Merge pull request #64 from wolberlab/update-black-formatting

Update package w.r.t. new black & pandas versions

dynophores/cli.py

@@ -238,7 +238,7 @@ def _update_paths_in_notebook(notebook_path, dyno_path, pdb_path, dcd_path=None)
         filedata = f.read()
 
     # Replace the target string
-    for (search_str, replace_str) in search_replace_tuples:
+    for search_str, replace_str in search_replace_tuples:
         filedata = filedata.replace(search_str, replace_str)
 
     # Write the file out again

dynophores/core/chemicalfeaturecloud3d.py

@@ -20,7 +20,6 @@ class ChemicalFeatureCloud3D:
     """
 
     def __init__(self, center, points, **kwargs):
-
         self.center = center
         self.points = [
             point

dynophores/core/chemicalfeaturecloud3dpoint.py

@@ -24,7 +24,6 @@ class ChemicalFeatureCloud3DPoint:
     """
 
     def __init__(self, x, y, z, frame_ix, weight, **kwargs):
-
         self.x = x
         self.y = y
         self.z = z

dynophores/core/dynophore.py

@@ -37,7 +37,6 @@ def __init__(
         superfeatures,
         **kwargs,
     ):
-
         self.id = id
         self.ligand = ligand if isinstance(ligand, Ligand) else Ligand(**ligand)
         self.superfeatures = {
@@ -66,7 +65,6 @@ def from_dir(cls, dynophore_path):
         dynophore_path = Path(dynophore_path)
 
         if dynophore_path.is_dir():
-
             # Set JSON path
             json_path = list(dynophore_path.glob("*.json"))
             if len(json_path) == 1:

dynophores/core/envpartner.py

@@ -28,7 +28,6 @@ class EnvPartner:
     def __init__(
         self, id, residue_name, residue_number, chain, atom_numbers, occurrences, distances
     ):
-
         if len(occurrences) != len(distances):
             raise ValueError("Occurrences and distances must be of same length.")
 

dynophores/core/ligand.py

@@ -30,7 +30,6 @@ def __init__(
         atom_serials,
         **kwargs,
     ):
-
         self.name = name
         self.smiles = smiles
         self.mdl_mol_buffer = mdl_mol_buffer

dynophores/core/superfeature.py

@@ -34,7 +34,6 @@ class SuperFeature:
     """
 
     def __init__(self, id, feature_type, atom_numbers, occurrences, envpartners, color, cloud):
-
         self.id = id
         self.feature_type = feature_type
         self.atom_numbers = atom_numbers
@@ -185,7 +184,7 @@ def _count(self, property_envpartners_occurrences):
         )
         envpartners_count = property_envpartners_occurrences.sum()
 
-        return superfeature_count.append(envpartners_count)
+        return pd.concat([superfeature_count, envpartners_count])
 
     @property
     def frequency(self):
@@ -279,7 +278,6 @@ def _data_collapsed(self):
         # For each unique residue ID,
         # we want to aggregate data for all environmental partners that belong to the same residue
         for residue_id in residue_ids:
-
             # Get all environmental partner IDs that belong to this residue
             ids_to_be_collapsed = [_id for _id in ids if _id.startswith(residue_id)]
 

dynophores/parsers.py

@@ -83,7 +83,6 @@ def _pml_to_dict(pml_path):
 
     feature_clouds = dynophore3d_xml.findall("featureCloud")
     for feature_cloud in feature_clouds:
-
         # Superfeature ID
         superfeature_feature_name = feature_cloud.get("name")
         superfeature_atom_numbers = feature_cloud.get("involvedAtomSerials")

dynophores/tests/conftest.py

@@ -15,40 +15,34 @@
 
 @pytest.fixture(scope="module")
 def dynophore():
-
     dynophore = Dynophore.from_dir(PATH_TEST_DATA / "out")
     return dynophore
 
 
 @pytest.fixture(scope="module")
 def superfeature(dynophore):
-
     superfeature = dynophore.superfeatures["H[4615,4623,4622,4613,4621,4614]"]
     return superfeature
 
 
 @pytest.fixture(scope="module")
 def chemicalfeaturecloud3d(superfeature):
-
     cloud = superfeature.cloud
     return cloud
 
 
 @pytest.fixture(scope="module")
 def chemicalfeaturecloud3dpoint(superfeature):
-
     point = next(iter(superfeature.cloud.points))
     return point
 
 
 @pytest.fixture(scope="module")
 def envpartner(superfeature):
-
     envpartner = superfeature.envpartners["ILE-10-A[169,171,172]"]
     return envpartner
 
 
 @pytest.fixture(scope="module")
 def ligand(dynophore):
-
     return dynophore.ligand

dynophores/tests/core/test_chemicalfeaturecloud3d.py

@@ -22,7 +22,6 @@ class TestsChemicalFeatureCloud3D:
     """
 
     def test_init(self):
-
         dynophore_dict = parsers._json_pml_to_dict(
             PATH_TEST_DATA / "out/1KE7_dynophore.json",
             PATH_TEST_DATA / "out/1KE7_dynophore.pml",

dynophores/tests/core/test_chemicalfeaturecloud3dpoint.py

@@ -22,7 +22,6 @@ class TestsChemicalFeatureCloud3DPoint:
     """
 
     def test_init(self):
-
         dynophore_dict = parsers._json_pml_to_dict(
             PATH_TEST_DATA / "out/1KE7_dynophore.json",
             PATH_TEST_DATA / "out/1KE7_dynophore.pml",

dynophores/tests/core/test_dynophore.py

@@ -25,7 +25,6 @@ class TestsDynophore:
 
     @pytest.mark.parametrize("id", ["dynophore_1KE7"])
     def test_attributes(self, dynophore, id):
-
         dynophore_dict = parsers._json_pml_to_dict(
             PATH_TEST_DATA / "out/1KE7_dynophore.json",
             PATH_TEST_DATA / "out/1KE7_dynophore.pml",
@@ -48,12 +47,10 @@ def test_attributes(self, dynophore, id):
 
     @pytest.mark.parametrize("filepath", [PATH_TEST_DATA / "out"])
     def test_from_dir(self, filepath):
-
         dynophore = Dynophore.from_dir(filepath)
         assert isinstance(dynophore, Dynophore)
 
     def test_clouds_and_cloud_by_superfeature(self, dynophore):
-
         # Property `cloud`
         assert isinstance(dynophore.clouds, dict)
         assert list(dynophore.clouds.keys()) == list(dynophore.superfeatures.keys())
@@ -88,7 +85,6 @@ def test_clouds_and_cloud_by_superfeature(self, dynophore):
         ],
     )
     def test_superfeatures_occurrences(self, dynophore, column_names, counts_sum):
-
         data = dynophore.superfeatures_occurrences
         assert data.columns.to_list() == column_names
         assert data.index.to_list() == list(range(0, dynophore.n_frames))
@@ -115,7 +111,6 @@ def test_superfeatures_occurrences(self, dynophore, column_names, counts_sum):
     def test_envpartners_occurrences_and_envpartners_occurrences_by_superfeature(
         self, dynophore, counts_sum_dict
     ):
-
         # Test `envpartners_occurrences`
         assert sorted(list(dynophore.envpartners_occurrences.keys())) == sorted(
             list(counts_sum_dict.keys())
@@ -150,7 +145,6 @@ def test_envpartners_occurrences_and_envpartners_occurrences_by_superfeature(
         ],
     )
     def test_envpartners_distances(self, dynophore, distances_sum_dict):
-
         assert sorted(list(dynophore.envpartners_distances.keys())) == sorted(
             list(distances_sum_dict.keys())
         )
@@ -161,12 +155,10 @@ def test_envpartners_distances(self, dynophore, distances_sum_dict):
 
     @pytest.mark.parametrize("n_superfeatures", [10])
     def test_n_superfeatures(self, dynophore, n_superfeatures):
-
         assert dynophore.n_superfeatures == n_superfeatures
 
     @pytest.mark.parametrize("n_frames", [1002])
     def test_n_frames(self, dynophore, n_frames):
-
         assert dynophore.n_frames == n_frames
 
     @pytest.mark.parametrize(
@@ -218,7 +210,6 @@ def test_n_frames(self, dynophore, n_frames):
     def test_count_frequency(
         self, dynophore, count_sum, frequency_sum, superfeature_ids, envpartner_names
     ):
-
         # TODO remove this when fixed in DynophoreApp json export
         envpartner_names = [i.replace("_", "-") for i in envpartner_names]
 
@@ -240,22 +231,19 @@ def test_count_frequency(
     def test_raise_keyerror_if_invalid_superfeature_id(
         self, dynophore, valid_superfeature, superfeature_id
     ):
-
         if valid_superfeature:
             assert dynophore._raise_keyerror_if_invalid_superfeature_id(superfeature_id) is None
         else:
             with pytest.raises(KeyError):
                 dynophore._raise_keyerror_if_invalid_superfeature_id(superfeature_id)
 
     def test_superfeatures_atom_serials(self, dynophore):
-
         atom_serials = dynophore.superfeatures_atom_serials
         assert isinstance(atom_serials, dict)
         assert list(atom_serials) == list(dynophore.superfeatures)
         assert isinstance(next(iter(atom_serials.values()))[0], int)
 
     def test_superfeatures_colors(self, dynophore):
-
         colors = dynophore.superfeatures_colors
         assert isinstance(colors, dict)
         assert list(colors) == list(dynophore.superfeatures)

dynophores/tests/core/test_envpartner.py

@@ -21,7 +21,6 @@ class TestsEnvPartner:
     """
 
     def test_init(self):
-
         dynophore_dict = parsers._json_pml_to_dict(
             PATH_TEST_DATA / "out/1KE7_dynophore.json",
             PATH_TEST_DATA / "out/1KE7_dynophore.pml",
@@ -64,7 +63,6 @@ def test_init(self):
         ],
     )
     def test_init_raises(self, envpartner_dict):
-
         with pytest.raises(ValueError):
             EnvPartner(**envpartner_dict)
 

dynophores/tests/core/test_ligand.py

@@ -19,7 +19,6 @@ class TestsLigand:
     """
 
     def test_init(self):
-
         dynophore_dict = parsers._json_pml_to_dict(
             PATH_TEST_DATA / "out/1KE7_dynophore.json",
             PATH_TEST_DATA / "out/1KE7_dynophore.pml",

dynophores/tests/core/test_superfeature.py

@@ -24,7 +24,6 @@ class TestsSuperFeature:
     """
 
     def test_init(self):
-
         dynophore_dict = parsers._json_pml_to_dict(
             PATH_TEST_DATA / "out/1KE7_dynophore.json",
             PATH_TEST_DATA / "out/1KE7_dynophore.pml",

dynophores/tests/test_cli.py

@@ -136,6 +136,5 @@ def test_update_paths_in_notebook_raises(notebook_path, dyno_path, pdb_path, dcd
     ],
 )
 def test_open_notebook_raises(notebook):
-
     with pytest.raises(RuntimeError):
         cli._open_notebook(notebook)

dynophores/tests/viz/test_plot_static.py

@@ -23,7 +23,6 @@
     ],
 )
 def test_superfeatures_vs_envpartners(dynophore, superfeature_ids, annotate_heatmap):
-
     fig, ax = plot.static.superfeatures_vs_envpartners(
         dynophore, superfeature_ids, annotate_heatmap
     )
@@ -34,7 +33,6 @@ def test_superfeatures_vs_envpartners(dynophore, superfeature_ids, annotate_heat
 
 @pytest.mark.parametrize("superfeature_ids", ["xxx"])
 def test_superfeatures_vs_envpartners_raises(dynophore, superfeature_ids):
-
     with pytest.raises(KeyError):
         plot.static.superfeatures_vs_envpartners(dynophore, superfeature_ids)
 
@@ -58,7 +56,6 @@ def test_superfeatures_vs_envpartners_raises(dynophore, superfeature_ids):
 def test_superfeatures_occurrences(
     dynophore, superfeature_ids, color_by_feature_type, frames_range, frames_step_size
 ):
-
     fig, ax = plot.static.superfeatures_occurrences(
         dynophore, superfeature_ids, color_by_feature_type, frames_range, frames_step_size
     )
@@ -69,7 +66,6 @@ def test_superfeatures_occurrences(
 
 @pytest.mark.parametrize("superfeature_ids", ["xxx"])
 def test_superfeatures_occurrences_raises(dynophore, superfeature_ids):
-
     with pytest.raises(KeyError):
         plot.static.superfeatures_occurrences(dynophore, superfeature_ids)
 
@@ -105,7 +101,6 @@ def test_superfeatures_occurrences_raises(dynophore, superfeature_ids):
 def test_envpartners_occurrences(
     dynophore, superfeature_ids, frames_range, frames_step_size, occurrence_min, collapse_residues
 ):
-
     fig, axes = plot.static.envpartners_occurrences(
         dynophore,
         superfeature_ids,
@@ -125,7 +120,6 @@ def test_envpartners_occurrences(
 
 @pytest.mark.parametrize("superfeature_id", ["xxx", ["AR[4605,4607,4603,4606,4604]", "xxx"]])
 def test_envpartners_occurrences_raises(dynophore, superfeature_id):
-
     with pytest.raises(KeyError):
         plot.static.envpartners_occurrences(dynophore, superfeature_id)
 
@@ -139,7 +133,6 @@ def test_envpartners_occurrences_raises(dynophore, superfeature_id):
     ],
 )
 def test_envpartners_distances(dynophore, superfeature_ids, kind):
-
     fig, axes = plot.static.envpartners_distances(dynophore, superfeature_ids, kind)
     assert isinstance(fig, matplotlib.figure.Figure)
     if isinstance(superfeature_ids, str):
@@ -154,7 +147,6 @@ def test_envpartners_distances(dynophore, superfeature_ids, kind):
     "superfeature_id, kind", [("xxx", "line"), ("AR[4605,4607,4603,4606,4604]", "xxx")]
 )
 def test_envpartner_distances_raises(dynophore, superfeature_id, kind):
-
     with pytest.raises(KeyError):
         plot.static.envpartners_distances(dynophore, superfeature_id, kind)
 
@@ -167,7 +159,6 @@ def test_envpartner_distances_raises(dynophore, superfeature_id, kind):
     ],
 )
 def test_envpartners_all_in_one(dynophore, superfeature_id, frames_range, frames_step_size):
-
     fig, axes = plot.static.envpartners_all_in_one(
         dynophore, superfeature_id, frames_range, frames_step_size
     )
@@ -179,6 +170,5 @@ def test_envpartners_all_in_one(dynophore, superfeature_id, frames_range, frames
 
 @pytest.mark.parametrize("superfeature_id", ["xxx"])
 def test_envpartners_all_in_one_raises(dynophore, superfeature_id):
-
     with pytest.raises(KeyError):
         plot.static.envpartners_all_in_one(dynophore, superfeature_id)

dynophores/tests/viz/test_view2d_static.py

@@ -29,12 +29,10 @@ def test_show(dynophore, show_superfeatures, show_pdb_serial_numbers):
 
     @pytest.mark.parametrize("show_pdb_serial_numbers", [False, True])
     def test_view2d(self, ligand, show_pdb_serial_numbers):
-
         mol = ligand.view2d(show_pdb_serial_numbers)
         assert isinstance(mol, Chem.rdchem.Mol)
 
     @pytest.mark.parametrize("show_pdb_serial_numbers", [False, True])
     def test_view2d_superfeatures(self, ligand, show_pdb_serial_numbers):
-
         img = ligand.view2d_superfeatures(show_pdb_serial_numbers)
         assert isinstance(img, Image)

dynophores/tests/viz/test_view3d_interactive.py

@@ -68,7 +68,6 @@ def test_show(
 def test_show_raises(
     dynophore, pdb_path, dcd_path, visualization_type, color_cloud_by_frame, frame_range
 ):
-
     with pytest.raises(ValueError):
         view3d.show(
             dynophore,