Sync

.github/workflows/_install_opt_unit_deps.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+set -euo pipefail
+set -x
+
+# Use a custom bin directory for easier GitHub Actions caching
+BIN_DIR="${1:-$PWD/opt/bin}" && mkdir -p "$BIN_DIR"
+
+# Install BoltzTraP
+wget --no-verbose -O BoltzTraP.tar.bz2 https://owncloud.tuwien.ac.at/index.php/s/s2d55LYlZnioa3s/download
+tar -jxf BoltzTraP.tar.bz2
+cp boltztrap-1.2.5/src/{BoltzTraP,x_trans} "$BIN_DIR"
+
+# Install Vampire 5.0
+# TODO: Accepts self-signed cert (https://github.com/richard-evans/vampire/issues/122)
+wget --no-verbose --no-check-certificate https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
+tar -zxf vampire-5.0-linux.tar.gz && mv linux vampire-5.0
+cp vampire-5.0/vampire-serial "$BIN_DIR"
+
+# Install Voro++ and ZEO++
+wget --no-verbose http://www.zeoplusplus.org/zeo++-0.3.tar.gz
+tar -xzf zeo++-0.3.tar.gz
+make -C zeo++-0.3/voro++/src -s CFLAGS="-w"
+make -C zeo++-0.3 -s CFLAGS="-w"
+cp zeo++-0.3/voro++/src/voro++ "$BIN_DIR"
+cp zeo++-0.3/network "$BIN_DIR"
+
+# Install mcsqs (from ATAT)
+# TODO: cannot build on MacOS
+if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+  wget --no-verbose https://axelvandewalle.github.io/www-avdw/atat/atat3_50.tar.gz
+  tar -zxf atat3_50.tar.gz
+
+  # Replace `BINDIR` in makefile
+  sed -i "s|^BINDIR=.*|BINDIR=$BIN_DIR|" atat/makefile
+
+  sudo apt install csh -y -q
+  make -C atat && make -C atat install
+fi
+
+# Add to path
+echo "$BIN_DIR" >> "$GITHUB_PATH"

.github/workflows/lint.yml

@@ -22,8 +22,7 @@ jobs:
           cache-dependency-glob: "uv.lock"
       - name: Install dependencies
         run: |
-          uv sync --group lint
-          uv pip install -e .
+          uv sync
 
       - name: ruff
         run: |

.github/workflows/test.yml

@@ -21,7 +21,7 @@ jobs:
     if: github.repository == 'materialsproject/pymatgen'
     defaults:
       run:
-        shell: bash -l {0} # Enable conda/mamba env activation by reading bash profile
+        shell: bash -leo pipefail {0} # Enable mamba env activation by reading bash profile
     strategy:
       fail-fast: false
       matrix:
@@ -31,31 +31,29 @@ jobs:
         # newest version (currently 3.13) on ubuntu (to get complete coverage on unix).
         config:
           - os: windows-latest
-            python: "3.11"
+            python: "3.10"
             resolution: highest
-            extras: ci,optional,prototypes
+            extras: optional,prototypes
           - os: windows-latest
             python: "3.11"
             resolution: highest
-            extras: ci,prototypes,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
-          - os: ubuntu-latest
-            python: "3.13"
-            resolution: lowest-direct
-            extras: ci,prototypes,optional
+            extras: prototypes,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
           - os: macos-latest
             python: "3.12"
             resolution: lowest-direct
-            extras: ci,prototypes # test with only required dependencies installed
+            extras: prototypes # test with only required dependencies installed
+          - os: ubuntu-latest
+            python: "3.13"
+            resolution: lowest-direct
+            extras: prototypes,optional
 
         # 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:
-      MPLBACKEND: Agg  # non-interactive backend for matplotlib
-      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-      PYTHONWARNDEFAULTENCODING: "true"  # PEP 597: Enable optional EncodingWarning
+      OPT_BIN_DIR: ${{ github.workspace }}/opt/bin  # for optional Unix dependencies
     steps:
       - name: Check out repo
         uses: actions/checkout@v4
@@ -64,6 +62,7 @@ jobs:
         uses: mamba-org/setup-micromamba@main
         with:
           environment-name: pmg
+          cache-environment: true
           create-args: >-
             python=${{ matrix.config.python }}
 
@@ -79,48 +78,34 @@ jobs:
 
       - name: Install pymatgen and dependencies via uv
         run: |
-          micromamba activate pmg
-
           # Install from wheels to test the content
           uv build --wheel --no-build-logs
           WHEEL_FILE=$(ls dist/pymatgen*.whl)
-          uv pip install $WHEEL_FILE[${{matrix.config.extras}}] --resolution=${{matrix.config.resolution}}
+          uv pip install $WHEEL_FILE[${{matrix.config.extras}}] --group test \
+            --resolution=${{matrix.config.resolution}}
 
-      - name: Install DGL and MatGL specially on ubuntu.
-        if: matrix.config.os == 'ubuntu-latest' && matrix.config.python < '3.13'
-        run: |
-          micromamba activate pmg
-          pip install --upgrade dgl -f https://data.dgl.ai/wheels/torch-2.4/repo.html
-          pip install --upgrade matgl>=1.2.6
-          pip install torch==2.2.0 torchdata==0.7.1
-
-      - name: Install optional Ubuntu and macOS dependencies
+      - name: Restore cache for optional Ubuntu/MacOS dependencies
         if: matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-latest'
-        run: |
-          # Install BoltzTraP
-          wget -q -O BoltzTraP.tar.bz2 https://owncloud.tuwien.ac.at/index.php/s/s2d55LYlZnioa3s/download
-          tar -jxf BoltzTraP.tar.bz2 && realpath boltztrap-1.2.5/src/ >> $GITHUB_PATH
-
-          # Install Vampire 5.0
-          wget -q https://vampire.york.ac.uk/resources/release-5/vampire-5.0-linux.tar.gz
-          tar -zxf vampire-5.0-linux.tar.gz && mv linux vampire-5.0
-          realpath vampire-5.0/ >> $GITHUB_PATH
-
-          # Install Voro++ and ZEO++
-          wget -q http://www.zeoplusplus.org/zeo++-0.3.tar.gz && tar -xzf zeo++-0.3.tar.gz
+        id: optbin-cache
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.OPT_BIN_DIR }}
+          key: opt-bin-${{ runner.os }}-${{ hashFiles('.github/workflows/_install_opt_unit_deps.sh') }}
 
-          cd zeo++-0.3/voro++/src && make -s CFLAGS="-w" && realpath . >> $GITHUB_PATH && cd ../..
-          make -s CFLAGS="-w" && realpath . >> $GITHUB_PATH
+      - name: Build optional Ubuntu/MacOS dependencies (when cache misses)
+        if: (matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-latest') && steps.optbin-cache.outputs.cache-hit != 'true'
+        run: bash .github/workflows/_install_opt_unit_deps.sh "$OPT_BIN_DIR"
 
       - name: pytest split ${{ matrix.split }}
         env:
           MPLBACKEND: Agg  # non-interactive backend for matplotlib
           PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
           PMG_TEST_FILES_DIR: "${{ github.workspace }}/tests/files"
+          PYTHONWARNDEFAULTENCODING: "true"  # PEP 597: Enable optional EncodingWarning
         run: |
-          micromamba activate pmg
-
-          pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
+          pytest tests \
+            --splits 10 --group ${{ matrix.split }} \
+            --durations-path tests/files/.pytest-split-durations \
 
   trigger_atomate2_ci:
     needs: test
@@ -141,6 +126,7 @@ jobs:
             -d '{"event_type": "pymatgen-ci-trigger", "client_payload": {"pymatgen_ref": "${{ github.sha }}"}}'
 
   all_pass:
+    # This step is added to indicate all the tests have passed to make it easier to do auto-merge of PRs.
     needs: test
     runs-on: ubuntu-latest
     steps:

.pre-commit-config.yaml

@@ -8,24 +8,23 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.12.11
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.17.1
     hooks:
       - id: mypy
-        additional_dependencies: [numpy>=1.2.5]
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
@@ -37,7 +36,7 @@ repos:
         exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.6
+    rev: v0.16.7
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]
@@ -66,6 +65,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.401
+    rev: v1.1.404
     hooks:
       - id: pyright

ADMIN.md

@@ -1,40 +1,30 @@
 # Introduction
 
-This documentation provides a guide for `pymatgen` administrators. The following assumes you are using `miniconda`
-or Anaconda.
+This documentation provides a guide for `pymatgen` administrators.
 
 ## Releases
 
 The general procedure for releasing `pymatgen` comprises the following steps:
 
 1. Make sure all CI checks are green. We don't want to release known bugs.
 2. Update changelog.
-3. Run `invoke make-doc` to update the HTML docs.
+3. Run `uv run invoke make-doc` to update the HTML docs.
 4. Tag the latest commit with `git tag v<yyyy.mm.dd>`.
 5. Make a GitHub release with auto-generated release notes.
 6. Make sure the release action runs that publishes the new version to PyPI and conda-forge runs to completion.
 
-## Initial setup
-
-Pymatgen uses [invoke](https://pyinvoke.org) to automate releases.
-You will also need `sphinx` and `doc2dash`.
-
-```sh
-pip install --upgrade invoke sphinx
-```
-
 ## Doing the release
 
 First update the change log. The autogenerated change log is simply a list of commit messages since the last version. Make sure to edit the log for brevity and to attribute significant features to appropriate developers:
 
 ```sh
-invoke update-changelog
+uv run invoke update-changelog
 ```
 
 Then, do the release:
 
 ```sh
-invoke release
+uv run invoke release
 ```
 
-Double check that the releases are properly done on Pypi.
+Double check that the releases are properly done on PyPI.

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -131,9 +131,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 continue
     n_cols = 5
     n_lines = int(np.ceil(float(len(sep_plane_cgs)) / n_cols))
-    sep_plane_cgs_grid = []
-    for _ in range(n_lines):
-        sep_plane_cgs_grid.append([""] * n_cols)
+    sep_plane_cgs_grid = [[""] * n_cols for _ in range(n_lines)]
     for line_idx in range(n_lines):
         for col_idx in range(n_cols):
             ii = line_idx * n_cols + col_idx