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Bump mamba-org/setup-micromamba from 1 to 2 #3902

Bump mamba-org/setup-micromamba from 1 to 2

Bump mamba-org/setup-micromamba from 1 to 2 #3902

Workflow file for this run

name: ci
on:
push:
branches:
- main
- develop
pull_request:
branches:
- main
- develop
schedule:
- cron: "0 0 * * *"
workflow_dispatch:
defaults:
run:
shell: bash -l {0}
jobs:
test:
name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, Pydantic ${{ matrix.pydantic-version }}, OpenEye ${{ matrix.openeye }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os:
- macos-12
- ubuntu-latest
python-version:
- "3.10"
- "3.11"
pydantic-version:
- "2"
openeye:
- true
- false
openmm:
- true
- false
env:
OE_LICENSE: ${{ github.workspace }}/oe_license.txt
COV: --cov=openff/interchange --cov-report=xml --cov-config=setup.cfg --cov-append
steps:
- uses: actions/checkout@v4
- name: Install conda environment
uses: mamba-org/setup-micromamba@v2
with:
micromamba-version: '1.5.10-0'
environment-file: devtools/conda-envs/test_env.yaml
create-args: >-
python=${{ matrix.python-version }}
pydantic=${{ matrix.pydantic-version }}
- name: Install package
run: |
# These packages are brought in by conda (via the toolkit) and must be removed manually
# since pip doesn't know about the -base split and does not uninstall the -base package
micromamba remove --force openff-interchange openff-interchange-base
python -m pip install . plugins/
- name: Install and license OpenEye Toolkits
if: ${{ matrix.openeye == true }}
run: |
micromamba install "openeye-toolkits =2024.1.0" -c openeye
echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
env:
SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
- name: Install OpenMM
if: ${{ matrix.openmm == true }}
run: |
micromamba install openmm -c conda-forge
- name: Uninstall OpenMM
if: ${{ matrix.openmm == false && matrix.openeye == true }}
run: |
micromamba remove openmm mdtraj
# Removing mBuild also removes some leaves, need to re-install them
micromamba install rdkit packmol "lammps >=2023.08.02"
- name: Install AmberTools and RDKit
if: ${{ matrix.openeye == false }}
# Unclear why, but around October 2023 this downgrades JAX to broken 0.1.x builds
# and also uninstalls RDKit
run: micromamba install rdkit "ambertools =23" "lammps >=2023.08.02" "jax >=0.3" "jaxlib >=0.3" -c conda-forge
- name: Install Foyer
run: micromamba install "foyer >=0.12.1" -c conda-forge -yq
- name: Run tests
if: always()
run: |
python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
- name: Run small molecule regression tests
if: ${{ matrix.openeye == true && matrix.openmm == true }}
run: |
micromamba install "deepdiff =5" rich click -c conda-forge
python -m pip install git+https://github.com/openforcefield/interchange-regression-testing.git@fa07b62824c39af591142b402bd68103f4043f8b
create_openmm_systems \
--input "regression_tests/small-molecule/input-topologies.json" \
--output "regression_tests/small-molecule/" \
--using-interchange \
--force-field "openff-2.0.0.offxml" \
--n-procs 2
# Don't trust the interchange version here, for some reason, just put it in a new directory
mkdir regression_tests/small-molecule/omm-systems-interchange-latest/
mv regression_tests/small-molecule/omm-systems-interchange-*/*xml regression_tests/small-molecule/omm-systems-interchange-latest/
compare_openmm_systems \
--input-dir-a "regression_tests/small-molecule/omm-systems-toolkit-0.10.6" \
--input-dir-b "regression_tests/small-molecule/omm-systems-interchange-latest" \
--output "regression_tests/differences.json" \
--settings "regression_tests/default-comparison-settings.json" \
--expected-changes "regression_tests/toolkit-to-interchange.json" \
--n-procs 2
python devtools/scripts/molecule-regressions.py
- name: Run mypy
if: ${{ matrix.python-version == '3.10' }}
run: |
# As of 01/23, JAX with mypy is too slow to use without a pre-built cache
# https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875
micromamba remove jax
python -m mypy -p "openff.interchange" --exclude "openff/interchange/_tests/"
python -m mypy plugins/nonbonded_plugins/
- name: Codecov
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
file: ./coverage.xml
fail_ci_if_error: false