merge master

.github/workflows/issue-metrics.yml

@@ -26,7 +26,7 @@ jobs:
           # Calculate the last day of the previous month
           last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
 
-          #Set an environment variable with the date range
+          # Set an environment variable with the date range
           echo "$first_day..$last_day"
           echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
 

.github/workflows/lint.yml

@@ -26,7 +26,6 @@ jobs:
 
       - name: ruff
         run: |
-          ruff --version
           ruff check .
           ruff format --check .
 

.github/workflows/release.yml

@@ -1,4 +1,5 @@
-name: Release # makes PyPI releases
+# Make PyPI releases
+name: Release
 
 on:
   release:
@@ -26,12 +27,12 @@ jobs:
       - name: Check out repo
         uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        name: Install Python
+      - name: Install Python
+        uses: actions/setup-python@v5
         with:
           python-version: "3.13"
 
-      - name: Build sdist
+      - name: Build source distribution
         run: |
           pip install build
           python -m build --sdist
@@ -65,8 +66,11 @@ jobs:
   release:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pymatgen
     permissions:
-      # For pypi trusted publishing
+      # For PyPI trusted publishing
       id-token: write
     steps:
       - name: Set up Python
@@ -81,9 +85,8 @@ jobs:
           merge-multiple: true
           path: dist
 
-      - name: Publish to PyPi or TestPyPI
+      - name: Publish to PyPI or TestPyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           skip-existing: true
           verbose: true
-          repository-url: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.task == 'test-release' && 'https://test.pypi.org/legacy/' || '' }}

.github/workflows/test.yml

@@ -55,7 +55,7 @@ jobs:
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-      PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files
+      MPLBACKEND: Agg  # non-interactive backend for matplotlib
 
     steps:
       - name: Check out repo
@@ -80,7 +80,12 @@ jobs:
 
           pip install uv
 
-          uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
+          # Install from wheels to test the content
+          uv pip install build
+          python -m build --wheel
+
+          uv pip install dist/*.whl
+          uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
@@ -97,6 +102,8 @@ jobs:
           echo "$(realpath vampire-5.0/)" >> $GITHUB_PATH
 
       - name: pytest split ${{ matrix.split }}
+        env:
+          PMG_TEST_FILES_DIR: "${{ github.workspace }}/tests/files"
         run: |
           micromamba activate pmg
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

.pre-commit-config.yaml

@@ -8,29 +8,29 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.7.2
     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: v1.13.0
     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: 1.19.1
     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
@@ -59,12 +59,12 @@ repos:
         args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.0
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.379
+    rev: v1.1.387
     hooks:
       - id: pyright

CONTRIBUTING.md

@@ -10,25 +10,29 @@ For developers interested in expanding `pymatgen` for their own purposes, we rec
 
 1. Create a free GitHub account (if you don't already have one) and perform the necessary setup (e.g., install SSH keys etc.).
 
-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.
+2. 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 to your own GitHub account.
 
-1. Install `git` on your local machine (if you don't already have it).
+3. Install `git` on your local machine (if you haven't already).
 
-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:
+4. 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 https://github.com/<username>/pymatgen
+
+    # (Alternative/Much Faster) If you don't need a full commit history/other branches
+    # git clone --depth 1 https://github.com/<username>/pymatgen
+    # git pull --unshallow  # if you need the complete repo at some point
     ```
 
     Note that the entire Github repo is fairly large because of the presence of test files, but these are necessary for rigorous testing.
 
-1. Make a new branch for your contributions
+5. 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.
+6. 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 https://github.com/materialsproject/pymatgen
@@ -48,19 +52,19 @@ For developers interested in expanding `pymatgen` for their own purposes, we rec
 
     Remember, pull is a combination of the commands fetch and merge, so there may be merge conflicts to be manually resolved.
 
-1. Publish your contributions. Assuming that you now have a couple of commits that you would like to contribute to the main repository. Please follow the following steps:
+7. Publish your contributions. Assuming that you now have a couple of commits that you would like to contribute to the main repository. Please follow the following steps:
 
     1. If your change is based on a relatively old state of the main repository, then you should probably bring your repository up-to-date first to see if the change is not creating any merge conflicts.
 
-    1. Check that everything compiles cleanly and passes all tests. The `pymatgen` repo comes with a complete set of tests for all modules. If you have written new modules or methods, you must write tests for the new code as well (see [Coding Guidelines](#coding-guidelines)). Install and run `pytest` in your local repo directory and fix all errors before continuing further.
+    2. Check that everything compiles cleanly and passes all tests. The `pymatgen` repo comes with a complete set of tests for all modules. If you have written new modules or methods, you must write tests for the new code as well (see [Coding Guidelines](#coding-guidelines)). Install and run `pytest` in your local repo directory and fix all errors before continuing further.
 
-    1. If everything is ok, publish the commits to your GitHub repository.
+    3. If everything is ok, publish the commits to your GitHub repository:
 
     ```sh
     git push origin master
     ```
 
-1. Now that your commit is published, it doesn't mean that it has already been merged into the main repository. You should issue a merge request to `pymatgen` maintainers. They will pull your commits and run their own tests before releasing.
+8. Now that your commit is published, it doesn't mean that it has already been merged into the main repository. You should issue a merge request to `pymatgen` maintainers. They will pull your commits and run their own tests before releasing.
 
 "Work-in-progress" pull requests are encouraged, especially if this is your first time contributing to `pymatgen`, and the maintainers will be happy to help or provide code review as necessary. Put "\[WIP\]" in the title of your pull request to indicate it's not ready to be merged.
 
@@ -69,16 +73,30 @@ 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.
-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
+   To run the testsuite in you repository follow these steps:
+
+   ```sh
+   cd path/to/repo
+
+   # Option One (Recommended): Install in editable mode
+   pip install -e '.[ci]'  # or more optional dependencies
+   pytest tests
+
+   # Option Two: Use environment variable PMG_TEST_FILES_DIR
+   pip install '.[ci]'
+   PMG_TEST_FILES_DIR=$(pwd)/tests/files pytest tests  # run the test suite providing the path for the test files
+   ```
+
+2. **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 should 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
    pre-commit install  # ensures linters are run prior to all future commits
    pre-commit run --files path/to/changed/files  # ensure your current uncommitted changes don't offend linters
    # or
-    pre-commit run --all-files  # ensure your entire codebase passes linters
+   pre-commit run --all-files  # ensure your entire codebase passes linters
    ```
 
-1. **Python 3**. We only support Python 3.10+.
-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.
+3. **Python 3**. We only support Python 3.10+.
+4. **Documentation** is required for all modules, classes and methods. We prefer [Google Style Docstrings](https://www.sphinx-doc.org/en/master/usage/extensions/example_google.html). 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.

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -46,7 +46,8 @@
         perms_on_file = f"Permutations on file in this algorithm ({len(sep_plane_algo._permutations)}) "
         print(f"{perms_on_file}\n{sep_plane_algo._permutations}")
         permutations = sep_plane_algo.safe_separation_permutations(
-            ordered_plane=sep_plane_algo.ordered_plane, ordered_point_groups=sep_plane_algo.ordered_point_groups
+            ordered_plane=sep_plane_algo.ordered_plane,
+            ordered_point_groups=sep_plane_algo.ordered_point_groups,
         )
 
         sep_plane_algo._permutations = permutations
@@ -56,7 +57,10 @@
         lgf = LocalGeometryFinder()
         lgf.setup_parameters(structure_refinement=lgf.STRUCTURE_REFINEMENT_NONE)
         lgf.setup_test_perfect_environment(
-            cg_symbol, randomness=True, indices=range(cg.coordination_number), max_random_dist=0.05
+            cg_symbol,
+            randomness=True,
+            indices=range(cg.coordination_number),
+            max_random_dist=0.05,
         )
 
         lgf.perfect_geometry = AbstractGeometry.from_cg(cg=cg)
@@ -65,27 +69,40 @@
         local_plane = None
         found = False
         for n_points in range(
-            sep_plane_algo.minimum_number_of_points, min(sep_plane_algo.maximum_number_of_points, 4) + 1
+            sep_plane_algo.minimum_number_of_points,
+            min(sep_plane_algo.maximum_number_of_points, 4) + 1,
         ):
             if found:
                 break
             for ipoints in itertools.combinations(sep_plane_algo.plane_points, n_points):
                 points_combination = [lgf.local_geometry.coords[ipoint] for ipoint in ipoints]
                 if n_points == 2:
                     if collinear(
-                        points_combination[0], points_combination[1], lgf.local_geometry.central_site, tolerance=0.25
+                        points_combination[0],
+                        points_combination[1],
+                        lgf.local_geometry.central_site,
+                        tolerance=0.25,
                     ):
                         continue
                     local_plane = Plane.from_3points(
-                        points_combination[0], points_combination[1], lgf.local_geometry.central_site
+                        points_combination[0],
+                        points_combination[1],
+                        lgf.local_geometry.central_site,
                     )
                     found = True
                     break
                 elif n_points == 3:
-                    if collinear(points_combination[0], points_combination[1], points_combination[2], tolerance=0.25):
+                    if collinear(
+                        points_combination[0],
+                        points_combination[1],
+                        points_combination[2],
+                        tolerance=0.25,
+                    ):
                         continue
                     local_plane = Plane.from_3points(
-                        points_combination[0], points_combination[1], points_combination[2]
+                        points_combination[0],
+                        points_combination[1],
+                        points_combination[2],
                     )
                     found = True
                     break
@@ -123,7 +140,7 @@
         for icsm, csm in enumerate(csms):
             found = False
             for csm2 in csms_with_recorded_permutation:
-                if np.isclose(csm, csm2, rtol=0.0, atol=1.0e-6):
+                if np.isclose(csm, csm2, rtol=0.0, atol=1e-6):
                     found = True
                     break
             if not found:

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -167,7 +167,10 @@ def random_permutations_iterator(initial_permutation, n_permutations):
 
         # Setup the random environment
         lgf.setup_test_perfect_environment(
-            cg_symbol, randomness=True, indices=range(cg.coordination_number), max_random_dist=0.05
+            cg_symbol,
+            randomness=True,
+            indices=range(cg.coordination_number),
+            max_random_dist=0.05,
         )
         lgf.perfect_geometry = AbstractGeometry.from_cg(cg=cg)
         points_perfect = lgf.perfect_geometry.points_wcs_ctwcc()
@@ -201,7 +204,8 @@ def random_permutations_iterator(initial_permutation, n_permutations):
 
             # Setup of safe permutations
             permutations = algo.safe_separation_permutations(
-                ordered_plane=algo.ordered_plane, ordered_point_groups=algo.ordered_point_groups
+                ordered_plane=algo.ordered_plane,
+                ordered_point_groups=algo.ordered_point_groups,
             )
             algo._permutations = permutations
             print(f"Safe permutations found ({len(permutations)})")
@@ -234,7 +238,10 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 )
 
                 sym_measures = [c["symmetry_measure"] for c in csms]
-                prt1(string="Continuous symmetry measures", printing_volume=printing_volume)
+                prt1(
+                    string="Continuous symmetry measures",
+                    printing_volume=printing_volume,
+                )
                 prt1(string=sym_measures, printing_volume=printing_volume)
                 csms_with_recorded_permutation: list = []
                 explicit_permutations = []
@@ -345,7 +352,11 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 )
                 # Setup of the local and perfect geometries
                 lgf.setup_test_perfect_environment(
-                    cg_symbol, indices=indices_perm, randomness=True, max_random_dist=0.02, random_rotation=True
+                    cg_symbol,
+                    indices=indices_perm,
+                    randomness=True,
+                    max_random_dist=0.02,
+                    random_rotation=True,
                 )
                 lgf.perfect_geometry = AbstractGeometry.from_cg(cg=cg)
                 points_perfect = lgf.perfect_geometry.points_wcs_ctwcc()

dev_scripts/chemenv/plane_multiplicity.py

@@ -20,7 +20,20 @@
 
     # I:12
     if cg_symbol == "I:12":
-        opposite_points = {0: 3, 1: 2, 2: 1, 3: 0, 4: 7, 5: 6, 6: 5, 7: 4, 8: 11, 9: 10, 10: 9, 11: 8}
+        opposite_points = {
+            0: 3,
+            1: 2,
+            2: 1,
+            3: 0,
+            4: 7,
+            5: 6,
+            6: 5,
+            7: 4,
+            8: 11,
+            9: 10,
+            10: 9,
+            11: 8,
+        }
         edges = cg._edges
         for edge in edges:
             opposite_edge = [opposite_points[edge[0]], opposite_points[edge[1]]]