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b/tests/ase_traj/HeAlO.traj similarity index 100% rename from tests/ase/HeAlO.traj rename to tests/ase_traj/HeAlO.traj diff --git a/tests/pymatgen/FA-001.vasp b/tests/pymatgen_data/FA-001.vasp similarity index 100% rename from tests/pymatgen/FA-001.vasp rename to tests/pymatgen_data/FA-001.vasp diff --git a/tests/pymatgen/FA-001.xyz b/tests/pymatgen_data/FA-001.xyz similarity index 100% rename from tests/pymatgen/FA-001.xyz rename to tests/pymatgen_data/FA-001.xyz diff --git a/tests/pymatgen/mol2-new.vasp b/tests/pymatgen_data/mol2-new.vasp similarity index 100% rename from tests/pymatgen/mol2-new.vasp rename to tests/pymatgen_data/mol2-new.vasp diff --git a/tests/pymatgen/mol2.vasp b/tests/pymatgen_data/mol2.vasp similarity index 100% rename from tests/pymatgen/mol2.vasp rename to tests/pymatgen_data/mol2.vasp diff --git a/tests/test_amber_md.py b/tests/test_amber_md.py index 758c6d002..d3189a0d6 100644 --- a/tests/test_amber_md.py +++ b/tests/test_amber_md.py @@ -3,7 +3,12 @@ import shutil from context import dpdata from comp_sys import CompLabeledSys, IsPBC - +try: + import parmed +except ModuleNotFoundError: + skip_parmed_related_test=True +else: + skip_parmed_related_test=False class TestAmberMD(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : @@ -19,6 +24,7 @@ def tearDown(self) : if os.path.exists('tmp.deepmd.npy'): shutil.rmtree('tmp.deepmd.npy') +@unittest.skipIf(skip_parmed_related_test,"skip parmed related test. install parmed to fix") class TestAmberMDTarget(unittest.TestCase, CompLabeledSys, IsPBC): def setUp(self): ll="amber/corr/low_level" @@ -35,4 +41,4 @@ def setUp(self): self.v_places = 6 if __name__ == '__main__': - unittest.main() \ No newline at end of file + unittest.main() diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py index 43ecaa023..6c37a31ce 100644 --- a/tests/test_ase_traj.py +++ b/tests/test_ase_traj.py @@ -3,23 +3,31 @@ import unittest from context import dpdata from comp_sys import CompLabeledSys, IsPBC +try: + import ase +except ModuleNotFoundError: + skip_ase = True +else: + skip_ase = False +@unittest.skipIf(skip_ase,"skip ase related test. install ase to fix") class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : - self.multi_systems = dpdata.MultiSystems.from_file('ase/HeAlO.traj', fmt='ase/structure') + self.multi_systems = dpdata.MultiSystems.from_file('ase_traj/HeAlO.traj', fmt='ase_traj/structure') self.system_1 = self.multi_systems.systems['Al0He4O0'] - self.system_2 = dpdata.LabeledSystem('ase/Al0He4O0', fmt='deepmd') + self.system_2 = dpdata.LabeledSystem('ase_traj/Al0He4O0', fmt='deepmd') self.places = 6 self.e_places = 6 self.f_places = 6 self.v_places = 4 +@unittest.skipIf(skip_ase,"skip ase related test. install ase to fix") class TestASEtraj1(unittest.TestCase, CompLabeledSys, IsPBC): def setUp (self) : - self.system_temp0 = dpdata.MultiSystems.from_file(file_name='ase/HeAlO.traj', fmt='ase/structure') + self.system_temp0 = dpdata.MultiSystems.from_file(file_name='ase_traj/HeAlO.traj', fmt='ase/structure') self.system_1 = self.system_temp0.systems['Al2He1O3'] # .sort_atom_types() - self.system_temp1 = dpdata.LabeledSystem('ase/Al2He1O3', fmt='deepmd') - self.system_temp2 = dpdata.LabeledSystem('ase/Al4He4O6', fmt='deepmd') + self.system_temp1 = dpdata.LabeledSystem('ase_traj/Al2He1O3', fmt='deepmd') + self.system_temp2 = dpdata.LabeledSystem('ase_traj/Al4He4O6', fmt='deepmd') self.system_temp3 = dpdata.MultiSystems(self.system_temp2, self.system_temp1) self.system_2 = self.system_temp3.systems['Al2He1O3'] self.places = 6 diff --git a/tests/test_pymatgen_molecule.py b/tests/test_pymatgen_molecule.py index 4a1eb0291..d80acc922 100644 --- a/tests/test_pymatgen_molecule.py +++ b/tests/test_pymatgen_molecule.py @@ -2,17 +2,24 @@ import numpy as np import unittest from context import dpdata +try: + import pymatgen +except ModuleNotFoundError: + skip_pymatgen=True +else: + skip_pymatgen=False +@unittest.skipIf(skip_pymatgen,"skip pymatgen related test. install pymatgen to fix") class TestPOSCARCart(unittest.TestCase): def setUp(self): self.system = dpdata.System() - self.system.from_pymatgen_molecule(os.path.join('pymatgen', 'FA-001.xyz')) + self.system.from_pymatgen_molecule(os.path.join('pymatgen_data', 'FA-001.xyz')) self.assertEqual(list(self.system["atom_types"]), [0, 1, 2, 1, 1, 2, 1, 1]) def test_poscar_to_molecule(self): tmp_system = dpdata.System() - tmp_system.from_vasp_poscar(os.path.join('pymatgen', 'mol2.vasp')) + tmp_system.from_vasp_poscar(os.path.join('pymatgen_data', 'mol2.vasp')) natoms = len(tmp_system['coords'][0]) tmpcoord = tmp_system['coords'][0] cog = np.average(tmpcoord, axis = 0)