fixed: failed image creation in periodic hops

.github/workflows/testing.yml

@@ -23,6 +23,86 @@ jobs:
 
       - uses: pre-commit/action@v3.0.0
 
+  test-forcefields:
+    # 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:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+        dep-group: ["generic", "torch-limited", "e3nn-limited", "numpy-limited"]
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+        with:
+          environment-name: a2
+          cache-environment: false
+          create-args: >-
+            python=${{ matrix.python-version }}
+
+      - name: Install uv
+        run: micromamba run -n a2 pip install uv
+
+      - name: Install conda dependencies
+        run: |
+          micromamba install -n a2 -c conda-forge packmol --yes
+
+      - name: Install dependencies
+        run: |
+          micromamba activate a2
+          python -m pip install --upgrade pip
+          mkdir -p ~/.abinit/pseudos
+          cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
+          uv pip install .[strict,strict-forcefields-${{ matrix.dep-group }},abinit,approxneb,aims] --group 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: |
+          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 }}
+
+        # torch-limited loads the heaviest MLIP stack (matgl + nequip + torch);
+        # running it single-process avoids the OOM that kills the runner when
+        # xdist spawns multiple workers each holding a copy of the models.
+        run: |
+          micromamba activate a2
+          pytest -n ${{ matrix.dep-group == 'torch-limited' && '1' || 'auto' }} --cov=atomate2 --cov-report=xml tests/forcefields
+          #pytest -n auto --cov=atomate2 --cov-report=xml tests/forcefields
+
+      - name: Forcefield tutorial
+        if: matrix.dep-group == 'torch-limited'
+        env:
+          MP_API_KEY: ${{ secrets.MP_API_KEY }}
+        run: |
+          micromamba activate a2
+          pytest -n auto --nbmake ./tutorials/force_fields
+
+      - uses: codecov/codecov-action@v1
+        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/atomate2'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          name: coverage${{ matrix.split }}
+          file: ./coverage.xml
+
   test-non-ase:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/atomate2'
@@ -38,6 +118,7 @@ jobs:
       run:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
+      fail-fast: false
       matrix:
         python-version: ["3.11", "3.12"]
         split: [1, 2, 3]
@@ -67,7 +148,7 @@ jobs:
           python -m pip install --upgrade pip
           mkdir -p ~/.abinit/pseudos
           cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
-          uv pip install .[strict,strict-forcefields,abinit,approxneb,aims] --group tests
+          uv pip install .[strict,abinit,approxneb,aims] --group tests
           uv pip install torch-runstats torch_dftd
           uv pip install --no-deps nequip==0.5.6
 
@@ -88,7 +169,7 @@ jobs:
         # However this `splitting-algorithm` means that tests cannot depend sensitively on the order they're executed in.
         run: |
           micromamba activate a2
-          pytest -n auto --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --ignore=tests/openff_md --ignore=tests/openmm_md --cov=atomate2 --cov-report=xml
+          pytest -n auto --splits 3 --group ${{ matrix.split }} --durations-path tests/.pytest-split-durations --splitting-algorithm least_duration --ignore=tests/ase --ignore=tests/openff_md --ignore=tests/openmm_md --ignore=tests/forcefields --cov=atomate2 --cov-report=xml
 
 
       - uses: codecov/codecov-action@v1
@@ -132,7 +213,7 @@ jobs:
         run: micromamba run -n a2 pip install uv
 
       - name: Install conda dependencies
-        run: |
+        run: |  # TODO: migrate openff tests to use non smirnoff99frosst forcefields as recommended by devs
           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
@@ -195,7 +276,7 @@ jobs:
 
       - 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
+          micromamba install -n a2 -c conda-forge enumlib packmol openbabel --yes
 
       - name: Install dependencies
         run: |
@@ -206,14 +287,16 @@ jobs:
 
       - 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@${{ github.event.client_payload.pymatgen_ref }}'
+        run: |
+          micromamba activate a2
+          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
       - name: Test Notebooks
         env:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
-          pytest -n auto --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields
+          pytest -n auto --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb --ignore=./tutorials/force_fields --ignore=./tutorials/torchsim_tutorial.ipynb --ignore=./tutorials/lammps_workflow.ipynb 
 
       - name: Test ASE
         env:
@@ -228,7 +311,7 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
 
-  test-force-field-notebook:
+  test-torchsim:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/atomate2'
 
@@ -241,10 +324,7 @@ jobs:
     runs-on: ubuntu-latest
     defaults:
       run:
-        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
-    strategy:
-      matrix:
-        python-version: ["3.11", "3.12"]
+        shell: bash -l {0}
 
     steps:
       - name: Check out repo
@@ -256,54 +336,39 @@ jobs:
           environment-name: a2
           cache-environment: false
           create-args: >-
-            python=${{ matrix.python-version }}
+            python=3.12
 
       - 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
-          mkdir -p ~/.abinit/pseudos
-          cp -r tests/test_data/abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4 ~/.abinit/pseudos
-          uv pip install .[strict,strict-forcefields,abinit,aims] --group tests
-          uv pip install torch-runstats
-          uv pip install --no-deps nequip==0.5.6
+          uv pip install torch --index-url https://download.pytorch.org/whl/cpu
+          uv pip install .[torchsim,ase,phonons] --group tests
+          uv pip install mace-torch>=0.3.3
 
-      - name: Install pymatgen from master if triggered by pymatgen repo dispatch
-        if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
+      - name: Test TorchSim
+        env:
+          MP_API_KEY: ${{ secrets.MP_API_KEY }}
         run: |
           micromamba activate a2
-          uv pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
+          pytest -n auto tests/torchsim --cov=atomate2 --cov-report=xml
 
-      - name: Forcefield tutorial
+      - name: Test TorchSim notebook
         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 -n auto --nbmake ./tutorials/force_fields
-
+          pytest -n auto --nbmake ./tutorials/torchsim_tutorial.ipynb
 
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/atomate2'
+        if: github.repository == 'materialsproject/atomate2'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          name: coverage
           file: ./coverage.xml
 
-
-
   docs:
     runs-on: ubuntu-latest
 
@@ -319,13 +384,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install .[strict,strict-forcefields] --group docs
+          pip install .[strict,strict-forcefields-generic] --group docs
 
       - name: Build
         run: sphinx-build docs docs_build
 
   automerge:
-    needs: [docs, lint, test-force-field-notebook, test-non-ase, test-notebooks-and-ase, test-openff]
+    needs: [docs, lint, test-forcefields, test-non-ase, test-notebooks-and-ase, test-openff, test-torchsim]
     runs-on: ubuntu-latest
 
     permissions:

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.14.2
+  rev: v0.15.10
   hooks:
   - id: ruff
     args: [--fix]
@@ -16,7 +16,7 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.21.0
+  rev: v3.21.2
   hooks:
     - id: pyupgrade
 - repo: https://github.com/asottile/blacken-docs
@@ -33,22 +33,22 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.18.2
+  rev: v1.20.1
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.4.1
+  rev: v2.4.2
   hooks:
   - id: codespell
     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
+  rev: 0.9.1
   hooks:
     - id: nbstripout
       args:

applications/__init__.py

@@ -0,0 +1,9 @@
+"""Demo custom applications of atomate2.
+
+This namespace is reserved primarily for workflows / jobs
+which may be too niche to be in the core atomate2 library,
+but which may be valuable for the community to access.
+
+This could include workflows from published works which are
+funded by the Materials Project.
+"""