push to stash changes before switching over to CI fix branch

MDAnalysis · Jul 24, 2024 · 9bc9b74 · 9bc9b74
1 parent 5f13117
commit 9bc9b74
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Showing 3 changed files with 7 additions and 8 deletions.
diff --git a/mda_openbabel_converter/OpenBabelParser.py b/mda_openbabel_converter/OpenBabelParser.py
@@ -40,8 +40,9 @@
     from openbabel import OBElementTable
     HAS_OBABEL = True
 except ImportError:
+    # import breaks with version 3.x
     warnings.warn("Cannot find openbabel, install with `mamba install -c "
-                  "conda-forge openbabel`")
+                  "conda-forge openbabel==2.4.0`")
 
 
 class StereoEnum(StrEnum):
@@ -168,7 +169,7 @@ def parse(self, **kwargs):
 
         # Atom name set with element and id, as name not supported by OpenBabel
         for atom in ob.OBMolAtomIter(mol):
-            name = "%s%d" % (OBElementTable().GetSymbol(atom.GetAtomicNum()), 
+            name = "%s%d" % (OBElementTable().GetSymbol(atom.GetAtomicNum()),
                              atom.GetIdx())
             names.append(name)
         attrs.append(Atomnames(np.array(names, dtype=object)))

diff --git a/mda_openbabel_converter/data/files.py b/mda_openbabel_converter/data/files.py
@@ -13,7 +13,5 @@
 ]
 
 from importlib.resources import files
-# from . import data
-# MDANALYSIS_LOGO = importlib.resources.files(__name__) / "mda.txt"
 MDANALYSIS_LOGO = files("mda_openbabel_converter") / "data" / "mda.txt"
 
diff --git a/mda_openbabel_converter/tests/test_openbabel_parser.py b/mda_openbabel_converter/tests/test_openbabel_parser.py
@@ -17,7 +17,7 @@
 
 import mda_openbabel_converter.OpenBabelParser  # version 2.7.0
 
-# *** can run with "python -m pytest" but not "pytest" (can't find 
+# *** can run with "python -m pytest" but not "pytest" (can't find
 # MDAnalysis) - need to fix this! ***
 
 
@@ -27,7 +27,7 @@ class OpenBabelParserBase(ParserBase):
     expected_attrs = ['ids', 'names', 'elements', 'masses', 'aromaticities',
                       'resids', 'resnums', 'chiralities',
                       'segids', 'bonds',
-                    ]
+                      ]
 
     expected_n_atoms = 0
     expected_n_residues = 0
@@ -53,7 +53,7 @@ def filename(self):
 
     def test_mandatory_attributes(self, top):
         for attr in self.mandatory_attrs:
-            assert (hasattr(top, attr), 
+            assert (hasattr(top, attr),
                     'Missing required attribute: {}'.format(attr))
 
     def test_attrs_total_counts(self, top):
@@ -102,7 +102,7 @@ def test_aromaticities(self, top, filename):
 
     def test_elements(self, top, filename):
         expected = np.array([
-            OBElementTable().GetSymbol(atom.GetAtomicNum()) for atom in 
+            OBElementTable().GetSymbol(atom.GetAtomicNum()) for atom in
             ob.OBMolAtomIter(filename)])
         assert_equal(expected, top.elements.values)