fix tests data file path

tests/test_file_io.py

@@ -1,6 +1,10 @@
 import unittest
 from cosymlib import file_io
 from numpy import testing
+import os
+
+
+data_dir = os.path.join(os.path.dirname(__file__), 'data')
 
 
 class TestPointGroup(unittest.TestCase):
@@ -16,7 +20,7 @@ def test_reading_xyz(self):
                     [ 0.2051,  0.8240, -0.6786],
                     [ 0.3345, -0.9314, -0.4496],
                     [-1.0685, -0.0537,  0.1921]]
-        structure = file_io.get_geometry_from_file_xyz('data/file_io/test.xyz', read_multiple=True)
+        structure = file_io.get_geometry_from_file_xyz(data_dir + '/file_io/test.xyz', read_multiple=True)
         testing.assert_array_equal(structure[0].get_positions(), methane)
         testing.assert_array_equal(structure[1].get_positions(), ammonium)
         self.assertEqual(structure[0].get_symbols(), ['C', 'H', 'H', 'H', 'H'])
@@ -35,7 +39,7 @@ def test_reading_cor(self):
                       [7.85296,  1.80990,  1.32660],
                       [4.85354,  1.20560, -1.32660],
                       [8.03285,  0.37875, -0.26075]]
-        structures = file_io.get_geometry_from_file_cor('data/file_io/test.cor', read_multiple=True)
+        structures = file_io.get_geometry_from_file_cor(data_dir +'/file_io/test.cor', read_multiple=True)
         testing.assert_array_equal(structures[0].get_positions(), structure1)
         testing.assert_array_equal(structures[1].get_positions(), structure2)
         self.assertEqual(structures[0].get_symbols(), ['Pd', 'N', 'N', 'N', 'N'])
@@ -48,7 +52,7 @@ def test_reading_fchk(self):
         beta_occupancy = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
         alpha_electrons = 18
         beta_electrons = 18
-        molecule = file_io.get_molecule_from_file_fchk('data/file_io/test.fchk', read_multiple=False)
+        molecule = file_io.get_molecule_from_file_fchk(data_dir + '/file_io/test.fchk', read_multiple=False)
         self.assertEqual(molecule.electronic_structure.alpha_occupancy, alpha_occupancy)
         self.assertEqual(molecule.electronic_structure.beta_occupancy, beta_occupancy)
         self.assertEqual(molecule.electronic_structure.alpha_electrons, alpha_electrons)
@@ -59,7 +63,7 @@ def test_readinf_molden(self):
         beta_occupancy = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0]
         alpha_electrons = 13
         beta_electrons = 13
-        molecule = file_io.get_molecule_from_file_molden('data/file_io/test.molden', read_multiple=False)
+        molecule = file_io.get_molecule_from_file_molden(data_dir + '/file_io/test.molden', read_multiple=False)
         self.assertEqual(molecule.electronic_structure.alpha_occupancy, alpha_occupancy)
         self.assertEqual(molecule.electronic_structure.beta_occupancy, beta_occupancy)
         self.assertEqual(molecule.electronic_structure.alpha_electrons, alpha_electrons)

tests/test_point_group.py

@@ -1,5 +1,9 @@
 import unittest
 from cosymlib import file_io, Cosymlib
+import os
+
+
+data_dir = os.path.join(os.path.dirname(__file__), 'data')
 
 
 class TestPointGroup(unittest.TestCase):
@@ -8,7 +12,7 @@ def test(self):
         point_groups = ['C1', 'Cs', 'Ci', 'Cinfh', 'Dinfh', 'C2', 'C3', 'C2h', 'C3h', 'C2v', 'C3v', 'C4v', 'C5v', 'D2',
                         'D3', 'D2h', 'D3h', 'D4h', 'D5h', 'D6h', 'D7h', 'D8h', 'D2d', 'D3d', 'D4d', 'D5d', 'D6d', 'D8d',
                         'S4', 'T', 'Th', 'Td', 'O', 'Oh']
-        molecules = file_io.read_generic_structure_file('data/point_group/sym_molecules.xyz', read_multiple=True)
+        molecules = file_io.read_generic_structure_file(data_dir + '/point_group/sym_molecules.xyz', read_multiple=True)
         symobj = Cosymlib(molecules)
         calculated_point_groups = [pg for pg in (symobj.get_point_group())]
         for pg1, pg2 in zip(point_groups, calculated_point_groups):

tests/test_shape.py

@@ -5,12 +5,16 @@
 from cosymlib import file_io
 import cosymlib.shape as shape
 import cosymlib.shape.maps as maps
+import os
+
+
+data_dir = os.path.join(os.path.dirname(__file__), 'data')
 
 
 class TestShape(unittest.TestCase):
 
     def test_example01(self):
-        molecules, options = classic_inputs.read_old_input('data/shape/example01.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example01.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -29,7 +33,7 @@ def test_example02(self):
                          [5.047, 36.698],
                          [5.234, 36.822],
                          [5.1, 36.733]]
-        molecules, options = classic_inputs.read_old_input('data/shape/example02.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example02.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -44,7 +48,7 @@ def test_example02(self):
     def test_example03(self):
         nice_measures = [[31.375, 0.97],
                          [33.44, 0.16]]
-        molecules, options = classic_inputs.read_old_input('data/shape/example03.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example03.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -79,7 +83,7 @@ def test_example04(self):
                            [-5.66862241e-01, -1.42522607e+00, 1.26951447e+00],
                            [-1.72449417e+00, 9.49990377e-01, 2.96491640e-01],
                            [1.72449417e+00, -9.49990377e-01, -2.96491640e-01]]
-        molecules, options = classic_inputs.read_old_input('data/shape/example04.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example04.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -125,7 +129,7 @@ def test_example05(self):
                                           [15.097, 0.05],
                                           [16.737, 0.]])
 
-        molecules, options = classic_inputs.read_old_input('data/shape/example05.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example05.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -164,7 +168,7 @@ def test_example06(self):
                          4.4, 1.6, 3.5, 3.8, 3.6, 4.7, 4.8, 3.7, 1.8, 1.6, 2.3, 3.7, 3.,
                          1.3, 0.9, 2.8, 0.9, 4.1, 3.2, 4.6, 1.7, 0.8, 1., 0.7, 0.6, 0.2,
                          4.6, 1.5, 1.5, 1.7, 2.5, 2.9, 0.5, 0.8, 1.3]
-        molecules, options = classic_inputs.read_old_input('data/shape/example06.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example06.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -179,7 +183,7 @@ def test_example06(self):
         self.assertTrue(np.allclose(nice_dev_path, devpath, atol=1e-1))
 
     def test_example07(self):
-        molecules, options = classic_inputs.read_old_input('data/shape/example06.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example06.dat')
         reference_polyhedron = []
         for number in options['%labels']:
             reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -195,13 +199,13 @@ def test_example07(self):
     def test_example08(self):
         nice_measures = [[1.976, 3.699],
                          [6.955, 0.602]]
-        molecules, options = classic_inputs.read_old_input('data/shape/example08.dat')
+        molecules, options = classic_inputs.read_old_input(data_dir + '/shape/example08.dat')
         central_atom = options['%central_atom']
         reference_polyhedron = []
         if options['%labels'] != 0:
             for number in options['%labels']:
                 if int(number) == 0:
-                    for ref in file_io.get_geometry_from_file_ref('data/shape/example08.ref', read_multiple=True):
+                    for ref in file_io.get_geometry_from_file_ref(data_dir + '/shape/example08.ref', read_multiple=True):
                         reference_polyhedron.append(ref)
                 else:
                     reference_polyhedron.append(shape.tools.get_shape_label(int(number), options['%n_atoms']))
@@ -226,5 +230,5 @@ def test_example08(self):
     #     ref_str1 = shape.shape_tools.order_coordinates(ref_str1, [len(ref_str1), central_atom])
     #     ref_str2 = shape.shape_tools.get_test_structure('CSAPR-9', central_atom)
     #     ref_str2 = shape.shape_tools.order_coordinates(ref_str2, [len(ref_str2), central_atom])
-    #     good_results = np.loadtxt('data/shape/example09_results')
+    #     good_results = np.loadtxt(data_dir + '/shape/example09_results')
     #     self.assertTrue(np.allclose(good_results, ref_str1, atol=1e-3))

tests/test_symgroup.py

@@ -2,12 +2,16 @@
 from cosymlib import file_io
 from numpy import testing
 from cosymlib.molecule.geometry import Geometry
+import os
+
+
+data_dir = os.path.join(os.path.dirname(__file__), 'data')
 
 
 class TestSymgroupFchk(unittest.TestCase):
 
     def setUp(self):
-        self._structure = file_io.read_generic_structure_file('data/wfnsym/tih4_5d.fchk')
+        self._structure = file_io.read_generic_structure_file(data_dir + '/wfnsym/tih4_5d.fchk')
         self._geometry = self._structure.geometry
 
     def test_symmetry_measure(self):

tests/test_wfnsym.py

@@ -1,12 +1,16 @@
 import unittest
 from cosymlib import file_io
 from numpy import testing
+import os
+
+
+data_dir = os.path.join(os.path.dirname(__file__), 'data')
 
 
 class TestWfnsym(unittest.TestCase):
 
     def setUp(self):
-        self.structure = file_io.read_generic_structure_file('data/wfnsym/tih4_5d.fchk')
+        self.structure = file_io.read_generic_structure_file(data_dir + '/wfnsym/tih4_5d.fchk')
 
     def test_symmetry_overlap_analysis(self):
         td_labels = ['E', '2C3', '2C3', '2C3', '2C3', 'C2', 'C2', 'C2', '2S4', '2S4', '2S4',