fix prospector errors

tests/domain/test_aminoacidlist.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 from deeprank2.domain.aminoacidlist import (amino_acids, cysteine, lysine,
                                             pyrrolysine, selenocysteine)
 
@@ -16,10 +17,10 @@ def test_all_different_onehot():
             if other != amino_acid:
                 try:
                     assert not np.all(amino_acid.onehot == other.onehot)
-                except AssertionError:
+                except AssertionError as exc:
                     if other in EXCEPTIONS[0] and amino_acid in EXCEPTIONS[0]:
                         assert np.all(amino_acid.onehot == other.onehot)
                     elif other in EXCEPTIONS[1] and amino_acid in EXCEPTIONS[1]:
                         assert np.all(amino_acid.onehot == other.onehot)
                     else:
-                        raise AssertionError(f"one-hot index {amino_acid.index} is occupied by both {amino_acid} and {other}")
+                        raise AssertionError(f"one-hot index {amino_acid.index} is occupied by both {amino_acid} and {other}") from exc

tests/molstruct/test_structure.py

@@ -2,17 +2,18 @@
 import pickle
 from multiprocessing.connection import _ForkingPickler
 
+from pdb2sql import pdb2sql
+
 from deeprank2.molstruct.structure import PDBStructure
 from deeprank2.utils.buildgraph import get_structure
-from pdb2sql import pdb2sql
 
 
 def _get_structure(path) -> PDBStructure:
     pdb = pdb2sql(path)
     try:
         structure = get_structure(pdb, "101M")
     finally:
-        pdb._close()
+        pdb._close() # pylint: disable=protected-access
 
     assert structure is not None
 
@@ -45,3 +46,4 @@ def test_serialization_fork():
     assert loaded_structure.get_chain("A").get_residue(0) == structure.get_chain("A").get_residue(0)
     assert loaded_structure.get_chain("A").get_residue(0).amino_acid == structure.get_chain("A").get_residue(0).amino_acid
     assert loaded_structure.get_chain("A").get_residue(0).atoms[0] == structure.get_chain("A").get_residue(0).atoms[0]
+    assert loaded_structure.get_chain("A").get_residue(0).atoms[0] == structure.get_chain("A").get_residue(0).atoms[0]

tests/utils/test_exporters.py

@@ -7,6 +7,7 @@
 
 import h5py
 import pandas as pd
+
 from deeprank2.utils.exporters import (HDF5OutputExporter,
                                        OutputExporterCollection,
                                        ScatterPlotExporter,
@@ -95,7 +96,7 @@ def test_scatter_plot(self):
 
         assert os.path.isfile(scatterplot_exporter.get_filename(epoch_number))
 
-    def test_hdf5_output(self):
+    def test_hdf5_output(self): # pylint: disable=too-many-locals
         output_exporter = HDF5OutputExporter(self._work_dir)
         path_output_exporter = os.path.join(self._work_dir, 'output_exporter.hdf5')
         entry_names = ["entry1", "entry2", "entry3"]
@@ -147,3 +148,6 @@ def test_hdf5_output(self):
         # assert there are 6 columns ('phase', 'epoch', 'entry', 'output', 'target', 'loss')
         assert df_test_1[df_test_1.phase == pass_name_1].shape[1] == 6
         assert df_test_2[df_test_2.phase == pass_name_2].shape[1] == 6
+        # assert there are 6 columns ('phase', 'epoch', 'entry', 'output', 'target', 'loss')
+        assert df_test_1[df_test_1.phase == pass_name_1].shape[1] == 6
+        assert df_test_2[df_test_2.phase == pass_name_2].shape[1] == 6

tests/utils/test_grid.py

@@ -1,11 +1,12 @@
 import h5py
 import numpy as np
+
 from deeprank2.query import (ProteinProteinInterfaceAtomicQuery,
                              ProteinProteinInterfaceResidueQuery)
 from deeprank2.utils.grid import Grid, GridSettings, MapMethod
 
 
-def test_residue_grid_orientation():
+def test_residue_grid_orientation(): # pylint: disable=too-many-locals
 
     coord_error_margin = 1.0  # Angstrom
 
@@ -53,7 +54,7 @@ def test_residue_grid_orientation():
     assert np.all(np.abs(grid.zs - target_zs) < coord_error_margin), f"\n{grid.zs} != \n{target_zs}"
 
 
-def test_atomic_grid_orientation():
+def test_atomic_grid_orientation(): # pylint: disable=too-many-locals
 
     coord_error_margin = 1.0  # Angstrom
 
@@ -99,3 +100,6 @@ def test_atomic_grid_orientation():
 
     assert grid.zs.shape == target_zs.shape
     assert np.all(np.abs(grid.zs - target_zs) < coord_error_margin), f"\n{grid.zs} != \n{target_zs}"
+
+    assert grid.zs.shape == target_zs.shape
+    assert np.all(np.abs(grid.zs - target_zs) < coord_error_margin), f"\n{grid.zs} != \n{target_zs}"