Merge remote-tracking branch 'upstream/master' into dev

Author: Jingyang Wang

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.284
+    rev: v0.0.285
     hooks:
       - id: ruff
         args: [--fix]
@@ -26,7 +26,7 @@ repos:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.5.1
     hooks:
       - id: mypy
 

CONTRIBUTING.md

@@ -12,22 +12,26 @@ For developers interested in expanding `pymatgen` for their own purposes, we rec
 
 1. Fork the `pymatgen` GitHub repo, i.e., go to the main [`pymatgen` GitHub repo](https://github.com/materialsproject/pymatgen) and click fork to create a copy of the `pymatgen` code base on your own GitHub account.
 
-1. Install git on your local machine (if you don't already have it).
+1. Install `git` on your local machine (if you don't already have it).
 
 1. Clone *your forked repo* to your local machine. You will work mostly with your local repo and only publish changes when they are ready to be merged:
 
     ```sh
-    git clone git@github.com:YOURNAME/pymatgen
+    git clone https://github.com/<username>/pymatgen
     ```
 
-    Note that the entire Github repo is fairly large because of the presence of test files, but these are absolutely necessary for rigorous testing of the code.
+    Note that the entire Github repo is fairly large because of the presence of test files, but these are necessary for rigorous testing.
 
-1. It is highly recommended you install all the optional dependencies as well.
+1. Make a new branch for your contributions
+
+    ```sh
+    git checkout -b my-new-fix-or-feature # should be run from up-to-date master
+    ```
 
 1. Code (see [Coding Guidelines](#coding-guidelines)). Commit early and commit often. Keep your code up to date. You need to add the main repository to the list of your remotes.
 
     ```sh
-    git remote add upstream git://github.com/materialsproject/`pymatgen`
+    git remote add upstream https://github.com/materialsproject/pymatgen
     ```
 
     Make sure your repository is clean (no uncommitted changes) and is currently on the master branch. If not, commit or stash any changes and switch to the master.
@@ -75,6 +79,6 @@ Given that `pymatgen` is intended to be a long-term code base, we adopt very str
    ```
 
 1. **Python 3**. We only support Python 3.8+.
-1. **Documentation** is required for all modules, classes and methods. In particular, the method doc strings should make clear the arguments expected and the return values. For complex algorithms (e.g., an Ewald summation), a summary of the algorithm should be provided, and preferably with a link to a publication outlining the method in detail.
+1. **Documentation** is required for all modules, classes and methods. In particular, the method doc strings should make clear the arguments expected and the return values. For complex algorithms (e.g., an Ewald summation), a summary of the algorithm should be provided and preferably with a link to a publication outlining the method in detail.
 
 For the above, if in doubt, please refer to the core classes in `pymatgen` for examples of what is expected.

README.md

@@ -6,13 +6,17 @@ height="70">
   </picture>
 </h1>
 
+<h4 align="center">
+
 [![CI Status](https://github.com/materialsproject/pymatgen/actions/workflows/test.yml/badge.svg)](https://github.com/materialsproject/pymatgen/actions/workflows/test.yml)
 [![codecov](https://codecov.io/gh/materialsproject/pymatgen/branch/master/graph/badge.svg?token=XC47Un1LV2)](https://codecov.io/gh/materialsproject/pymatgen)
 [![PyPI Downloads](https://img.shields.io/pypi/dm/pymatgen?logo=pypi&logoColor=white&color=blue&label=PyPI)](https://pypi.org/project/pymatgen)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/pymatgen?logo=condaforge&color=blue&label=Conda)](https://anaconda.org/conda-forge/pymatgen)
 [![Requires Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 [![arXiv](https://img.shields.io/badge/J.ComMatSci-2012.10.028-blue)](https://doi.org/10.1016/j.commatsci.2012.10.028)
 
+</h4>
+
 Pymatgen (Python Materials Genomics) is a robust, open-source Python
 library for materials analysis. These are some of the main features:
 

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -121,16 +121,16 @@ def figure_fractions(self, weights_options: dict, morphing_factors: Sequence[flo
         fig_height = fig_height_cm / 2.54
 
         fig = plt.figure(num=1, figsize=(fig_width, fig_height))
-        subplot = fig.add_subplot(111)
+        ax = fig.add_subplot(111)
 
-        subplot.plot(
+        ax.plot(
             morphing_factors,
             fractions_initial_environment,
             "b-",
             label=self.initial_environment_symbol,
             linewidth=1.5,
         )
-        subplot.plot(
+        ax.plot(
             morphing_factors,
             fractions_final_environment,
             "g--",
@@ -301,16 +301,16 @@ def get_weights(self, weights_options):
         self_weight_max_csms_per_cn[ce1.split(":")[1]].append(params["self_weight_max_csm"])
 
     fig = plt.figure(1)
-    subplot = fig.add_subplot(111)
+    ax = fig.add_subplot(111)
 
     for idx, cn_pair in enumerate(all_cn_pairs):
         if len(self_weight_max_csms[cn_pair]) == 0:
             continue
-        subplot.plot(idx * np.ones_like(self_weight_max_csms[cn_pair]), self_weight_max_csms[cn_pair], "rx")
-        subplot.plot(idx * np.ones_like(delta_csm_mins[cn_pair]), delta_csm_mins[cn_pair], "b+")
+        ax.plot(idx * np.ones_like(self_weight_max_csms[cn_pair]), self_weight_max_csms[cn_pair], "rx")
+        ax.plot(idx * np.ones_like(delta_csm_mins[cn_pair]), delta_csm_mins[cn_pair], "b+")
 
-    subplot.set_xticks(range(len(all_cn_pairs)))
-    subplot.set_xticklabels(all_cn_pairs, rotation="vertical")
+    ax.set_xticks(range(len(all_cn_pairs)))
+    ax.set_xticklabels(all_cn_pairs, rotation="vertical")
     fig.savefig("self_delta_params.pdf")
 
     fig2 = plt.figure(2)

docs/conf.py

@@ -1,4 +1,3 @@
-"""
-This package provides the modules for performing large scale transformations on
+"""This package provides the modules for performing large scale transformations on
 a large number of structures.
 """

docs/contributing.md

@@ -17,16 +17,14 @@
 
 
 class AbstractStructureFilter(MSONable, metaclass=abc.ABCMeta):
-    """
-    AbstractStructureFilter that defines an API to perform testing of
+    """AbstractStructureFilter that defines an API to perform testing of
     Structures. Structures that return True to a test are retained during
     transmutation while those that return False are removed.
     """
 
     @abc.abstractmethod
     def test(self, structure: Structure):
-        """
-        Method to execute the test.
+        """Method to execute the test.
 
         Args:
             structure (Structure): Input structure to test
@@ -39,8 +37,7 @@ def test(self, structure: Structure):
 
 
 class ContainsSpecieFilter(AbstractStructureFilter):
-    """
-    Filter for structures containing certain elements or species.
+    """Filter for structures containing certain elements or species.
     By default compares by atomic number.
     """
 
@@ -60,8 +57,7 @@ def __init__(self, species, strict_compare=False, AND=True, exclude=False):
         self._exclude = exclude
 
     def test(self, structure: Structure):
-        """
-        Method to execute the test.
+        """Method to execute the test.
 
         Returns: True if structure do not contain specified species.
         """
@@ -121,8 +117,7 @@ def from_dict(cls, dct):
 
 
 class SpecieProximityFilter(AbstractStructureFilter):
-    """
-    This filter removes structures that have certain species that are too close
+    """This filter removes structures that have certain species that are too close
     together.
     """
 
@@ -139,8 +134,7 @@ def __init__(self, specie_and_min_dist_dict):
         self.specie_and_min_dist = {get_el_sp(k): v for k, v in specie_and_min_dist_dict.items()}
 
     def test(self, structure: Structure):
-        """
-        Method to execute the test.
+        """Method to execute the test.
 
         Args:
             structure (Structure): Input structure to test
@@ -185,8 +179,7 @@ class RemoveDuplicatesFilter(AbstractStructureFilter):
     """This filter removes exact duplicate structures from the transmuter."""
 
     def __init__(self, structure_matcher: dict | StructureMatcher | None = None, symprec: float | None = None) -> None:
-        """
-        Remove duplicate structures based on the structure matcher
+        """Remove duplicate structures based on the structure matcher
         and symmetry (if symprec is given).
 
         Args:
@@ -235,8 +228,7 @@ class RemoveExistingFilter(AbstractStructureFilter):
     """This filter removes structures existing in a given list from the transmuter."""
 
     def __init__(self, existing_structures, structure_matcher=None, symprec=None):
-        """
-        Remove existing structures based on the structure matcher
+        """Remove existing structures based on the structure matcher
         and symmetry (if symprec is given).
 
         Args:
@@ -256,8 +248,7 @@ def __init__(self, existing_structures, structure_matcher=None, symprec=None):
             self.structure_matcher = structure_matcher or StructureMatcher(comparator=ElementComparator())
 
     def test(self, structure: Structure):
-        """
-        Method to execute the test.
+        """Method to execute the test.
 
         Args:
             structure (Structure): Input structure to test
@@ -291,8 +282,7 @@ def as_dict(self):
 
 
 class ChargeBalanceFilter(AbstractStructureFilter):
-    """
-    This filter removes structures that are not charge balanced from the
+    """This filter removes structures that are not charge balanced from the
     transmuter. This only works if the structure is oxidation state
     decorated, as structures with only elemental sites are automatically
     assumed to have net charge of 0.
@@ -302,8 +292,7 @@ def __init__(self):
         """No args required."""
 
     def test(self, structure: Structure):
-        """
-        Method to execute the test.
+        """Method to execute the test.
 
         Args:
             structure (Structure): Input structure to test
@@ -314,8 +303,7 @@ def test(self, structure: Structure):
 
 
 class SpeciesMaxDistFilter(AbstractStructureFilter):
-    """
-    This filter removes structures that do have two particular species that are
+    """This filter removes structures that do have two particular species that are
     not nearest neighbors by a predefined max_dist. For instance, if you are
     analyzing Li battery materials, you would expect that each Li+ would be
     nearest neighbor to lower oxidation state transition metal for
@@ -336,8 +324,7 @@ def __init__(self, sp1, sp2, max_dist):
         self.max_dist = max_dist
 
     def test(self, structure: Structure):
-        """
-        Method to execute the test.
+        """Method to execute the test.
 
         Args:
             structure (Structure): Input structure to test