remove functional tests

bug fix with rbt analysis

MDANSE/Framework/Jobs/RigidBodyTrajectory.py

@@ -235,7 +235,7 @@ class RigidBodyTrajectory(IJob):
         # The NetCDF variable that stores the rigid-body fit.
         FIT = outputFile.createVariable('fit', numpy.dtype(numpy.float64).char, ('NGROUPS','NFRAMES'))
  
-        outputFile.info = self._info
+        outputFile.info = str(self)
  
         # Loop over the groups.
         for comp in range(self.configuration['atom_selection']['selection_length']):

Tests/FunctionalTests/Jobs/BuildJobTests.py

 from MDANSE import REGISTRY
 
-for v in REGISTRY['job'].itervalues():
+for k,v in REGISTRY['job'].items():
+    
+    # Skip the mcstas test because mcstas executable is not available on all platform
+    if k=='mvi':
+        continue
     v.build_test("Test_%s.py" % v.type)

Tests/FunctionalTests/Jobs/Test_ac.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestAC(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['axis_selection'] = ('Water', ('OW', 'HW'))
-        parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['per_axis'] = False
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['ac']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestAC))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_apm.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestAPM(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['axis'] = ['a', 'b']
-        parameters['frames'] = (0, 10, 1)
-        parameters['name'] = 'DMPC'
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/dmpc_in_periodic_universe.nc'
-        job = REGISTRY['job']['apm']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestAPM))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_btt.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestBTT(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['btt']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestBTT))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_castep.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestCASTEP(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['castep_file'] = '../../../Data/Trajectories/CASTEP/PBAnew.md'
-        parameters['output_file'] = ('/tmp/output', ['netcdf'])
-        job = REGISTRY['job']['castep']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestCASTEP))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_ccf.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestCCF(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['atom_transmutation'] = None
-        parameters['frames'] = (0, 10, 1)
-        parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
-        parameters['normalize'] = False
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 5, 0.1)})
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['weights'] = 'b_coherent'
-        job = REGISTRY['job']['ccf']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestCCF))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_charmm.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestCHARMM(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['dcd_file'] = '../../../Data/Trajectories/CHARMM/2vb1.dcd'
-        parameters['fold'] = False
-        parameters['output_file'] = ('/tmp/output', ['netcdf'])
-        parameters['pdb_file'] = '../../../Data/Trajectories/CHARMM/2vb1.pdb'
-        job = REGISTRY['job']['charmm']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestCHARMM))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_cn.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestCN(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['atom_transmutation'] = None
-        parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['r_values'] = (0, 10, 1)
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['cn']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestCN))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_comt.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestCOMT(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['frames'] = (0, 1, 1)
-        parameters['grouping_level'] = 'atom'
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['comt']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestCOMT))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_ct.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestCT(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['ct']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestCT))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_dacf.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDACF(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_charges'] = {0: 0.5, 1: 1.2, 2: -0.2}
-        parameters['atom_selection'] = 'atom_index 0,1,2'
-        parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['dacf']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDACF))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_dcsf.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDCSF(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['atom_transmutation'] = None
-        parameters['frames'] = (0, 10, 1)
-        parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 5, 0.1)})
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['weights'] = 'b_coherent'
-        job = REGISTRY['job']['dcsf']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDCSF))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_den.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDEN(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['frames'] = (0, 10, 1)
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        job = REGISTRY['job']['den']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDEN))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_dftb.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDFTB(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['output_file'] = ('/tmp/output', ['netcdf'])
-        parameters['trj_file'] = '../../../Data/Trajectories/Forcite/nylon66_rho100_500K_v300K.trj'
-        parameters['xtd_file'] = '../../../Data/Trajectories/Forcite/nylon66_rho100_500K_v300K.xtd'
-        job = REGISTRY['job']['dftb']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDFTB))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_discover.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDISCOVER(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['his_file'] = '../../../Data/Trajectories/Discover/sushi.his'
-        parameters['output_file'] = ('/tmp/output', ['netcdf'])
-        parameters['xtd_file'] = '../../../Data/Trajectories/Discover/sushi.xtd'
-        job = REGISTRY['job']['discover']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDISCOVER))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_disf.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDISF(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['atom_transmutation'] = None
-        parameters['frames'] = (0, 10, 1)
-        parameters['grouping_level'] = 'atom'
-        parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['projection'] = None
-        parameters['q_vectors'] = ('spherical_lattice', {'width': 0.1, 'n_vectors': 50, 'shells': (0.1, 5, 0.1)})
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['weights'] = 'b_incoherent2'
-        job = REGISTRY['job']['disf']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDISF))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_dl_poly.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDL_POLY(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_aliases'] = {}
-        parameters['field_file'] = '../../../Data/Trajectories/DL_Poly/FIELD_cumen'
-        parameters['history_file'] = '../../../Data/Trajectories/DL_Poly/HISTORY_cumen'
-        parameters['output_file'] = ('/tmp/output', ['netcdf'])
-        parameters['version'] = '2'
-        job = REGISTRY['job']['dl_poly']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDL_POLY))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_dmol.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDMOL(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['his_file'] = '../../../Data/Trajectories/Discover/sushi.his'
-        parameters['output_file'] = ('/tmp/output', ['netcdf'])
-        parameters['xtd_file'] = '../../../Data/Trajectories/Discover/sushi.xtd'
-        job = REGISTRY['job']['dmol']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDMOL))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)

Tests/FunctionalTests/Jobs/Test_dos.py

-#!/usr/bin/python
-
-import unittest
-from Tests.UnitTests.UnitTest import UnitTest
-from MDANSE import REGISTRY
-
-class TestDOS(UnitTest):
-
-    def test(self):
-        parameters = {}
-        parameters['atom_selection'] = 'all'
-        parameters['atom_transmutation'] = None
-        parameters['frames'] = (0, 10, 1)
-        parameters['grouping_level'] = 'atom'
-        parameters['instrument_resolution'] = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
-        parameters['interpolation_order'] = 'no interpolation'
-        parameters['output_files'] = ('/tmp/output', ['netcdf'])
-        parameters['projection'] = None
-        parameters['running_mode'] = ('monoprocessor', 1)
-        parameters['trajectory'] = '../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
-        parameters['weights'] = 'equal'
-        job = REGISTRY['job']['dos']()
-        self.assertNotRaises(job.run, parameters, status=False)
-
-def suite():
-    loader = unittest.TestLoader()
-    s = unittest.TestSuite()
-    s.addTest(loader.loadTestsFromTestCase(TestDOS))
-    return s
-
-if __name__ == '__main__':
-    unittest.main(verbosity=2)