Merge pull request #1843 from peastman/tests

Fixed tests on Windows
deepchem · May 5, 2020 · f53936c · f53936c
2 parents 4fed7c2 + 8c69efe
commit f53936c
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Showing 2 changed files with 18 additions and 19 deletions.
diff --git a/deepchem/molnet/tests/test_molnet.py b/deepchem/molnet/tests/test_molnet.py
@@ -36,7 +36,7 @@ def test_delaney_graphconvreg(self):
         split=split,
         out_path=out_path,
         reload=False)
-    with open(os.path.join(out_path, 'results.csv'), 'r') as f:
+    with open(os.path.join(out_path, 'results.csv'), newline='\n') as f:
       reader = csv.reader(f)
       for lastrow in reader:
         pass
@@ -59,7 +59,7 @@ def test_qm7_multitask(self):
         split=split,
         out_path=out_path,
         reload=False)
-    with open(os.path.join(out_path, 'results.csv'), 'r') as f:
+    with open(os.path.join(out_path, 'results.csv'), newline='\n') as f:
       reader = csv.reader(f)
       for lastrow in reader:
         pass
@@ -82,7 +82,7 @@ def test_clintox_multitask(self):
         out_path=out_path,
         test=True,
         reload=False)
-    with open(os.path.join(out_path, 'results.csv'), 'r') as f:
+    with open(os.path.join(out_path, 'results.csv'), newline='\n') as f:
       reader = csv.reader(f)
       for lastrow in reader:
         pass

diff --git a/deepchem/utils/test/test_rdkit_util.py b/deepchem/utils/test/test_rdkit_util.py
@@ -72,45 +72,44 @@ def test_write_molecule(self):
     xyz, mol = rdkit_util.load_molecule(
         ligand_file, calc_charges=False, add_hydrogens=False)
 
-    outfile = "/tmp/mol.sdf"
-    rdkit_util.write_molecule(mol, outfile)
+    with tempfile.TemporaryDirectory() as tmp:
+      outfile = os.path.join(tmp, "mol.sdf")
+      rdkit_util.write_molecule(mol, outfile)
 
-    xyz, mol2 = rdkit_util.load_molecule(
-        outfile, calc_charges=False, add_hydrogens=False)
+      xyz, mol2 = rdkit_util.load_molecule(
+          outfile, calc_charges=False, add_hydrogens=False)
 
     assert_equal(mol.GetNumAtoms(), mol2.GetNumAtoms())
     for atom_idx in range(mol.GetNumAtoms()):
       atom1 = mol.GetAtoms()[atom_idx]
       atom2 = mol.GetAtoms()[atom_idx]
       assert_equal(atom1.GetAtomicNum(), atom2.GetAtomicNum())
-    os.remove(outfile)
 
   def test_pdbqt_to_pdb(self):
     current_dir = os.path.dirname(os.path.realpath(__file__))
     protein_file = os.path.join(current_dir,
                                 "../../dock/tests/1jld_protein.pdb")
     xyz, mol = rdkit_util.load_molecule(
         protein_file, calc_charges=False, add_hydrogens=False)
-    out_pdb = "/tmp/mol.pdb"
-    out_pdbqt = "/tmp/mol.pdbqt"
+    with tempfile.TemporaryDirectory() as tmp:
+      out_pdb = os.path.join(tmp, "mol.pdb")
+      out_pdbqt = os.path.join(tmp, "mol.pdbqt")
 
-    rdkit_util.write_molecule(mol, out_pdb)
-    rdkit_util.write_molecule(mol, out_pdbqt, is_protein=True)
+      rdkit_util.write_molecule(mol, out_pdb)
+      rdkit_util.write_molecule(mol, out_pdbqt, is_protein=True)
 
-    pdb_block = rdkit_util.pdbqt_to_pdb(out_pdbqt)
-    from rdkit import Chem
-    pdb_mol = Chem.MolFromPDBBlock(pdb_block, sanitize=False, removeHs=False)
+      pdb_block = rdkit_util.pdbqt_to_pdb(out_pdbqt)
+      from rdkit import Chem
+      pdb_mol = Chem.MolFromPDBBlock(pdb_block, sanitize=False, removeHs=False)
 
-    xyz, pdbqt_mol = rdkit_util.load_molecule(
-        out_pdbqt, add_hydrogens=False, calc_charges=False)
+      xyz, pdbqt_mol = rdkit_util.load_molecule(
+          out_pdbqt, add_hydrogens=False, calc_charges=False)
 
     assert_equal(pdb_mol.GetNumAtoms(), pdbqt_mol.GetNumAtoms())
     for atom_idx in range(pdb_mol.GetNumAtoms()):
       atom1 = pdb_mol.GetAtoms()[atom_idx]
       atom2 = pdbqt_mol.GetAtoms()[atom_idx]
       assert_equal(atom1.GetAtomicNum(), atom2.GetAtomicNum())
-    os.remove(out_pdb)
-    os.remove(out_pdbqt)
 
   def test_merge_molecules_xyz(self):
     current_dir = os.path.dirname(os.path.realpath(__file__))