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mattwthompsonmattwthompson
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Revert "Debug"
This reverts commit afaaa70.
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‎.github/workflows/ci.yaml‎

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name: ci
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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schedule:
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- cron: "0 5 * * *"
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workflow_dispatch:
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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test:
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name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, OpenEye ${{ matrix.openeye }}, RDKit ${{ matrix.rdkit }}, AmberTools ${{ matrix.ambertools }}, NAGL ${{ matrix.nagl }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os:
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- macos-latest
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- ubuntu-latest
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python-version:
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- "3.11"
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- "3.12"
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- "3.13"
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openeye:
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- true
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- false
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rdkit:
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- true
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ambertools:
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- true
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- false
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nagl:
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- true
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- false
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openmm:
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- true
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exclude:
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- python-version: "3.13"
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openeye: true
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- ambertools: false
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openeye: false
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env:
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OE_LICENSE: ${{ github.workspace }}/oe_license.txt
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COV: --cov=openff/interchange --cov-report=xml --cov-config=pyproject.toml --cov-append
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steps:
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- uses: actions/checkout@v5
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with:
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fetch-depth: 0
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- name: Install conda environment
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: devtools/conda-envs/test_env.yaml
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create-args: >-
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python=${{ matrix.python-version }}
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- name: Install and license OpenEye Toolkits
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if: ${{ matrix.openeye == true }}
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run: |
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micromamba install "openeye-toolkits =2025" -c openeye
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echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
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python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
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env:
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SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
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- name: Install OpenMM
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if: ${{ matrix.openmm == true }}
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run: |
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micromamba install openmm -c conda-forge
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- name: Install RDKit
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if: ${{ matrix.rdkit == true }}
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run: |
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micromamba install rdkit "ambertools =24" intermol -c conda-forge
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- name: Remove AmberTools
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if: ${{ matrix.ambertools == false }}
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run: |
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micromamba remove ambertools parmed
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micromamba install "packmol >=20.15.0" "lammps>=2024" "numpy>=2.3"
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- name: Install OpenFF NAGL
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if: ${{ matrix.nagl == true }}
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run: |
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micromamba install openff-nagl -c conda-forge
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- name: Install Python <3.13 dependencies
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if: ${{ matrix.python-version != '3.13' && matrix.ambertools == true }}
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run: micromamba install --file devtools/conda-envs/test_not_py313.yaml python=${{ matrix.python-version }}
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- name: Install package
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run: python -m pip install . plugins/
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- name: Run tests
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run: |
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# https://github.com/openforcefield/openff-units/issues/111
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python -c "from openff.toolkit import *"
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python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
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- name: Run small molecule regression tests
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if: ${{ matrix.openeye == true && matrix.openmm == true }}
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run: |
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micromamba install "openmm=8.4.0" "deepdiff <=8" rich click -c conda-forge
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python -m pip install git+https://github.com/openforcefield/interchange-regression-testing.git@443480732f5caf3fc63f5442fdd763176c63e72f
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create_openmm_systems \
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--input "regression_tests/small-molecule/input-topologies.json" \
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--output "regression_tests/small-molecule/" \
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--using-interchange \
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--force-field "openff-2.0.0.offxml" \
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--n-procs 4
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# Don't trust the interchange version here, for some reason, just put it in a new directory
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mkdir regression_tests/small-molecule/omm-systems-interchange-latest/
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mv regression_tests/small-molecule/omm-systems-interchange-*/*xml regression_tests/small-molecule/omm-systems-interchange-latest/
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compare_openmm_systems \
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--input-dir-a "regression_tests/small-molecule/omm-systems-toolkit-0.10.6" \
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--input-dir-b "regression_tests/small-molecule/omm-systems-interchange-latest" \
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--output "regression_tests/differences.json" \
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--settings "regression_tests/default-comparison-settings.json" \
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--expected-changes "regression_tests/toolkit-to-interchange.json" \
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--n-procs 4
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python devtools/scripts/molecule-regressions.py
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- name: Run mypy
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run: |
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# As of 01/23, JAX with mypy is too slow to use without a pre-built cache
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# https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875
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micromamba remove jax
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python -m mypy -p "openff.interchange" --exclude "openff/interchange/_tests/"
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python -m mypy plugins/nonbonded_plugins/
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- name: Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./coverage.xml

‎.github/workflows/examples.yaml‎

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- name: Run docexamples
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run: python -m pytest -c pyproject.toml --doctest-modules openff/interchange/ --ignore=openff/interchange/_tests
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- name: Debug import/build failures
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- name: Run example notebooks
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run: |
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python -c "from openff.interchange import Interchange, __version__; print(Interchange.__module__, __version__)"
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python -m pytest -xv -c pyproject.toml --nbval-lax --durations=20 examples/ligand_in_water/
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python -m pytest -x -c pyproject.toml --nbval-lax --dist loadscope -n logical --durations=20 examples/ \
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--ignore=examples/deprecated/ \
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--ignore=examples/experimental/ \
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--ignore=examples/lammps/

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