Description: Skip tests requiring network access. Author: Andrius Merkys Forwarded: not-needed --- a/test/test_parmed_formats.py +++ b/test/test_parmed_formats.py @@ -2206,6 +2206,7 @@ def setUp(self): self.url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/' + @unittest.skip("Not running tests requiring network access") def test_download_off(self): """ Tests automatic loading of downloaded OFF files """ self.assertTrue(amber.AmberOFFLibrary.id_format(self.url + 'amino12.lib')) @@ -2214,24 +2215,28 @@ for key, item in off.items(): self.assertIsInstance(item, ResidueTemplate) + @unittest.skip("Not running tests requiring network access") def test_download_amber_prmtop(self): """ Tests automatic loading of downloaded AmberParm object """ self.assertTrue(amber.AmberFormat.id_format(self.url + 'tip4p.parm7')) parm = amber.AmberFormat.parse(self.url + 'tip4p.parm7') self.assertIsInstance(parm, amber.AmberParm) + @unittest.skip("Not running tests requiring network access") def test_download_amoeba_prmtop(self): """ Tests automatic loading of downloaded AmoebaParm object """ self.assertTrue(amber.AmberFormat.id_format(self.url + 'nma.parm7')) parm = amber.AmberFormat.parse(self.url + 'nma.parm7') self.assertIsInstance(parm, amber.AmoebaParm) + @unittest.skip("Not running tests requiring network access") def test_download_chamber_prmtop(self): """ Tests automatic loading of downloaded ChamberParm object """ self.assertTrue(amber.AmberFormat.id_format(self.url + 'ala_ala_ala.parm7')) parm = amber.AmberFormat.parse(self.url + 'ala_ala_ala.parm7') self.assertIsInstance(parm, amber.ChamberParm) + @unittest.skip("Not running tests requiring network access") def test_download_raw_amber_format(self): """ Tests automatic loading of downloaded AmberFormat object """ self.assertTrue(amber.AmberFormat.id_format(self.url + 'cSPCE.mdl')) @@ -2239,36 +2244,42 @@ self.assertIsInstance(parm, amber.AmberFormat) self.assertNotIsInstance(parm, amber.AmberParm) + @unittest.skip("Not running tests requiring network access") def test_download_amber_restart_ascii(self): """ Tests automatic loading of downloaded Amber ASCII restart file """ self.assertTrue(amber.AmberAsciiRestart.id_format(self.url + 'trx.inpcrd')) parm = amber.AmberAsciiRestart(self.url + 'trx.inpcrd') self.assertIsInstance(parm, amber.AmberAsciiRestart) + @unittest.skip("Not running tests requiring network access") def test_download_amber_traj_ascii(self): """ Tests automatic loading of downloaded Amber mdcrd file """ self.assertTrue(amber.AmberMdcrd.id_format(self.url + 'tz2.truncoct.crd')) crd = amber.AmberMdcrd(self.url + 'tz2.truncoct.crd', natom=5827, hasbox=True) self.assertIsInstance(crd, amber.AmberMdcrd) + @unittest.skip("Not running tests requiring network access") def test_download_charmm_psf(self): """ Tests automatic loading of downloaded CHARMM PSF file """ self.assertTrue(formats.PSFFile.id_format(self.url + 'ala_ala_ala.psf')) parm = formats.PSFFile.parse(self.url + 'ala_ala_ala.psf') self.assertIsInstance(parm, charmm.CharmmPsfFile) + @unittest.skip("Not running tests requiring network access") def test_download_charmm_crd(self): """ Tests automatic loading of downloaded CHARMM crd file """ self.assertTrue(charmm.CharmmCrdFile.id_format(self.url + 'dhfr_min_charmm.crd')) crd = charmm.CharmmCrdFile(self.url + 'dhfr_min_charmm.crd') self.assertIsInstance(crd, charmm.CharmmCrdFile) + @unittest.skip("Not running tests requiring network access") def test_download_charmm_restart(self): """ Tests automatic loading of downloaded CHARMM restart file """ self.assertTrue(charmm.CharmmRstFile.id_format(self.url + 'sample-charmm.rst')) crd = charmm.CharmmRstFile(self.url + 'sample-charmm.rst') self.assertIsInstance(crd, charmm.CharmmRstFile) + @unittest.skip("Not running tests requiring network access") def test_download_pdb(self): """ Tests automatic loading of downloaded PDB files """ self.assertTrue(formats.PDBFile.id_format(self.url + '4lzt.pdb')) @@ -2276,6 +2287,7 @@ self.assertIsInstance(pdb, Structure) self.assertEqual(len(pdb.atoms), 1164) + @unittest.skip("Not running tests requiring network access") def test_download_cif(self): """ Tests automatic loading of downloaded PDBx/mmCIF files """ self.assertTrue(formats.CIFFile.id_format(self.url + '4LZT.cif')) @@ -2283,6 +2295,7 @@ self.assertIsInstance(cif, Structure) self.assertEqual(len(cif.atoms), 1164) + @unittest.skip("Not running tests requiring network access") def test_download_mol2(self): """ Tests automatic loading of downloaded mol2 and mol3 files """ self.assertTrue(formats.Mol2File.id_format(self.url + 'test_multi.mol2')) @@ -2292,6 +2305,7 @@ mol3 = formats.Mol2File.parse(self.url + 'tripos9.mol2') self.assertIsInstance(mol3, ResidueTemplate) + @unittest.skip("Not running tests requiring network access") @unittest.skipUnless(HAS_GROMACS, "Cannot run GROMACS tests without GROMACS") def test_download_gromacs_topology(self): """ Tests automatic loading of downloaded Gromacs topology file """ @@ -2299,12 +2313,14 @@ top = gromacs.GromacsTopologyFile(self.url + '1aki.charmm27.top') self.assertIsInstance(top, gromacs.GromacsTopologyFile) + @unittest.skip("Not running tests requiring network access") def test_download_gromacs_gro(self): """ Tests automatic loading of downloaded Gromacs GRO file """ self.assertTrue(gromacs.GromacsGroFile.id_format(self.url + '1aki.ff99sbildn.gro')) gro = gromacs.GromacsGroFile.parse(self.url + '1aki.ff99sbildn.gro') self.assertIsInstance(gro, Structure) + @unittest.skip("Not running tests requiring network access") def test_download_netcdf(self): """ Tests that NetCDF files always fail when trying to download them """ self.assertFalse(amber.NetCDFRestart.id_format(self.url + 'ncinpcrd.rst7')) --- a/test/test_parmed_genopen.py +++ b/test/test_parmed_genopen.py @@ -53,18 +53,21 @@ text = bz2.BZ2File(self.get_fn('test.bz2', written=True), 'r').read() self.assertEqual(text.decode('ascii'), ALPHABET) + @unittest.skip("Not running tests requiring network access") def test_read_normal_URL(self): """ Tests genopen reading a remote file """ url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/tripos1.mol2' with closing(genopen(url, 'r')) as f: self.assertEqual(f.read(), open(get_fn('tripos1.mol2')).read()) + @unittest.skip("Not running tests requiring network access") def test_read_bzipped_URL(self): """ Tests genopen reading a bzipped remote file """ url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/4lzt.pdb.bz2' with closing(genopen(url, 'r')) as f: self.assertEqual(f.read(), genopen(get_fn('4lzt.pdb.bz2')).read()) + @unittest.skip("Not running tests requiring network access") def test_read_gzipped_URL(self): """ Tests genopen reading a gzipped remote file """ url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/4lzt.pdb.gz' @@ -105,12 +108,14 @@ text = bz2.BZ2File(self.get_fn('test.txt.bz2', written=True)).read() self.assertEqual(text.decode('ascii'), ALPHABET*2) + @unittest.skip("Not running tests requiring network access") def test_append_remote_file(self): """ Tests that genopen appending a remote file fails """ url = 'http://q4md-forcefieldtools.org/REDDB/projects/W-73/tripos1.mol2' self.assertRaises(ValueError, lambda: genopen(url, 'a')) self.assertRaises(ValueError, lambda: genopen(url, 'w')) + @unittest.skip("Not running tests requiring network access") def test_read_bad_URL(self): """ Tests proper exception handling of non-existent URL """ self.assertRaises(IOError, lambda: genopen('http://asdkfjasdf.lib')) --- a/test/test_parmed_structure.py +++ b/test/test_parmed_structure.py @@ -1384,6 +1384,7 @@ self.assertEqual(len(self.sys2.cmaps), len(x2.cmaps)) self.assertEqual(len(self.sys3.cmaps), len(x3.cmaps)) + @unittest.skip("Not running tests requiring network access") def test_save_psf2(self): """ Test saving PSF file for unparametrized system """ url = 'http://ambermd.org/tutorials/advanced/tutorial1/files/polyAT.pdb'