Merge branch 'materialsproject:master' into install_data_files

materialsproject · Aug 24, 2021 · fd9004d · fd9004d
2 parents 8a3f596 + 405a0b2
commit fd9004d
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Showing 20 changed files with 45 additions and 135 deletions.
diff --git a/pymatgen/alchemy/tests/test_materials.py b/pymatgen/alchemy/tests/test_materials.py
@@ -55,9 +55,7 @@ def test_append_filter(self):
         self.trans.append_filter(f3)
 
     def test_get_vasp_input(self):
-        SETTINGS["PMG_VASP_PSP_DIR"] = os.path.abspath(
-            os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
-        )
+        SETTINGS["PMG_VASP_PSP_DIR"] = PymatgenTest.TEST_FILES_DIR
         potcar = self.trans.get_vasp_input(MPRelaxSet)["POTCAR"]
         self.assertEqual("Na_pv\nFe_pv\nP\nO", "\n".join([p.symbol for p in potcar]))
         self.assertEqual(len(self.trans.structures), 2)

diff --git a/pymatgen/analysis/chemenv/connectivity/tests/test_environment_nodes.py b/pymatgen/analysis/chemenv/connectivity/tests/test_environment_nodes.py
@@ -20,13 +20,7 @@
     bson = None
 
 json_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "json_test_files",
 )

diff --git a/...gen/analysis/chemenv/coordination_environments/tests/test_coordination_geometry_finder.py b/...gen/analysis/chemenv/coordination_environments/tests/test_coordination_geometry_finder.py
@@ -19,13 +19,7 @@
 from pymatgen.util.testing import PymatgenTest
 
 json_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "json_test_files",
 )

diff --git a/pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py b/pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py
@@ -31,26 +31,15 @@
     DetailedVoronoiContainer,
 )
 from pymatgen.core.structure import Structure
+from pymatgen.util.testing import PymatgenTest
 
 json_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "json_test_files",
 )
 se_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "structure_environments_files",
 )

diff --git a/pymatgen/analysis/chemenv/coordination_environments/tests/test_structure_environments.py b/pymatgen/analysis/chemenv/coordination_environments/tests/test_structure_environments.py
@@ -23,13 +23,7 @@
 from pymatgen.util.testing import PymatgenTest
 
 se_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "structure_environments_files",
 )

diff --git a/pymatgen/analysis/chemenv/coordination_environments/tests/test_voronoi.py b/pymatgen/analysis/chemenv/coordination_environments/tests/test_voronoi.py
@@ -19,24 +19,12 @@
 from pymatgen.util.testing import PymatgenTest
 
 json_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "json_test_files",
 )
 img_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "images",
 )

diff --git a/pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py b/pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py
@@ -23,13 +23,7 @@
 from pymatgen.util.testing import PymatgenTest
 
 se_files_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "structure_environments_files",
 )

diff --git a/pymatgen/analysis/chemenv/utils/tests/test_chemenv_config.py b/pymatgen/analysis/chemenv/utils/tests/test_chemenv_config.py
@@ -11,15 +11,10 @@
 
 from pymatgen.core import SETTINGS
 from pymatgen.analysis.chemenv.utils.chemenv_config import ChemEnvConfig
+from pymatgen.util.testing import PymatgenTest
 
 config_file_dir = os.path.join(
-    os.path.dirname(__file__),
-    "..",
-    "..",
-    "..",
-    "..",
-    "..",
-    "test_files",
+    PymatgenTest.TEST_FILES_DIR,
     "chemenv",
     "config",
 )

diff --git a/pymatgen/analysis/structure_prediction/tests/test_substitution_probability.py b/pymatgen/analysis/structure_prediction/tests/test_substitution_probability.py
@@ -13,6 +13,7 @@
     SubstitutionProbability,
 )
 from pymatgen.core.periodic_table import Species
+from pymatgen.util.testing import PymatgenTest
 
 
 def get_table():
@@ -22,12 +23,7 @@ def get_table():
     default lambda table.
     """
     data_dir = os.path.join(
-        os.path.dirname(__file__),
-        "..",
-        "..",
-        "..",
-        "..",
-        "test_files",
+        PymatgenTest.TEST_FILES_DIR,
         "struct_predictor",
     )
 

diff --git a/pymatgen/analysis/structure_prediction/tests/test_substitutor.py b/pymatgen/analysis/structure_prediction/tests/test_substitutor.py
@@ -20,12 +20,7 @@ def get_table():
     default lambda table.
     """
     data_dir = os.path.join(
-        os.path.dirname(__file__),
-        "..",
-        "..",
-        "..",
-        "..",
-        "test_files",
+        PymatgenTest.TEST_FILES_DIR,
         "struct_predictor",
     )
     json_file = os.path.join(data_dir, "test_lambda.json")

diff --git a/pymatgen/analysis/tests/test_graphs.py b/pymatgen/analysis/tests/test_graphs.py
@@ -37,7 +37,7 @@
 __date__ = "August 2017"
 
 module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
-molecule_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files", "molecules")
+molecule_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules")
 
 
 class StructureGraphTest(PymatgenTest):
@@ -83,21 +83,15 @@ def setUp(self):
         # MoS2 example, structure graph obtained from critic2
         # (not ground state, from mp-1023924, single layer)
         stdout_file = os.path.join(
-            os.path.dirname(__file__),
-            "..",
-            "..",
-            "..",
-            "test_files/critic2/MoS2_critic2_stdout.txt",
+            PymatgenTest.TEST_FILES_DIR,
+            "critic2/MoS2_critic2_stdout.txt",
         )
         with open(stdout_file, "r") as f:
             reference_stdout = f.read()
         self.structure = Structure.from_file(
             os.path.join(
-                os.path.dirname(__file__),
-                "..",
-                "..",
-                "..",
-                "test_files/critic2/MoS2.cif",
+                PymatgenTest.TEST_FILES_DIR,
+                "critic2/MoS2.cif",
             )
         )
         c2o = Critic2Analysis(self.structure, reference_stdout)
@@ -229,9 +223,7 @@ def test_insert_remove(self):
         self.assertEqual(square_copy.graph.number_of_edges(), 3)
 
     def test_substitute(self):
-        structure = Structure.from_file(
-            os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files", "Li2O.cif")
-        )
+        structure = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "Li2O.cif"))
         molecule = FunctionalGroups["methyl"]
 
         structure_copy = copy.deepcopy(structure)
@@ -471,11 +463,8 @@ def test_from_edges(self):
     def test_extract_molecules(self):
 
         structure_file = os.path.join(
-            os.path.dirname(__file__),
-            "..",
-            "..",
-            "..",
-            "test_files/H6PbCI3N_mp-977013_symmetrized.cif",
+            PymatgenTest.TEST_FILES_DIR,
+            "H6PbCI3N_mp-977013_symmetrized.cif",
         )
 
         s = Structure.from_file(structure_file)
@@ -539,11 +528,8 @@ def setUp(self):
 
         cyclohexene = Molecule.from_file(
             os.path.join(
-                os.path.dirname(__file__),
-                "..",
-                "..",
-                "..",
-                "test_files/graphs/cyclohexene.xyz",
+                PymatgenTest.TEST_FILES_DIR,
+                "graphs/cyclohexene.xyz",
             )
         )
         self.cyclohexene = MoleculeGraph.with_empty_graph(
@@ -568,11 +554,8 @@ def setUp(self):
 
         butadiene = Molecule.from_file(
             os.path.join(
-                os.path.dirname(__file__),
-                "..",
-                "..",
-                "..",
-                "test_files/graphs/butadiene.xyz",
+                PymatgenTest.TEST_FILES_DIR,
+                "graphs/butadiene.xyz",
             )
         )
         self.butadiene = MoleculeGraph.with_empty_graph(butadiene, edge_weight_name="strength", edge_weight_units="")
@@ -588,11 +571,8 @@ def setUp(self):
 
         ethylene = Molecule.from_file(
             os.path.join(
-                os.path.dirname(__file__),
-                "..",
-                "..",
-                "..",
-                "test_files/graphs/ethylene.xyz",
+                PymatgenTest.TEST_FILES_DIR,
+                "graphs/ethylene.xyz",
             )
         )
         self.ethylene = MoleculeGraph.with_empty_graph(ethylene, edge_weight_name="strength", edge_weight_units="")
@@ -602,7 +582,7 @@ def setUp(self):
         self.ethylene.add_edge(1, 4, weight=1.0)
         self.ethylene.add_edge(1, 5, weight=1.0)
 
-        self.pc = Molecule.from_file(os.path.join(module_dir, "..", "..", "..", "test_files", "graphs", "PC.xyz"))
+        self.pc = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "graphs", "PC.xyz"))
         self.pc_edges = [
             [5, 10],
             [5, 12],
@@ -618,11 +598,9 @@ def setUp(self):
             [6, 0],
             [6, 2],
         ]
-        self.pc_frag1 = Molecule.from_file(
-            os.path.join(module_dir, "..", "..", "..", "test_files", "graphs", "PC_frag1.xyz")
-        )
+        self.pc_frag1 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "graphs", "PC_frag1.xyz"))
         self.pc_frag1_edges = [[0, 2], [4, 2], [2, 1], [1, 3]]
-        self.tfsi = Molecule.from_file(os.path.join(module_dir, "..", "..", "..", "test_files", "graphs", "TFSI.xyz"))
+        self.tfsi = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "graphs", "TFSI.xyz"))
         self.tfsi_edges = (
             [14, 1],
             [1, 4],
@@ -920,11 +898,8 @@ def test_find_rings(self):
     def test_isomorphic(self):
         ethylene = Molecule.from_file(
             os.path.join(
-                os.path.dirname(__file__),
-                "..",
-                "..",
-                "..",
-                "test_files/graphs/ethylene.xyz",
+                PymatgenTest.TEST_FILES_DIR,
+                "graphs/ethylene.xyz",
             )
         )
         # switch carbons

diff --git a/pymatgen/analysis/tests/test_path_finder.py b/pymatgen/analysis/tests/test_path_finder.py
@@ -9,6 +9,7 @@
 from pymatgen.analysis.path_finder import ChgcarPotential, NEBPathfinder
 from pymatgen.core.periodic_table import Element
 from pymatgen.io.vasp import Chgcar, Poscar
+from pymatgen.util.testing import PymatgenTest
 
 __author__ = "Ziqin (Shaun) Rong"
 __version__ = "0.1"
@@ -23,7 +24,7 @@ class PathFinderTest(unittest.TestCase):
 
     def test_image_num(self):
         module_dir = os.path.dirname(os.path.abspath(__file__))
-        test_file_dir = os.path.join(module_dir, "..", "..", "..", "test_files", "path_finder")
+        test_file_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "path_finder")
         start_s = Poscar.from_file(os.path.join(test_file_dir, "LFP_POSCAR_s")).structure
         end_s = Poscar.from_file(os.path.join(test_file_dir, "LFP_POSCAR_e")).structure
         mid_s = start_s.interpolate(end_s, nimages=2, interpolate_lattices=False)[1]

diff --git a/pymatgen/analysis/tests/test_surface_analysis.py b/pymatgen/analysis/tests/test_surface_analysis.py
@@ -25,7 +25,7 @@
 
 def get_path(path_str):
     cwd = os.path.abspath(os.path.dirname(__file__))
-    path = os.path.join(cwd, "..", "..", "..", "test_files", "surface_tests", path_str)
+    path = os.path.join(PymatgenTest.TEST_FILES_DIR, "surface_tests", path_str)
     return path
 
 

diff --git a/pymatgen/command_line/tests/test_critic2_caller.py b/pymatgen/command_line/tests/test_critic2_caller.py
@@ -62,11 +62,8 @@ def test_from_structure(self):
         # uses promolecular density
         structure = Structure.from_file(
             os.path.join(
-                os.path.dirname(__file__),
-                "..",
-                "..",
-                "..",
-                "test_files/critic2/MoS2.cif",
+                PymatgenTest.TEST_FILES_DIR,
+                "critic2/MoS2.cif",
             )
         )
 

diff --git a/pymatgen/core/tests/test_surface.py b/pymatgen/core/tests/test_surface.py
@@ -29,7 +29,7 @@
 
 def get_path(path_str):
     cwd = os.path.abspath(os.path.dirname(__file__))
-    path = os.path.join(cwd, "..", "..", "..", "test_files", "surface_tests", path_str)
+    path = os.path.join(PymatgenTest.TEST_FILES_DIR, "surface_tests", path_str)
     return path
 
 

diff --git a/pymatgen/entries/computed_entries.py b/pymatgen/entries/computed_entries.py
@@ -701,7 +701,7 @@ def normalize(self, mode: str = "formula_unit") -> "ComputedStructureEntry":
         d = super().normalize(mode).as_dict()
         d["structure"] = self.structure.as_dict()
         entry = self.from_dict(d)
-        entry._composition /= factor  # type: ignore
+        entry._composition /= factor  # pylint: disable=E1101
         return entry
 
 

diff --git a/pymatgen/io/abinit/tests/test_inputs.py b/pymatgen/io/abinit/tests/test_inputs.py
@@ -21,7 +21,7 @@
 )
 from pymatgen.util.testing import PymatgenTest
 
-_test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", "test_files", "abinit")
+_test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "abinit")
 
 
 def abiref_file(filename):

diff --git a/pymatgen/io/abinit/tests/test_netcdf.py b/pymatgen/io/abinit/tests/test_netcdf.py
@@ -16,7 +16,7 @@
 except ImportError:
     netCDF4 = None
 
-_test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", "test_files", "abinit")
+_test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "abinit")
 
 
 def ref_file(filename):