Merge branch 'master' into fix_icohp

Signed-off-by: Katharina Ueltzen <[email protected]>

Author: kaueltzen

.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/jekyll-gh-pages.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup Pages
         uses: actions/configure-pages@v5
@@ -36,7 +36,7 @@ jobs:
           destination: ./_site
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
 
   deploy:
     environment:

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Linting
+name: Lint
 
 on:
   push:
@@ -13,24 +13,23 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv with python version.
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: '3.x'
+          python-version: "3.13"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff mypy pyright
+          uv sync
 
       - name: ruff
         run: |
-          ruff check .
-          ruff format --check .
-
-      - name: mypy
-        run: mypy src
+          uv run ruff check .
+          uv run ruff format --check .
 
       - name: pyright
-        run: pyright
+        run: uv run pyright src

.github/workflows/release.yml

@@ -25,12 +25,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Install Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.14"
 
       - name: Build source distribution
         run: |
@@ -39,21 +39,22 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
+          name: dist-sdist
           path: dist/*.tar.gz
 
   build_wheels:
     needs: test
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
-        python-version: ["310", "311", "312"]
+        os: [ubuntu-latest, macos-latest, macos-13, windows-latest, ubuntu-24.04-arm]
+        python-version: ["310", "311", "312", "313", "314"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v3.2.0
         env:
           CIBW_BUILD: cp${{ matrix.python-version }}-*
 
@@ -74,12 +75,12 @@ jobs:
       id-token: write
     steps:
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
-          python-version: "3.12"
+          python-version: "3.14"
 
       - name: Get build artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           pattern: dist-*
           merge-multiple: true

.github/workflows/test.yml

@@ -1,14 +1,28 @@
 # Run the complete test suite incl. many external command line dependencies (like Openbabel)
 # as well as the pymatgen.ext package. Coverage used to be computed based on this workflow.
-name: Tests
+name: test
 
 on:
   push:
     branches: [master]
-    paths-ignore: ["**/*.md", docs/**]
+    paths:
+      [
+        "src/**/*.*",
+        "tests/**/*.*",
+        ".github/workflows/*",
+        "pyproject.toml",
+        "setup.py",
+      ]
   pull_request:
     branches: [master]
-    paths-ignore: ["**/*.md", docs/**]
+    paths:
+      [
+        "src/**/*.*",
+        "tests/**/*.*",
+        ".github/workflows/*",
+        "pyproject.toml",
+        "setup.py",
+      ]
   workflow_dispatch:
   workflow_call: # make this workflow reusable by release.yml
 
@@ -21,96 +35,91 @@ 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:
-        # 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 3.10) on windows (seems most likely to surface errors) and with
-        # newest version (currently 3.12) on ubuntu (to get complete coverage on unix).
+        # 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 on windows (most likely to surface errors) and with
+        # newest version on Ubuntu (to get complete coverage).
         config:
           - os: windows-latest
-            python: "3.10"
-            resolution: highest
-            extras: ci,optional
+            python: "3.10"  # Test lowest supported Python version
+            resolution: lowest-direct
+            extras: optional,prototypes
           - os: windows-latest
-            python: "3.10"
+            python: "3.11"
             resolution: highest
-            extras: ci,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
-          - os: ubuntu-latest
-            python: "3.12"
-            resolution: lowest-direct
-            extras: ci,optional
+            extras: prototypes,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
           - os: macos-latest
-            python: "3.11"
+            python: "3.13"
             resolution: lowest-direct
-            extras: ci # test with only required dependencies installed
+            extras: prototypes # test with only required dependencies installed
+          - os: ubuntu-latest
+            python: "3.14"  # Test highest supported Python version
+            resolution: highest
+            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 Ubuntu dependencies
     steps:
       - name: Check out repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Create mamba environment
         uses: mamba-org/setup-micromamba@main
         with:
           environment-name: pmg
+          cache-environment: true
           create-args: >-
             python=${{ matrix.config.python }}
 
       - name: Install ubuntu-only conda dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |
           micromamba install -n pmg -c conda-forge bader enumlib \
-            openff-toolkit packmol pygraphviz tblite --yes
+            packmol pygraphviz tblite --yes
+            # openff-toolkit # TODO: doesn't support Python 3.13 yet
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
 
       - name: Install pymatgen and dependencies via uv
         run: |
-          micromamba activate pmg
-          # TODO1 (use uv over pip) uv install torch is flaky, track #3826
-          # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1,
-          # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
-          pip install torch==2.2.1
-
           # 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 optional Ubuntu dependencies
-        if: matrix.config.os == 'ubuntu-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
-          echo "$(realpath boltztrap-1.2.5/src/)" >> $GITHUB_PATH
+      - name: Restore cache for optional Ubuntu/MacOS dependencies
+        if: matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-latest'
+        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') }}
 
-          # 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
-          echo "$(realpath vampire-5.0/)" >> $GITHUB_PATH
+      - name: Build optional Ubuntu/MacOS dependencies (when cache misses)
+        if: (matrix.config.os == 'ubuntu-latest' || matrix.config.os == 'macos-latest') && steps.optbin-cache.outputs.cache-hit != 'true'
+        run: bash .github/workflows/_install_opt_unit_deps.sh "$OPT_BIN_DIR"
 
       - name: pytest split ${{ matrix.split }}
         env:
-          MPLBACKEND: Agg  # non-interactive backend for matplotlib
+          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 \
+            -n auto --splits 10 --group ${{ matrix.split }} \
+            --durations-path tests/files/.pytest-split-durations \
 
   trigger_atomate2_ci:
     needs: test
@@ -129,3 +138,11 @@ jobs:
             -H "X-GitHub-Api-Version: 2022-11-28" \
             https://api.github.com/repos/materialsproject/atomate2/dispatches \
             -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:
+      - name: Echo
+        run: echo "All tests pass"

.gitignore

@@ -1,14 +1,13 @@
 __pycache__/
 .DS_Store
-pymatgen.egg-info
+*.egg-info
 *.o
 *.so
 *.pyc
 *.swp
 *.swo
 *.pyd
 *.c
-pymatgen/pymatgen.cfg
 dist
 _build
 _site
@@ -21,13 +20,12 @@ build
 setuptools*
 .ipynb_checkpoints
 .cache
-.tox
 .eggs/
 .coverage
 .*_cache
 # VS Code
 .vscode/*
-
+*.code-workspace
 # Environments
 .env
 .venv