Merge branch 'main' of github.com:materialsproject/atomate2

pull trunk main

Author: VicTrqt

.github/release.yml

@@ -13,7 +13,7 @@ changelog:
         - enhancement
     - title: Documentation 📖
       labels:
-        - documentation
+        - docs
     - title: House-Keeping 🧹
       labels:
         - house-keeping

.github/workflows/deploy.yml

@@ -28,8 +28,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

.github/workflows/docs.yml

@@ -33,8 +33,6 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
           pip install .[strict,docs]
 
       - name: Build

.github/workflows/testing.yml

@@ -6,6 +6,8 @@ on:
     tags: ["v*"]
   pull_request:
   workflow_dispatch:
+  repository_dispatch:
+    types: [pymatgen-ci-trigger]
 
 jobs:
   lint:
@@ -15,54 +17,147 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.10"
           cache: pip
           cache-dependency-path: pyproject.toml
 
       - uses: pre-commit/[email protected]
 
-  test:
+  test-non-ase:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+
     services:
       local_mongodb:
         image: mongo:4.0
         ports:
           - 27017:27017
 
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
+        split: [1, 2, 3]
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out repo
+        uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
+        run: |
+          micromamba create -n a2 python=${{ matrix.python-version }} --yes
+
+      - name: Install uv
+        run: micromamba run -n a2 pip install uv
 
+      - name: Install conda dependencies
+        run: |
+          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes
 
       - name: Install dependencies
-        # ERROR: Cannot install atomate2 and atomate2[strict,tests]==0.0.1 because these package versions have conflicting dependencies.
-        # The conflict is caused by:
-        #   atomate2[strict,tests] 0.0.1 depends on pymatgen>=2023.10.4
-        #   atomate2[strict,tests] 0.0.1 depends on pymatgen==2023.10.4; extra == "strict"
-        # ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
-        #   chgnet 0.2.1 depends on pymatgen>=2023.5.31
-        #   emmet-core 0.70.0 depends on pymatgen>=2023.10.11
         run: |
+          micromamba activate a2
           python -m pip install --upgrade pip
           mkdir -p ~/.abinit/pseudos
           cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
-          pip install .[strict,tests,abinit]
-          pip install torch-runstats
-          pip install --no-deps nequip
+          uv pip install .[strict,strict-forcefields,tests,abinit]
+          uv pip install torch-runstats
+          uv pip install --no-deps nequip==0.5.6
+
+      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
+        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
+        run: |
+          micromamba activate a2
+          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
+
+      - name: Test split ${{ matrix.split }}
+        env:
+          MP_API_KEY: ${{ secrets.MP_API_KEY }}
+
+        # regenerate durations file with `pytest --store-durations --durations-path tests/.pytest-split-durations`
+        # Note the use of `--splitting-algorithm least_duration`.
+        # This helps prevent a test split having no tests to run, and then the GH action failing, see:
+        # https://github.com/jerry-git/pytest-split/issues/95
+        # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
+        run: |
+          micromamba activate a2
+          pytest --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --cov=atomate2 --cov-report=xml
+
+      - uses: codecov/codecov-action@v1
+        if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          name: coverage${{ matrix.split }}
+          file: ./coverage.xml
+
+  test-notebooks-and-ase:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/atomate2'
+    
+    # It seems like anything torch-dependent and tblite can't be installed in the same environment
+    # without the tblite tests failing in CI, see, e.g.:
+    # https://github.com/tblite/tblite/issues/116
+    # Outside of CI, having torch installed but not loaded seems not to affect tblite
+    # Set off ASE tests here, where tblite-dependent tests live
+    services:
+      local_mongodb:
+        image: mongo:4.0
+        ports:
+          - 27017:27017
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
+        run: |
+          micromamba create -n a2 python=${{ matrix.python-version }} --yes
+
+      - name: Install uv
+        run: micromamba run -n a2 pip install uv
+
+      - name: Install conda dependencies
+        run: |
+          micromamba install -n a2 -c conda-forge enumlib packmol bader openbabel openff-toolkit==0.16.2 openff-interchange==0.3.22 --yes
+
+      - name: Install dependencies
+        run: |
+          micromamba activate a2
+          python -m pip install --upgrade pip
+          uv pip install .[strict,tests]
+
+      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
+        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
+        run: uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
-      - name: Test
+      - name: Test Notebooks
+        run: |
+          micromamba activate a2
+          pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb
+
+      - name: Test ASE
         env:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
-        run: pytest --cov=atomate2 --cov-report=xml
+        run: |
+          micromamba activate a2
+          pytest --splits 1 --group 1 --cov=atomate2 --cov-report=xml tests/ase
 
       - uses: codecov/codecov-action@v1
         if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'
@@ -85,15 +180,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          # ase needed to get FrechetCellFilter used by ML force fields
-          pip install git+https://gitlab.com/ase/ase
-          pip install .[strict,docs]
+          pip install .[strict,strict-forcefields,docs]
 
       - name: Build
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [lint, test, docs]
+    needs: [lint, test-non-ase, test-notebooks-and-ase, docs]
     runs-on: ubuntu-latest
 
     permissions:

.github/workflows/update-precommit.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install pre-commit
         run: pip install pre-commit

.gitignore

@@ -64,5 +64,12 @@ docs/reference/atomate2.*
 
 .DS_Store
 
+# vim extensions
+*.swp
+*.swo
+
 # see https://github.com/materialsproject/atomate2/issues/345
 *.doctrees*
+
+.ipynb_checkpoints
+.aider*

.pre-commit-config.yaml

@@ -3,21 +3,21 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.3.5
+  rev: v0.8.0
   hooks:
   - id: ruff
     args: [--fix]
   - id: ruff-format
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v5.0.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.16.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,17 +30,25 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.9.0
+  rev: v1.13.0
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
   - id: codespell
-    stages: [commit, commit-msg]
+    stages: [pre-commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.8.1
+  hooks:
+    - id: nbstripout
+      args:
+        - --drop-empty-cells
+        - --strip-init-cells
+        - --extra-keys=metadata.kernelspec