Merge branch 'master' into master

.github/workflows/lint.yml

@@ -18,15 +18,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.x'
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff 'mypy<1.12' pyright
+          pip install --upgrade ruff mypy pyright
 
       - name: ruff
         run: |
-          ruff --version
           ruff check .
           ruff format --check .
 

.pre-commit-config.yaml

@@ -8,29 +8,29 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.12.0
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
+        stages: [pre-commit, commit-msg]
         exclude_types: [html]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
         exclude: src/pymatgen/analysis/aflow_prototypes.json
@@ -43,12 +43,12 @@ repos:
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.0
     hooks:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.41.0
+    rev: v0.42.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -65,6 +65,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.379
+    rev: v1.1.384
     hooks:
       - id: pyright

CONTRIBUTING.md

@@ -69,6 +69,14 @@ For developers interested in expanding `pymatgen` for their own purposes, we rec
 Given that `pymatgen` is intended to be a long-term code base, we adopt very strict quality control and coding guidelines for all contributions to `pymatgen`. The following must be satisfied for your contributions to be accepted into `pymatgen`.
 
 1. **Unit tests** are required for all new modules and methods. The only way to minimize code regression is to ensure that all code is well-tested. Untested contributions will not be accepted.
+   To run the testsuite in you repository follow these steps
+
+   ```sh
+   cd path/to/repo
+   pip install -e .  # install the package in your environment as "editable" == dev package
+   PMG_TEST_FILES_DIR=$(pwd)/tests/files pytest tests  # run the test suite providing the path for the datafiles
+   ```
+
 1. **Python PEP 8** [code style](https://python.org/dev/peps/pep-0008). We allow a few exceptions when they are well-justified (e.g., Element's atomic number is given a variable name of capital Z, in line with accepted scientific convention), but generally, PEP 8 must be observed. Code style will be automatically checked for all PRs and must pass before any PR is merged. To aid you, you can install and run the same set of formatters and linters that will run in CI using
 
    ```sh

pyproject.toml

@@ -21,7 +21,7 @@ Python Materials Genomics is a robust materials analysis code that defines core
 and molecules with support for many electronic structure codes. It is currently the core analysis code powering the
 Materials Project (https://materialsproject.org)."""
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.13"
 keywords = [
     "ABINIT",
     "VASP",
@@ -57,7 +57,7 @@ dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
     "monty>=2024.7.29",
-    "networkx>=2.2",
+    "networkx>=2.7",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=4.5.0",

requirements.txt

@@ -1,88 +1,88 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile pyproject.toml -o requirements.txt
-certifi==2024.7.4
-    # via requests
+certifi==2024.8.30
+# via requests
 charset-normalizer==3.3.2
-    # via requests
+# via requests
 contourpy==1.2.1
-    # via matplotlib
+# via matplotlib
 cycler==0.12.1
-    # via matplotlib
+# via matplotlib
 fonttools==4.53.0
-    # via matplotlib
+# via matplotlib
 idna==3.7
-    # via requests
+# via requests
 joblib==1.4.2
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 kiwisolver==1.4.5
-    # via matplotlib
+# via matplotlib
 latexcodec==3.0.0
-    # via pybtex
-matplotlib==3.9.0
-    # via pymatgen (pyproject.toml)
-monty==2024.7.30
-    # via pymatgen (pyproject.toml)
+# via pybtex
+matplotlib==3.9.2
+# via pymatgen (pyproject.toml)
+monty==2024.10.21
+# via pymatgen (pyproject.toml)
 mpmath==1.3.0
-    # via sympy
+# via sympy
 networkx==3.3
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 numpy==2.0.0
-    # via
-    #   pymatgen (pyproject.toml)
-    #   contourpy
-    #   matplotlib
-    #   pandas
-    #   scipy
-    #   spglib
+# via
+#   pymatgen (pyproject.toml)
+#   contourpy
+#   matplotlib
+#   pandas
+#   scipy
+#   spglib
 packaging==24.1
-    # via
-    #   matplotlib
-    #   plotly
+# via
+#   matplotlib
+#   plotly
 palettable==3.3.3
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 pandas==2.2.2
-    # via pymatgen (pyproject.toml)
-pillow==10.3.0
-    # via matplotlib
+# via pymatgen (pyproject.toml)
+pillow==11.0.0
+# via matplotlib
 plotly==5.22.0
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 pybtex==0.24.0
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 pyparsing==3.1.2
-    # via matplotlib
+# via matplotlib
 python-dateutil==2.9.0.post0
-    # via
-    #   matplotlib
-    #   pandas
+# via
+#   matplotlib
+#   pandas
 pytz==2024.1
-    # via pandas
-pyyaml==6.0.1
-    # via pybtex
+# via pandas
+pyyaml==6.0.2
+# via pybtex
 requests==2.32.3
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 ruamel-yaml==0.18.6
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 ruamel-yaml-clib==0.2.8
-    # via ruamel-yaml
+# via ruamel-yaml
 scipy==1.13.1
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 six==1.16.0
-    # via
-    #   pybtex
-    #   python-dateutil
+# via
+#   pybtex
+#   python-dateutil
 spglib==2.5.0
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 sympy==1.12.1
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 tabulate==0.9.0
-    # via pymatgen (pyproject.toml)
+# via pymatgen (pyproject.toml)
 tenacity==8.4.1
-    # via plotly
-tqdm==4.66.4
-    # via pymatgen (pyproject.toml)
+# via plotly
+tqdm==4.66.5
+# via pymatgen (pyproject.toml)
 tzdata==2024.1
-    # via pandas
+# via pandas
 uncertainties==3.2.1
-    # via pymatgen (pyproject.toml)
-urllib3==2.2.2
-    # via requests
+# via pymatgen (pyproject.toml)
+urllib3==2.2.3
+# via requests