Merge branch 'main' into fairchem_cpp

Author: misko

.github/workflows/build_docs.yml

@@ -12,6 +12,11 @@ on:
       - "contributor check"
     types:
       - completed
+env:
+  # `BASE_URL` determines, relative to the root of the domain, the URL that your site is served from.
+  # E.g., if your site lives at `https://mydomain.org/myproject`, set `BASE_URL=/myproject`.
+  # If, instead, your site lives at the root of the domain, at `https://mydomain.org`, set `BASE_URL=''`.
+  BASE_URL: ''
 
 jobs:
   build:
@@ -45,8 +50,15 @@ jobs:
       with:
           status-context: '${{ github.job }}'
 
-    - name: Install pandoc and ffmpeg
-      run: sudo apt-get update && sudo apt-get -y install pandoc ffmpeg
+    - uses: actions/setup-node@v6
+      with:
+        node-version: 18.x
+
+    - name: Install Jupyter Book (via myst)
+      run: npm install -g jupyter-book
+
+    - name: Install latexmk
+      run: sudo apt-get update && sudo apt-get -y install latexmk pandoc ffmpeg imagemagick texlive-xetex
 
     # Install dependencies
     - name: Set up Python
@@ -74,8 +86,8 @@ jobs:
       run: |
         # Convert MyST markdown files to Jupyter notebooks if needed to get download as ipynb buttons
         jupytext --to ipynb ./docs/uma_tutorials/*.md
-        # find ./docs/ -name "*.md" -exec grep -q "format_name: myst" {} \; -print0 | xargs -0 jupytext --to ipynb
-        jupyter-book build docs
+        find ./docs/ -name "*.md" -exec grep -q "format_name: myst" {} \; -print0 | xargs -0 jupytext --to ipynb
+        cd docs && jupyter-book build --html --execute --execute-parallel 1
 
     - name: Upload documentation artifact
       uses: actions/upload-artifact@v6
@@ -87,4 +99,4 @@ jobs:
       if: always()
       uses: ./.github/actions/multi-trigger-cleanup
       with:
-          status-context: '${{ github.job }}'
+          status-context: '${{ github.job }}'

.github/workflows/stale.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v10.1.1
+      - uses: actions/stale@v10.2.0
         with:
           days-before-stale: 30
           days-before-close: 14

.github/workflows/test.yml

@@ -35,7 +35,7 @@ jobs:
     strategy:
       max-parallel: 10
       matrix:
-        python_version: ['3.10', '3.13']
+        python_version: ['3.11', '3.13']
 
     steps:
       - name: Checkout code
@@ -84,13 +84,22 @@ jobs:
           make
           echo "$(readlink -f .)" >> $GITHUB_PATH
 
+      - name: Download large test files
+        run: coverage run -m fairchem.core.scripts.download_large_files oc
+
       - name: Core tests
         env:
           HF_TOKEN: ${{ secrets.HF_TOKEN }}
         run: |
-          NCCL_DEBUG=INFO pytest -n auto tests --durations=0 -vv --ignore=tests/demo/ocpapi/tests/integration/ --ignore=tests/applications/ --ignore=tests/perf --ignore=tests/lammps --cov-report=xml --cov=fairchem --junitxml=junit.xml -o junit_family=legacy -c ./packages/fairchem-core/pyproject.toml
+          NCCL_DEBUG=INFO pytest -n auto -m "not subprocess and not serial and not gpu" tests --durations=0 -vv --ignore=tests/demo/ocpapi/tests/integration/ --ignore=tests/applications/ --ignore=tests/perf --ignore=tests/lammps --cov-report=xml --cov=fairchem --cov-append --junitxml=junit.xml -o junit_family=legacy -c ./packages/fairchem-core/pyproject.toml
+
+      - name: Serial CPU tests
+        env:
+          HF_TOKEN: ${{ secrets.HF_TOKEN }}
+        run: |
+          pytest -m "serial and not gpu" tests -vv --ignore=tests/demo/ocpapi/tests/integration/ --ignore=tests/applications/ --ignore=tests/perf --ignore=tests/lammps --cov-report=xml --cov=fairchem --cov-append --junitxml=junit-serial.xml -o junit_family=legacy -c ./packages/fairchem-core/pyproject.toml
 
-      - if: ${{ matrix.python_version == '3.12' || matrix.python_version == '3.13' }}
+      - if: ${{ matrix.python_version == '3.13' }}
         name: codecov-coverage
         uses: codecov/codecov-action@v5
         with:
@@ -99,11 +108,11 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           verbose: true
 
-      - if: ${{ matrix.python_version == '3.12' || matrix.python_version == '3.13' }}
+      - if: ${{ matrix.python_version == '3.13' }}
         name: codecov-test-results
         uses: codecov/test-results-action@v1
         with:
-          files: ./junit.xml,./junit-gpu.xml
+          files: ./junit.xml,./junit-serial.xml,./junit-gpu.xml
           token: ${{ secrets.CODECOV_TOKEN }}
           commit_parent: ${{ env.HEAD_SHA }}
           verbose: true
@@ -146,7 +155,7 @@ jobs:
       - name: Install core dependencies and package
         run: |
           python -m pip install --upgrade pip
-          pip install packages/fairchem-core[dev] \
+          pip install packages/fairchem-core[dev,extras] \
           packages/fairchem-data-omol[dev] \
           packages/fairchem-data-omat \
           -r tests/requirements.txt # pin test packages

.github/workflows/trim-dependabot.yml

@@ -0,0 +1,28 @@
+name: Trim Dependabot PR description
+on:
+  pull_request:
+    types: [opened]
+
+jobs:
+  trim:
+    if: github.actor == 'dependabot[bot]'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/github-script@v7
+        with:
+          script: |
+            const { owner, repo } = context.repo;
+            const pull_number = context.payload.pull_request.number;
+            const body = context.payload.pull_request.body;
+            await github.rest.issues.createComment({
+              owner,
+              repo,
+              issue_number: pull_number,
+              body: `<details>\n<summary>Original Dependabot description</summary>\n\n${body}\n</details>`
+            });
+            await github.rest.pulls.update({
+              owner,
+              repo,
+              pull_number,
+              body: ""
+            });

.gitignore

@@ -134,3 +134,13 @@ docs/legacy_tutorials/data/*.extxyz
 docs/**.json
 
 
+node_modules/*
+cache.*.json
+docs/uma_tutorials/ni_tutorial_results/*
+docs/**/*.traj.*
+_build/*
+package.json
+package-lock.json
+bulks.pkl
+# MyST build outputs
+_build