pass
test_straight_to_helix_array Pass
test_straight_to_helix_v2 Pass
Total: 3, Pass: 3 -- Duration: 1.43 s
tests.test_featurizer.TestFeatures Status
test_add_all Pass
test_add_angles Pass
test_add_backbone_torsions Pass

158

test_add_chi1_torsions Pass
test_add_contacts Pass

Data variables: DistanceFeature (traj_num, frame_num, DISTANCEFEATURE) float32 1.0 ... 1... ContactFeature (traj_num, frame_num, CONTACTFEATURE) float32 1.0 ... 0.0

test_add_custom_feature Skip
test_add_dihedrals Pass
test_add_distances_ca Pass
test_add_group_COM Pass
test_add_inverse_distances Pass
test_add_minrmsd_to_ref Pass
test_add_residue_COM Pass
test_add_residue_mindist Pass
test_add_selection Pass
test_add_sidechain_torsions Skip
test_ala_dipeptide_correct_number_of_residues Pass
test_encodermap_features_1am7 Pass

446 (51, 446)

test_encodermap_features_ala10 Pass
test_encodermap_features_cartesians Pass

(6, 4, 3) [[[0. 0. 0.] [1. 0. 0.] [1. 1. 0.]] [[0. 0. 0.] [1. 0. 0.] [1. 1. 0.]] [[0. 0. 0.] [2. 0. 0.] [2. 1. 0.]] [[0. 0. 0.] [1. 0. 0.] [1. 1. 0.]] [[0. 0. 0.] [1. 0. 0.] [1. 1. 0.]] [[0. 0. 0.] [1. 0. 0.] [1. 1. 0.]]]

test_ensmble_with_diff_length Pass
Total: 20, Pass: 18, Skip: 2 -- Duration: 9.09 s
tests.test_interactive_plotting.TestInteractivePlotting Status
test_interactive_plotting Pass

Output files are saved to tmp as defined in 'main_path' in the parameters. For the ssupdate function to work encodermap/vmd/sscache.tcl will be sourced within vmd. If no Error is thrown the file is present.

Total: 1, Pass: 1 -- Duration: 110.70 s
tests.test_moldata.TestTrajinfo Status
test_compare_moldata_tf1_tf2 Pass
test_moldata_tf1 Pass

Loading Cartesians... Calculating dihedrals... Calculating sidedihedrals... Calculating angles... Calculating lengths...

test_moldata_tf2 Pass
Total: 3, Pass: 3 -- Duration: 1.20 s
tests.test_non_backbone_atoms.TestNonBackboneAtoms Status
test_guess_amide_H Pass
test_guess_amide_O Pass
Total: 2, Pass: 2 -- Duration: 402 ms
tests.test_optional_imports.TestOptionalImport Status
test_non_working_import Pass
test_working_import Pass
Total: 2, Pass: 2 -- Duration: 1 ms
encodermap Status
_optional_imports Pass
Total: 1, Pass: 1 -- Duration: 3 ms
tests.test_pairwise_distances.TestSigmoidDists Status
test_sigmoid Pass
Total: 1, Pass: 1 -- Duration: 137 ms
tests.test_pairwise_distances.TestPeriodicDistances Status
test_periodic_distance_np Pass
test_periodic_distance_tf Pass
test_periodic_many_points Pass
Total: 3, Pass: 3 -- Duration: 160 ms
tests.test_pairwise_distances.TestPairwiseDistances Status
test_compare_pairwise_dist_and_periodic_pairwise_dist Pass
test_pairwise_dist Pass
test_pairwise_dist_flat Pass
test_pairwise_dist_periodic Pass
test_pairwise_dist_periodic_not_periodic_case Pass
Total: 5, Pass: 5 -- Duration: 106 ms
tests.test_pairwise_distances.TestDistancesEm1Em2 Status
test_pairwise_dist Pass
test_pairwise_dist_periodic Pass
test_periodic_distance Pass
test_sigmoid Pass
Total: 4, Pass: 4 -- Duration: 44 ms
encodermap.misc.distances Status
periodic_distance Pass
Total: 1, Pass: 1 -- Duration: 6 ms
tests.test_trajinfo.TestTraj Status
test_CV_slicing_SingleTraj Pass
test_CVs_for_TrajEnsemble_containing_only_single_frames Pass
test_CVs_in_file Pass
test_CVs_stay_after_subsample Pass

Dimensions: (traj_num: 1, frame_num: 6, CENTRAL_ANGLES: 472) Coordinates: * traj_num (traj_num) object None traj_name (traj_num)

test_SingleTraj_equality Pass
test_SingleTraj_mdtraj_duplication Pass
test_SingleTraj_raises_error_on_wrong_dtype_for_traj Pass
test_SingleTraj_subsample Pass
test_SingleTraj_subsample_h5 Pass
test_SingleTraj_subsample_without_loading Pass
test_SingleTraj_throws_error_on_wrong_way_round Pass
test_adding_mixed_pyemma_features_with_custom_names Pass
test_addition_along_TrajEnsemble Pass
test_atom_slice Pass
test_double_slicing Pass

51 11 14 3 100 20

test_from_pdbid Pass
test_gen_ensemble Pass
test_gen_ensemble_no_files Pass
test_info_all_load_CVs_from_file Pass
test_info_all_load_CVs_from_numpy Pass
test_info_all_loading Pass
test_join Pass
test_load_CVs_TrajEnsemble Pass

encodermap.TrajEnsemble object. Current backend is no_load. Containing 2 trajs. Not containing any CVs. This `TrajEnsemble` object contains mulitple topologies. The output of _CVs can contain nans for some features. This `TrajEnsemble` object contains mulitple topologies. The output of _CVs can contain nans for some features. This `TrajEnsemble` object contains mulitple topologies. The output of _CVs can contain nans for some features.

test_load_CVs_for_single_traj_as_string Pass

Data and traj misaligned. traj_frames: 51, data.shape: (1, 3), attr_name: 1am7_center_of_mass, [[3.81903247 3.93509809 3.85774657]] Overwriting the following CVs with new values: {'center_of_mass_x'}. Overwriting the following CVs with new values: {'npy_data'}.

test_load_CVs_from_other_sources Pass

Overwriting the following CVs with new values: {'ones'}. Overwriting the following CVs with new values: {'pos_arr'}. Overwriting the following CVs with new values: {'ones2'}. Overwriting the following CVs with new values: {'ones3'}.

test_load_h5 Pass
test_load_h5_with_integer_index Pass
test_load_info_all_with_trajs_and_one_top_does_not_raise_error Pass
test_load_pdb_with_mdtraj_backend Pass
test_load_singletraj_with_traj_and_top Pass
test_load_uri_with_index Pass
test_load_url Pass
test_load_xtc Pass
test_n_frames_in_h5_file Pass
test_pyemma_indexing_and_get_single_frame Pass
test_single_traj_double_index_with_int Pass
test_singletraj_raises_error_on_file_not_found Pass
test_slicing_and_CVs_xtc_and_h5 Pass
test_slicing_and_indexing_mixed Pass

[[1 5]] [[ 1 0] [ 1 2] [ 1 4] [ 1 6] [ 1 8] [ 1 10] [ 1 12] [ 1 14] [ 1 16] [ 1 18] [ 1 20] [ 1 22] [ 1 24] [ 1 26] [ 1 28] [ 1 30] [ 1 32] [ 1 34] [ 1 36] [ 1 38] [ 1 40] [ 1 42] [ 1 44] [ 1 46] [ 1 48] [ 1 50]] [[1 1] [1 4] [1 5]] [[1 1]]

test_stack Pass
test_traj_ensemble_equality Pass
test_traj_id Pass
test_traj_joined Pass
test_wrong_formatted_CVs Pass

Data and traj misaligned. traj_frames: 16, data.shape: (1, 49), attr_name: test, [[ 0.59189999 1.31840003 0.91500002 -0.0763 2.08410001 -0.64749998 -0.7823 1.91110003 0.66850001 0.51679999 1.04900002 1.03410006 0.21349999 1.77909994 1.02849996 -0.1358 2.00769997 0.85170001 0.38049999 1.75810003 1.30719995 -0.70069999 1.39890003 -0.2476 -0.40360001 2.13050008 0.17399999 1.01880002 1.74220002 0.58289999 -0.1991 2.43149996 0.60360003 0.19 1.56169999 1.09739995 -0.0785 1.40530002 0.88139999 0.12980001 0.40279999 0.40400001 -0.45919999 1.65540004 1.13979995 0.2282 2.30620003 0.83399999 5. ]]

Total: 44, Pass: 44 -- Duration: 70.38 s
tests.test_version.TestVersion Status
test_version Pass
Total: 1, Pass: 1 -- Duration: 2 ms
encodermap.misc.xarray Status
add_one_by_one Pass
construct_xarray_from_numpy Pass
Total: 2, Pass: 2 -- Duration: 1.89 s