Fix _MPResterLegacy tests in pymatgen/ext/tests/test_matproj.py faili…

…ng due to new API key (#2700)

* pymatgen/ext/tests/test_matproj.py raise ValueError with specific err msg if 15 <= len(PMG_MAPI_KEY) <= 17

* pymatgen/ext/tests/test_*.py refactor skipIf website_is_up to website_down check

* fix pymatgen/ext/tests/test_matproj.py:402: AssertionError

assert mo_s3_112[0]["gb_energy"] == pytest.approx(0.47965)
E       assert 0.4796547330588574 == 0.47965 � 4.8e-07
E         comparison failed
E         Obtained: 0.4796547330588574
E         Expected: 0.47965 � 4.8e-07

* remove shebangs from test files

* fix TypeError: MPRester.__init__() got multiple values for argument 'api_key' from MPRester('xxxxxxxxxx')

pymatgen/analysis/chemenv/connectivity/tests/test_connected_components.py

@@ -1,6 +1,3 @@
-#!/usr/bin/env python
-
-
 import copy
 import json
 import os
@@ -467,15 +464,15 @@ def test_periodicity(self):
 
     def test_real_systems(self):
         # Initialize geometry and connectivity finders
-        strat = SimplestChemenvStrategy()
+        strategy = SimplestChemenvStrategy()
         lgf = LocalGeometryFinder()
         cf = ConnectivityFinder()
 
         # Connectivity of LiFePO4
         struct = self.get_structure("LiFePO4")
         lgf.setup_structure(structure=struct)
         se = lgf.compute_structure_environments(only_atoms=["Li", "Fe", "P"], maximum_distance_factor=1.2)
-        lse = LightStructureEnvironments.from_structure_environments(strategy=strat, structure_environments=se)
+        lse = LightStructureEnvironments.from_structure_environments(strategy=strategy, structure_environments=se)
         # Make sure the initial structure and environments are correct
         for isite in range(0, 4):
             assert lse.structure[isite].specie.symbol == "Li"
@@ -784,7 +781,7 @@ def test_real_systems(self):
         struct = Structure.from_file(os.path.join(self.TEST_FILES_DIR, "Li4Fe3Mn1(PO4)4.cif"))
         lgf.setup_structure(structure=struct)
         se = lgf.compute_structure_environments(only_atoms=["Li", "Fe", "Mn", "P"], maximum_distance_factor=1.2)
-        lse = LightStructureEnvironments.from_structure_environments(strategy=strat, structure_environments=se)
+        lse = LightStructureEnvironments.from_structure_environments(strategy=strategy, structure_environments=se)
         # Make sure the initial structure and environments are correct
         for isite in range(0, 4):
             assert lse.structure[isite].specie.symbol == "Li"

pymatgen/analysis/chemenv/connectivity/tests/test_environment_nodes.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import os
 
 from pymatgen.analysis.chemenv.connectivity.environment_nodes import EnvironmentNode
@@ -13,6 +8,8 @@
 except ModuleNotFoundError:
     bson = None
 
+__author__ = "waroquiers"
+
 json_files_dir = os.path.join(
     PymatgenTest.TEST_FILES_DIR,
     "chemenv",

pymatgen/analysis/chemenv/connectivity/tests/test_structure_connectivity.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import json
 import os
 
@@ -26,6 +21,8 @@
 except ModuleNotFoundError:
     bson = None
 
+__author__ = "waroquiers"
+
 
 class StructureConnectivityTest(PymatgenTest):
     def test_serialization(self):

pymatgen/analysis/chemenv/coordination_environments/tests/test_chemenv_strategies.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import unittest
 
 import pytest
@@ -16,6 +11,8 @@
 )
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 
 class StrategyOptionsTest(PymatgenTest):
     def test_options(self):

pymatgen/analysis/chemenv/coordination_environments/tests/test_coordination_geometries.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import unittest
 
 import numpy as np
@@ -16,6 +11,8 @@
 )
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 allcg = AllCoordinationGeometries()
 
 

pymatgen/analysis/chemenv/coordination_environments/tests/test_coordination_geometry_finder.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import os
 import unittest
 
@@ -20,6 +15,8 @@
 from pymatgen.core.structure import Lattice, Structure
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 json_files_dir = os.path.join(
     PymatgenTest.TEST_FILES_DIR,
     "chemenv",

pymatgen/analysis/chemenv/coordination_environments/tests/test_structure_environments.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import json
 import os
 import unittest
@@ -21,6 +16,8 @@
 from pymatgen.core.periodic_table import Species
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 se_files_dir = os.path.join(
     PymatgenTest.TEST_FILES_DIR,
     "chemenv",

pymatgen/analysis/chemenv/coordination_environments/tests/test_voronoi.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import os
 import random
 import unittest
@@ -17,6 +12,8 @@
 from pymatgen.core.structure import Structure
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 json_files_dir = os.path.join(
     PymatgenTest.TEST_FILES_DIR,
     "chemenv",

pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import json
 import os
 import unittest
@@ -24,6 +19,8 @@
 )
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 se_files_dir = os.path.join(
     PymatgenTest.TEST_FILES_DIR,
     "chemenv",

pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -48,8 +48,8 @@ def __init__(self, package_options=None):
         """
         :param package_options:
         """
-        if SETTINGS.get("PMG_MAPI_KEY", "") != "":
-            self.materials_project_configuration = SETTINGS.get("PMG_MAPI_KEY", "")
+        if SETTINGS.get("PMG_MAPI_KEY"):
+            self.materials_project_configuration = SETTINGS.get("PMG_MAPI_KEY")
         else:
             self.materials_project_configuration = None
 

pymatgen/analysis/chemenv/utils/tests/test_chemenv_config.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import os
 import unittest
 
@@ -12,19 +7,17 @@
 from pymatgen.core import SETTINGS
 from pymatgen.util.testing import PymatgenTest
 
-config_file_dir = os.path.join(
-    PymatgenTest.TEST_FILES_DIR,
-    "chemenv",
-    "config",
-)
+__author__ = "waroquiers"
+
+config_file_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "chemenv", "config")
 
 
 class ChemenvConfigTest(unittest.TestCase):
     def test_chemenv_config(self):
         with ScratchDir("."):
             config = ChemEnvConfig()
 
-            if SETTINGS.get("PMG_MAPI_KEY", "") != "":
+            if SETTINGS.get("PMG_MAPI_KEY"):
                 assert config.has_materials_project_access
             else:
                 assert not config.has_materials_project_access

pymatgen/analysis/chemenv/utils/tests/test_coordination_geometry_utils.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import itertools
 import random
 import unittest
@@ -12,6 +7,8 @@
 from pymatgen.analysis.chemenv.utils.coordination_geometry_utils import Plane
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 
 class PlanesUtilsTest(PymatgenTest):
     def setUp(self):

pymatgen/analysis/chemenv/utils/tests/test_func_utils.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import unittest
 
 import numpy as np
@@ -14,6 +9,8 @@
     DeltaCSMRatioFunction,
 )
 
+__author__ = "waroquiers"
+
 
 class FuncUtilsTest(unittest.TestCase):
     def test_CSMFiniteRatioFunction(self):

pymatgen/analysis/chemenv/utils/tests/test_math_utils.py

@@ -1,8 +1,3 @@
-#!/usr/bin/env python
-
-
-__author__ = "waroquiers"
-
 import unittest
 
 import numpy as np
@@ -22,6 +17,8 @@
 )
 from pymatgen.util.testing import PymatgenTest
 
+__author__ = "waroquiers"
+
 
 class MathUtilsTest(PymatgenTest):
     def test_list_cartesian_product(self):

pymatgen/analysis/tests/test_path_finder.py

@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-
 import os
 import unittest
 

pymatgen/ext/matproj.py

@@ -946,7 +946,6 @@ def get_exp_entry(self, formula):
         Returns:
             An ExpEntry object.
         """
-
         return ExpEntry(Composition(formula), self.get_exp_thermo_data(formula))
 
     def query(
@@ -1349,9 +1348,11 @@ def get_cohesive_energy(self, material_id, per_atom=False):
         Gets the cohesive for a material (eV per formula unit). Cohesive energy
             is defined as the difference between the bulk energy and the sum of
             total DFT energy of isolated atoms for atom elements in the bulk.
+
         Args:
             material_id (str): Materials Project material_id, e.g. 'mp-123'.
             per_atom (bool): Whether or not to return cohesive energy per atom
+
         Returns:
             Cohesive energy (eV).
         """
@@ -1412,7 +1413,6 @@ def get_all_substrates(self):
         Returns:
             list of material_ids corresponding to possible substrates
         """
-
         return self._make_request("/materials/all_substrate_ids")
 
     def get_surface_data(self, material_id, miller_index=None, inc_structures=False):
@@ -1433,6 +1433,7 @@ def get_surface_data(self, material_id, miller_index=None, inc_structures=False)
             of this specific plane will be returned.
             inc_structures (bool): Include final surface slab structures.
                 These are unnecessary for Wulff shape construction.
+
         Returns:
             Surface data for material. Energies are given in SI units (J/m^2).
         """
@@ -1457,6 +1458,7 @@ def get_wulff_shape(self, material_id):
 
         Args:
             material_id (str): Materials Project material_id, e.g. 'mp-123'.
+
         Returns:
             pymatgen.analysis.wulff.WulffShape
         """
@@ -1580,7 +1582,7 @@ def get_interface_reactions(
 
     def get_download_info(self, material_ids, task_types=None, file_patterns=None):
         """
-        get a list of URLs to retrieve raw VASP output files from the NoMaD repository
+        Get a list of URLs to retrieve raw VASP output files from the NoMaD repository
 
         Args:
             material_ids (list): list of material identifiers (mp-id's)
@@ -1762,23 +1764,16 @@ def __new__(cls, *args, **kwargs):
            *args: Pass through to either legacy or new MPRester.
            **kwargs: Pass through to either legacy or new MPRester.
         """
-
         if len(args) > 0:
             api_key = args[0]
         else:
-            api_key = kwargs.get("api_key", None)
-
-        if api_key is None:
-            api_key = SETTINGS.get("PMG_MAPI_KEY", "")
+            api_key = kwargs.get("api_key", SETTINGS.get("PMG_MAPI_KEY"))
             kwargs["api_key"] = api_key
 
         if not api_key:
             raise ValueError("Please supply an API key. See https://materialsproject.org/api for details.")
 
-        if len(api_key) == 32:
-            return _MPResterNew(*args, **kwargs)
-        else:
-            return _MPResterLegacy(*args, **kwargs)
+        return (_MPResterNew if len(api_key) == 32 else _MPResterLegacy)(*args, **kwargs)
 
 
 class MPRestError(Exception):

pymatgen/ext/tests/test_cod.py

@@ -11,12 +11,12 @@
 from pymatgen.ext.cod import COD
 
 try:
-    website_is_up = requests.get("https://www.crystallography.net").status_code == 200
+    website_down = requests.get("https://www.crystallography.net").status_code != 200
 except requests.exceptions.ConnectionError:
-    website_is_up = False
+    website_down = True
 
 
-@unittest.skipIf(not website_is_up, "www.crystallography.net is down.")
+@unittest.skipIf(website_down, "www.crystallography.net is down.")
 class CODTest(unittest.TestCase):
     _multiprocess_shared_ = True