Fix CI (#2767)

* fix typos

* fix AttributeError: 'range' object has no attribute 'remove' in dev_scripts/chemenv/equivalent_indices.py

* add missing doc strings in dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

* fix TypeError: Object of type ndarray is not JSON serializable

in         with open("tmp_dir/lse.json", "w") as f:
>           json.dump(lse.as_dict(), f)

pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py:81:

dev_scripts/chemenv/equivalent_indices.py

@@ -38,7 +38,7 @@
             for i2 in perp_plane[i0]:
                 # 3. point opposite to point 2.
                 i3 = opposite_points[i2]
-                remaining = range(6)
+                remaining = list(range(6))
                 remaining.remove(i0)
                 remaining.remove(i1)
                 remaining.remove(i2)

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -14,6 +14,7 @@
 
 import copy
 import json
+from typing import Sequence
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -41,6 +42,10 @@
 
 
 class CoordinationEnvironmentMorphing:
+    """
+    Class to morph a coordination environment into another one.
+    """
+
     def __init__(self, initial_environment_symbol, expected_final_environment_symbol, morphing_description):
         self.initial_environment_symbol = initial_environment_symbol
         self.expected_final_environment_symbol = expected_final_environment_symbol
@@ -50,6 +55,17 @@ def __init__(self, initial_environment_symbol, expected_final_environment_symbol
 
     @classmethod
     def simple_expansion(cls, initial_environment_symbol, expected_final_environment_symbol, neighbors_indices):
+        """
+        Simple expansion of a coordination environment.
+
+        Args:
+            initial_environment_symbol (str): The initial coordination environment symbol.
+            expected_final_environment_symbol (str): The expected final coordination environment symbol.
+            neighbors_indices (list): The indices of the neighbors to be expanded.
+
+        Returns:
+            CoordinationEnvironmentMorphing
+        """
         morphing_description = [
             {"ineighbor": i_nb, "site_type": "neighbor", "expansion_origin": "central_site"}
             for i_nb in neighbors_indices
@@ -60,7 +76,14 @@ def simple_expansion(cls, initial_environment_symbol, expected_final_environment
             morphing_description=morphing_description,
         )
 
-    def figure_fractions(self, weights_options, morphing_factors=None):
+    def figure_fractions(self, weights_options: dict, morphing_factors: Sequence[float] = None) -> None:
+        """
+        Plot the fractions of the initial and final coordination environments as a function of the morphing factor.
+
+        Args:
+            weights_options (dict): The weights options.
+            morphing_factors (list): The morphing factors.
+        """
         if morphing_factors is None:
             morphing_factors = np.linspace(1.0, 2.0, 21)
         # Set up the local geometry finder
@@ -69,7 +92,7 @@ def figure_fractions(self, weights_options, morphing_factors=None):
         # Set up the weights for the MultiWeights strategy
         weights = self.get_weights(weights_options)
         # Set up the strategy
-        strat = MultiWeightsChemenvStrategy(
+        strategy = MultiWeightsChemenvStrategy(
             dist_ang_area_weight=weights["DistAngArea"],
             self_csm_weight=weights["SelfCSM"],
             delta_csm_weight=weights["DeltaCSM"],
@@ -88,8 +111,8 @@ def figure_fractions(self, weights_options, morphing_factors=None):
             # Get the StructureEnvironments
             lgf.setup_structure(structure=struct)
             se = lgf.compute_structure_environments(only_indices=[0], valences=fake_valences)
-            strat.set_structure_environments(structure_environments=se)
-            result = strat.get_site_coordination_environments_fractions(
+            strategy.set_structure_environments(structure_environments=se)
+            result = strategy.get_site_coordination_environments_fractions(
                 site=se.structure[0], isite=0, return_strategy_dict_info=True, return_all=True
             )
             for res in result:

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

@@ -78,12 +78,10 @@ def test_read_write_structure_environments(self):
         )
 
         with open("tmp_dir/lse.json", "w") as f:
-            json.dump(lse.as_dict(), f)
+            json.dump(lse.as_dict(), f, default=lambda o: o.tolist() if hasattr(o, "tolist") else o)
 
         with open("tmp_dir/lse.json") as f:
-            dd = json.load(f)
-
-        lse2 = LightStructureEnvironments.from_dict(dd)
+            lse2 = LightStructureEnvironments.from_dict(json.load(f))
 
         assert lse == lse2
 

pymatgen/analysis/tests/test_functional_groups.py

@@ -34,15 +34,15 @@ def setUp(self):
 
         self.file = os.path.join(test_dir, "func_group_test.mol")
         self.mol = Molecule.from_file(self.file)
-        self.strat = OpenBabelNN()
-        self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strat)
+        self.strategy = OpenBabelNN()
+        self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strategy)
         self.extractor = FunctionalGroupExtractor(self.mg)
 
     def tearDown(self):
         warnings.simplefilter("default")
         del self.extractor
         del self.mg
-        del self.strat
+        del self.strategy
         del self.mol
         del self.file
 

pymatgen/io/qchem/inputs.py

@@ -982,8 +982,8 @@ def read_pcm_nonels(string: str) -> dict:
         pcm_nonels_table = read_table_pattern(string, header_pattern=header, row_pattern=row, footer_pattern=footer)
         if not pcm_nonels_table:
             print(
-                "No valid $pcm_nonels inputs found. Note that there should be no '=' \
-                 chracters in $pcm_nonels input lines."
+                "No valid $pcm_nonels inputs found. Note that there should be no '=' "
+                "characters in $pcm_nonels input lines."
             )
             return {}
 

pymatgen/io/qchem/sets.py

@@ -179,7 +179,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.
@@ -583,7 +583,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.
@@ -712,7 +712,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.
@@ -834,7 +834,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.
@@ -953,7 +953,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.
@@ -1069,7 +1069,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.
@@ -1205,7 +1205,7 @@ def __init__(
                 Other types of PCM calculations (e.g., IEF-PCM, SS(V)PE, etc.) may be requested by passing
                 custom keywords to overwrite_inputs, e.g.
                 overwrite_inputs = {"pcm": {"theory": "ssvpe"}}
-                Refer to the QChem manual for further details on the models availale.
+                Refer to the QChem manual for further details on the models available.
 
                 **Note that only one of pcm_dielectric, isosvp_dielectric, smd_solvent, or cmirs_solvent may be set.**
             isosvp_dielectric (float): Dielectric constant to use for isodensity SS(V)PE implicit solvation model.