Merge branch 'master' of https://github.com/materialsproject/pymatgen

.github/release.yml

@@ -2,6 +2,8 @@ changelog:
   exclude:
     authors: [dependabot, github-actions, pre-commit-ci]
   categories:
+    - title: 💥 Breaking Changes
+      labels: [breaking]
     - title: 🎉 New Features
       labels: [feature]
     - title: 🐛 Bug Fixes
@@ -20,8 +22,6 @@ changelog:
       labels: [refactor]
     - title: 🧪 Tests
       labels: [tests]
-    - title: 💥 Breaking Changes
-      labels: [breaking]
     - title: 🔒 Security Fixes
       labels: [security]
     - title: 🏥 Package Health

.github/workflows/test.yml

@@ -25,22 +25,29 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # pytest-split automatically distributes work load so parallel jobs finish in similar time
-        os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.12"]
-        split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-        # include/exclude is meant to maximize CI coverage of different platforms and python
-        # versions while minimizing the total number of jobs. We run all pytest splits with the
-        # oldest supported python version (currently 3.9) on windows (seems most likely to surface
-        # errors) and with newest version (currently 3.12) on ubuntu (to get complete and speedy
-        # coverage on unix). We ignore mac-os, which is assumed to be similar to ubuntu.
-        exclude:
+        # maximize CI coverage of different platforms and python versions while minimizing the
+        # total number of jobs. We run all pytest splits with the oldest supported python
+        # version (currently 3.9) on windows (seems most likely to surface errors) and with
+        # newest version (currently 3.12) on ubuntu (to get complete coverage on unix).
+        config:
           - os: windows-latest
-            python-version: "3.12"
+            python: "3.9"
+            resolution: highest
+            extras: ci,optional
           - os: ubuntu-latest
-            python-version: "3.9"
+            python: "3.12"
+            resolution: lowest-direct
+            extras: ci,optional
+          - os: macos-latest
+            python: "3.10"
+            resolution: lowest-direct
+            extras: ci # test with only required dependencies installed
 
-    runs-on: ${{ matrix.os }}
+        # pytest-split automatically distributes work load so parallel jobs finish in similar time
+        # update durations file with `pytest --store-durations --durations-path tests/files/.pytest-split-durations`
+        split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+
+    runs-on: ${{ matrix.config.os }}
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
@@ -55,13 +62,13 @@ jobs:
 
       - name: Create mamba environment
         run: |
-          micromamba create -n pmg python=${{ matrix.python-version }} --yes
+          micromamba create -n pmg python=${{ matrix.config.python }} --yes
 
       - name: Install uv
         run: micromamba run -n pmg pip install uv
 
       - name: Install ubuntu-only conda dependencies
-        if: matrix.os == 'ubuntu-latest'
+        if: matrix.config.os == 'ubuntu-latest'
         run: |
           micromamba install -n pmg -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
 
@@ -73,11 +80,7 @@ jobs:
           pip install torch
 
           uv pip install numpy cython
-
-          uv pip install --editable '.[dev,optional]'
-
-          # TODO remove next line installing ase from main branch when FrechetCellFilter is released
-          uv pip install --upgrade 'git+https://gitlab.com/ase/ase'
+          uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 
       - name: pytest split ${{ matrix.split }}
         run: |

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.8
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -27,7 +27,7 @@ repos:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
@@ -47,7 +47,7 @@ repos:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.40.0
+    rev: v0.41.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -64,6 +64,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.361
+    rev: v1.1.366
     hooks:
       - id: pyright

dev_scripts/regen_libxcfunc.py

@@ -2,7 +2,7 @@
 """
 This script regenerates the enum values in pymatgen.core.libxc_func.py.
 It requires in input the path of the `libxc_docs.txt` file contained in libxc/src
-The script parses this file, creates a new json file inside pymatgen.core
+The script parses this file, creates a new JSON file inside pymatgen.core
 and update the enum values declared in LibxcFunc.
 The script must be executed inside pymatgen/dev_scripts.
 """
@@ -16,10 +16,7 @@
 
 
 def parse_libxc_docs(path):
-    """
-    Parse libxc_docs.txt file, return dictionary with mapping:
-    libxc_id --> info_dict.
-    """
+    """Parse libxc_docs.txt file, return dictionary {libxc_id: info_dict}."""
 
     def parse_section(section):
         dct = {}
@@ -46,7 +43,7 @@ def parse_section(section):
 
 
 def write_libxc_docs_json(xc_funcs, json_path):
-    """Write json file with libxc metadata to path jpath."""
+    """Write JSON file with libxc metadata to path jpath."""
     xc_funcs = deepcopy(xc_funcs)
 
     # Remove XC_FAMILY from Family and XC_ from Kind to make strings more human-readable.
@@ -85,7 +82,7 @@ def main():
 
     xc_funcs = parse_libxc_docs(path)
 
-    # Generate new json file in pycore
+    # Generate new JSON file in pycore
     pmg_core = os.path.abspath("../pymatgen/core/")
     json_path = f"{pmg_core}/libxc_docs.json"
     write_libxc_docs_json(xc_funcs, json_path)

dev_scripts/update_pt_data.py

@@ -82,7 +82,7 @@ def parse_ionic_radii():
                 ionic_radii[int(header[tok_idx])] = float(match.group(1))
 
         if el in data:
-            data[el]["Ionic_radii" + suffix] = ionic_radii
+            data[el][f"Ionic_radii{suffix}"] = ionic_radii
             if suffix == "_hs":
                 data[el]["Ionic_radii"] = ionic_radii
         else: