TST: re-enabled CIF scraper tests

Conflicts: matador/tests/test_file_io.py
ml-evs · Jun 11, 2019 · 5d8ae99 · 5d8ae99
1 parent 106d33c
commit 5d8ae99
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/matador/scrapers/cif_scraper.py b/matador/scrapers/cif_scraper.py
@@ -233,7 +233,7 @@ def _cif_set_unreduced_sites(doc):
     unreduced_species = []
     for species in species_sites:
         unreduced_sites_spec, indices = np.unique(species_sites[species],
-                                                  return_index=True, axis=1)
+                                                  return_index=True, axis=0)
         unreduced_occupancies_spec = np.asarray(species_occ[species])[indices].tolist()
         unreduced_occupancies.extend(unreduced_occupancies_spec)
         unreduced_sites.extend(unreduced_sites_spec.tolist())

diff --git a/matador/tests/test_file_io.py b/matador/tests/test_file_io.py
@@ -845,7 +845,6 @@ def test_fortran_e100_bug(self):
         pdis, s = cell2dict(cell_fname, db=False, lattice=True, verbosity=VERBOSITY)
         self.assertTrue(s)
 
-    @unittest.skipIf(True, 'CIF tests temporarily disabled...')
     def test_cif(self):
         cif_fname = REAL_PATH + 'data/cif_files/AgBiI.cif'
         failed_open = False
@@ -859,9 +858,9 @@ def test_cif(self):
             test_dict, s = cif2dict(cif_fname)
             self.assertTrue(s, 'Failed entirely, oh dear! {}'.format(test_dict))
             self.assertAlmostEqual(test_dict['num_atoms'], 46.623999999999995, msg='Failed to read num_atoms!', places=5)
-            self.assertTrue(['Bi', 1.0] in test_dict['stoichiometry'], msg='Wrong stoichiometry!')
-            self.assertTrue(['I', 4.0] in test_dict['stoichiometry'], msg='Wrong stoichiometry!')
-            self.assertTrue(sorted(test_dict['stoichiometry']) == test_dict['stoichiometry'], msg='Wrong stoichiometry!')
+            Bi_ratio = [elem[1] for elem in test_dict['stoichiometry'] if elem[0] == 'Bi'][0]
+            I_ratio = [elem[1] for elem in test_dict['stoichiometry'] if elem[0] == 'I'][0]
+            self.assertEqual(I_ratio/Bi_ratio, 4)
             self.assertAlmostEqual(test_dict['cell_volume'], 1826.0028753, msg='Wrong cell volume!', places=3)
             self.assertEqual(test_dict['space_group'], 'Fd-3m', msg='Wrong space group!')
             self.assertEqual(len(test_dict['atom_types']), 64)
@@ -879,7 +878,7 @@ def test_cif(self):
             f.close()
             errored = False
             test_dict, s = cif2dict(cif_fname)
-            errored = isinstance(test_dict, RuntimeError) and 'RuntimeError' in test_dict
+            errored = isinstance(test_dict, RuntimeError) or 'RuntimeError' in test_dict
             self.assertTrue(errored, 'WARNING: malicious attack is possible through symops')
             self.assertFalse(s, 'This should have failed entirely, oh dear!')