Atomate2 OpenMM integration & broader classical MD framework (materia…

…lsproject#782) * Move remaining content from common.py to renamed base.py. * Update core.py with skeleton code for openff_job and generate_interchange methods. * Complete Calculation, CalculationInput, and CalculationOutput schemas for classical_md.openmm.tasks.py * Implement BaseOpenMMMaker for classical_md.openmm workflow * Update core jobs for classical_md.openmm to be compatible with new BaseOpenMMMaker * Add MoleculeSpec to classical_md.schemas and modify OpenMMTaskDoc * Implement attribute inheritance logic for base openmm maker and openmm jobs * Add from/as_dict functions for openff topology, interchange, molecule, and quantity * Fix serialization issues with conflicting pydantic versions between Interchange and atomate2 * Implement anneal and production workflows * Update resolve_attr logic to set missing attributes * Change ClassicalMDTaskDocument to OpenMMTaskDocument in base.py * Store interchange intermediate as a JSON string to fix parsing issues * Implement temperature change logic in TempChangeMaker * Improve state reporter to append to state file * Output taskdoc_json file to directory for easy building * Enhance documentation for all components * Implement micromamba for testing environment * Change all docstrings to numpy format * Add CodeCov for classical_md tests * Rename "steps" argument to "n_steps" and "output_steps" to "steps" in CalculationOutput * Add support for writing trajectory to HDF5 file * Implement MDAReporter for trajectory output * Add embed_traj argument to base_openmm_maker * Add traj_blob keyword and switch interchange to type HexBytes * Move classical_md schemas to emmet * Implement OPLS force field support through ligpargen * Create FauxInterchange object for OPLS compatibility * Refactor OpenMMFlowMaker and BaseOpenMMMaker * Add XMLMoleculeFF class for manipulating XML files representing OpenMM-compatible ForceFields * Split utilities and jobs in jobs/opls.py into separate files * Refactor utilities to isolate OpenFF dependency * Add support for MACE-based interchanges * Update OpenMM tutorial * Support BaseOpenMMMaker returning structures * Implement reading and writing of structure to/from OpenMMTaskDocument --------- Co-authored-by: Alex Ganose <[email protected]> Co-authored-by: Orion Cohen <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
hrushikesh-s · Nov 16, 2024 · 0258cd9 · 0258cd9
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commit 0258cd9
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diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -31,51 +31,58 @@ jobs:
           - 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"]
 
     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 enumlib
+      - name: Install conda dependencies
         run: |
-          cd ..
-          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.
+          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
-          pip install .[strict,tests,abinit]
-          pip install torch-runstats
-          pip install --no-deps nequip==0.5.6
+          uv pip install .[strict,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: 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
-        run: pytest --nbmake ./tutorials
+        run: | 
+          micromamba activate a2
+          pytest --nbmake ./tutorials --ignore=./tutorials/openmm_tutorial.ipynb
 
       - name: Test
         env:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}
-        run: pytest --cov=atomate2 --cov-report=xml
+        run: |
+          micromamba activate a2
+          pytest --cov=atomate2 --cov-report=xml
 
       - uses: codecov/codecov-action@v1
         if: matrix.python-version == '3.10' && github.repository == 'materialsproject/atomate2'