Pytest fixes (41654ab3) · Commits · 钟慕尧 / deepchem

deepchem/splits/tests/test_splitter.py

+0 −6

Original line number	Diff line number	Diff line
		@@ -549,9 +549,3 @@ class TestSplitter(unittest.TestCase):
		assert not np.array_equal(train1.X, train2.X)
		assert not np.array_equal(valid1.X, valid2.X)
		assert not np.array_equal(test1.X, test2.X)


		if __name__ == "__main__":
		import nose

		nose.run(defaultTest=__name__)

deepchem/utils/test/test_pdbqt_utils.py

+6 −7

Original line number	Diff line number	Diff line
		import unittest
		import os
		import tempfile
		from nose.tools import assert_equal
		from deepchem.utils import rdkit_util
		from deepchem.utils import pdbqt_utils

		@@ -33,11 +32,11 @@ class TestPDBQTUtils(unittest.TestCase):
		xyz, pdbqt_mol = rdkit_util.load_molecule(
		out_pdbqt, add_hydrogens=False, calc_charges=False)

		assert_equal(pdb_mol.GetNumAtoms(), pdbqt_mol.GetNumAtoms())
		assert 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())
		assert atom1.GetAtomicNum() == atom2.GetAtomicNum()

		def test_convert_mol_to_pdbqt(self):
		"""Test that a ligand molecule can be coverted to PDBQT."""
		@@ -52,11 +51,11 @@ class TestPDBQTUtils(unittest.TestCase):
		pdbqt_utils.convert_mol_to_pdbqt(mol, outfile)
		pdbqt_xyz, pdbqt_mol = rdkit_util.load_molecule(
		outfile, add_hydrogens=False, calc_charges=False)
		assert_equal(pdbqt_mol.GetNumAtoms(), pdbqt_mol.GetNumAtoms())
		assert pdbqt_mol.GetNumAtoms() == pdbqt_mol.GetNumAtoms()
		for atom_idx in range(pdbqt_mol.GetNumAtoms()):
		atom1 = pdbqt_mol.GetAtoms()[atom_idx]
		atom2 = pdbqt_mol.GetAtoms()[atom_idx]
		assert_equal(atom1.GetAtomicNum(), atom2.GetAtomicNum())
		assert atom1.GetAtomicNum() == atom2.GetAtomicNum()

		def test_convert_protein_to_pdbqt(self):
		"""Test a protein in a PDB can be converted to PDBQT."""
		@@ -71,8 +70,8 @@ class TestPDBQTUtils(unittest.TestCase):
		pdbqt_utils.convert_protein_to_pdbqt(mol, outfile)
		pdbqt_xyz, pdbqt_mol = rdkit_util.load_molecule(
		outfile, add_hydrogens=False, calc_charges=False)
		assert_equal(pdbqt_mol.GetNumAtoms(), pdbqt_mol.GetNumAtoms())
		assert pdbqt_mol.GetNumAtoms() == pdbqt_mol.GetNumAtoms()
		for atom_idx in range(pdbqt_mol.GetNumAtoms()):
		atom1 = pdbqt_mol.GetAtoms()[atom_idx]
		atom2 = pdbqt_mol.GetAtoms()[atom_idx]
		assert_equal(atom1.GetAtomicNum(), atom2.GetAtomicNum())
		assert atom1.GetAtomicNum() == atom2.GetAtomicNum()

pytest.ini

0 → 100644

+4 −0

Original line number	Diff line number	Diff line
		[pytest]
		markers =
		slow: marks tests as slow (deselect with '-m "not slow"')
		serial

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