Merge pull request #525 from DeepRank/hotfix_gcroci2

fix: installation bug due to missing domain files

Author: gcroci2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.1.0
+current_version = 2.1.1
 
 [comment]
 comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved

CITATION.cff

@@ -55,5 +55,5 @@ keywords:
   - DeepRank
 license: Apache-2.0
 commit: 4e8823758ba03f824b4281f5689cb6a335ab2f6c
-version: "2.1.0"
+version: "2.1.1"
 date-released: '2023-09-22'

deeprank2/__init__.py

@@ -1 +1 @@
-__version__ = "2.1.0"
+__version__ = "2.1.1"

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "deeprank2"
-version = "2.1.0"
+version = "2.1.1"
 description = "DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants."
 readme = "README.md"
 requires-python = ">=3.10"
@@ -82,4 +82,11 @@ source = ["deeprank2"]
 
 [tool.setuptools.packages.find]
 include = ["deeprank2*"]
-exclude = ["tests*"]
+exclude = ["tests*", "*tests.*", "*tests"]
+
+[tool.setuptools.package-data]
+"*" = [
+    "*.xlsx",
+    "*.param",
+    "*.top", 
+    "*residue-classes"]

tests/__init__.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/domain/test_aminoacidlist.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
 

tests/molstruct/test_structure.py

@@ -7,10 +7,13 @@
 
 import h5py
 import pandas as pd
-from deeprank2.utils.exporters import (HDF5OutputExporter,
-                                       OutputExporterCollection,
-                                       ScatterPlotExporter,
-                                       TensorboardBinaryClassificationExporter)
+
+from deeprank2.utils.exporters import (
+    HDF5OutputExporter,
+    OutputExporterCollection,
+    ScatterPlotExporter,
+    TensorboardBinaryClassificationExporter,
+)
 
 logging.getLogger(__name__)
 
@@ -95,7 +98,7 @@ 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"]

tests/utils/test_exporters.py

@@ -1,11 +1,14 @@
 import h5py
 import numpy as np
-from deeprank2.query import (ProteinProteinInterfaceAtomicQuery,
-                             ProteinProteinInterfaceResidueQuery)
+
+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 +56,7 @@ 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