Merge branch 'master' into pr/oashour/3463

Author: janosh

.coderabbit.yaml

@@ -0,0 +1,17 @@
+# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json
+language: "en-US"
+early_access: false
+reviews:
+  request_changes_workflow: false
+  high_level_summary: false
+  poem: false
+  review_status: false
+  collapse_walkthrough: false
+  auto_review:
+    enabled: true
+    ignore_title_keywords:
+      - "WIP"
+      - "DO NOT MERGE"
+    drafts: false
+chat:
+  auto_reply: true

.gitattributes

@@ -1,5 +1,4 @@
 # declare HTML, rST and test files as vendored/docs to exclude them when calculating repo languages on GitHub
 tests/files/**/* linguist-vendored
-cmd_line/* linguist-vendored
 docs/**/* linguist-generated
 dev_scripts/**/* linguist-vendored

.github/CODEOWNERS

@@ -2,3 +2,5 @@
 pymatgen/io/ase.py @Andrew-S-Rosen
 pymatgen/io/abinit/* @gmatteo
 pymatgen/io/lobster/* @JaGeo
+pymatgen/ext/* @ml-evs
+tests/ext/* @ml-evs

.github/release.yml

@@ -14,6 +14,8 @@ changelog:
       labels: [housekeeping]
     - title: 🚀 Performance
       labels: [performance]
+    - title: 🚧 CI
+      labels: [ci]
     - title: 💡 Refactoring
       labels: [refactor]
     - title: 🧪 Tests

.github/workflows/issue-metrics.yml

@@ -0,0 +1,42 @@
+name: Monthly issue metrics
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '3 2 1 * *'
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+    steps:
+    - name: Get dates for last month
+      shell: bash
+      run: |
+        # Calculate the first day of the previous month
+        first_day=$(date -d "last month" +%Y-%m-01)
+
+        # Calculate the last day of the previous month
+        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+
+        #Set an environment variable with the date range
+        echo "$first_day..$last_day"
+        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+
+    - name: Run issue-metrics tool
+      uses: github/issue-metrics@v3
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SEARCH_QUERY: 'repo:materialsproject/pymatgen is:issue created:${{ env.last_month }} -reason:"not planned"'
+
+    - name: Create issue
+      uses: peter-evans/create-issue-from-file@v5
+      with:
+        title: Monthly issue metrics report
+        token: ${{ secrets.GITHUB_TOKEN }}
+        content-filepath: ./issue_metrics.md

.github/workflows/jekyll-gh-pages.yml

@@ -1,15 +1,11 @@
-# Sample workflow for building and deploying a Jekyll site to GitHub Pages
 name: Deploy Jekyll with GitHub Pages dependencies preinstalled
 
 on:
-  # Runs on pushes targeting the default branch
   push:
     branches: ["master"]
+  workflow_dispatch: # enable manual workflow execution
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+# Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: read
   pages: write
@@ -22,23 +18,26 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  # Build job
   build:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+
       - name: Setup Pages
         uses: actions/configure-pages@v3
+
       - name: Build with Jekyll
         uses: actions/jekyll-build-pages@v1
         with:
           source: ./docs
           destination: ./_site
+
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2
 
-  # Deployment job
   deploy:
     environment:
       name: github-pages

.github/workflows/lint.yml

@@ -22,16 +22,16 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff mypy
+          pip install --upgrade ruff mypy pyright
 
       - name: ruff
         run: |
           ruff --version
-          ruff .
+          ruff check .
           ruff format --check .
 
       - name: mypy
-        run: |
-          mypy --version
-          rm -rf .mypy_cache
-          mypy ${{ github.event.repository.name }}
+        run: mypy ${{ github.event.repository.name }}
+
+      - name: pyright
+        run: pyright

.github/workflows/release.yml

@@ -29,14 +29,12 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
-
-      - run: |
-          python -m pip install build
-          pip install -e .
+          python-version: "3.12"
 
       - name: Build sdist
-        run: python -m build --sdist
+        run: |
+          pip install build
+          python -m build --sdist
 
       - uses: actions/upload-artifact@v3
         with:
@@ -47,7 +45,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["39", "310", "311"]
+        python-version: ["39", "310", "311", "312"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
@@ -70,10 +68,10 @@ jobs:
       # For pypi trusted publishing
       id-token: write
     steps:
-      - name: Set up Python 3.11
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Get build artifacts
         uses: actions/download-artifact@v3

.github/workflows/test.yml

@@ -10,8 +10,7 @@ on:
     branches: [master]
     paths-ignore: ["**/*.md", docs/**]
   workflow_dispatch:
-  # make this workflow reusable by release.yml
-  workflow_call:
+  workflow_call: # make this workflow reusable by release.yml
 
 permissions:
   contents: read
@@ -20,86 +19,67 @@ jobs:
   test:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/pymatgen'
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     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", "3.11"]
+        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 3.11) on ubuntu (to get complete and speedy
+        # 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:
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
           - os: ubuntu-latest
             python-version: "3.9"
 
     runs-on: ${{ matrix.os }}
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-      MPLBACKEND: Agg # https://github.com/orgs/community/discussions/26434
-      PMG_TEST_FILES_DIR: ${{ github.workspace }}/tests/files
-      GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries
       PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files
 
     steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: setup.py
-      - name: Copy GULP to bin
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/
-      - name: Install Bader
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          wget http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
-          tar xvzf bader_lnx_64.tar.gz
-          sudo mv bader /usr/local/bin/
-        continue-on-error: true # This is not critical to succeed.
-      - name: Install Enumlib
-        if: matrix.os == 'ubuntu-latest'
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
         run: |
-          git clone --recursive https://github.com/msg-byu/enumlib.git
-          cd enumlib/symlib/src
-          export F90=gfortran
-          make
-          cd ../../src
-          make enum.x
-          sudo mv enum.x /usr/local/bin/
-          cd ..
-          sudo cp aux_src/makeStr.py /usr/local/bin/
-        continue-on-error: true # This is not critical to succeed.
-      - name: Install Packmol
+          micromamba create -n pmg python=${{ matrix.python-version }} --yes
+
+      - name: Install uv
+        run: micromamba run -n pmg pip install uv
+
+      - name: Install ubuntu-only conda dependencies
         if: matrix.os == 'ubuntu-latest'
         run: |
-          wget -O packmol.tar.gz https://github.com/m3g/packmol/archive/refs/tags/v20.14.2.tar.gz
-          tar xvzf packmol.tar.gz
-          export F90=gfortran
-          cd packmol-20.14.2
-          ./configure
-          make
-          sudo mv packmol /usr/local/bin/
-          cd ..
-        continue-on-error: true # This is not critical to succeed.
-      - name: Install dependencies
+          micromamba install -n pmg -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
+
+      - name: Install pymatgen and dependencies
         run: |
-          python -m pip install numpy cython
+          micromamba activate pmg
+          # TODO remove temporary fix. added since uv install torch is flaky.
+          # track https://github.com/astral-sh/uv/issues/1921 for resolution
+          pip install torch
+
+          uv pip install numpy cython
 
-          # TODO remove next line installing ase from main branch until FrechetCellFilter is released
-          pip install git+https://gitlab.com/ase/ase
+          uv pip install --editable '.[dev,optional]'
 
-          python -m pip install -e '.[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'
 
       - name: pytest split ${{ matrix.split }}
         run: |
+          micromamba activate pmg
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

.pre-commit-config.yaml

@@ -1,28 +1,28 @@
-exclude: ^(docs|tests/files|cmd_line|tasks.py)
+exclude: ^(docs|tests/files|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [mypy]
+  skip: [mypy, pyright]
   autofix_commit_msg: pre-commit auto-fixes
   autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.1
+    rev: v0.4.2
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.10.0
     hooks:
       - id: mypy
 
@@ -35,7 +35,7 @@ repos:
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.0
+    rev: v0.16.2
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]
@@ -62,3 +62,8 @@ repos:
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]
+
+  - repo: https://github.com/RobertCraigie/pyright-python
+    rev: v1.1.360
+    hooks:
+      - id: pyright