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|
Description: Skip tests requiring network access.
Author: Andrius Merkys <merkys@debian.org>
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
@@ -53,24 +53,28 @@
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'
with closing(genopen(url, 'r')) as f:
self.assertEqual(f.read(), genopen(get_fn('4lzt.pdb.gz')).read())
+ @unittest.skip("Not running tests requiring network access")
@unittest.skipUnless(is_local(), 'Cannot download files from PDB with CI systems')
def test_read_ftp_URL(self):
""" Tests genopen reading a ftp remote file """
@@ -104,12 +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'
|
