diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml index bf415296b..e7fde9068 100644 --- a/.github/workflows/examples.yml +++ b/.github/workflows/examples.yml @@ -24,7 +24,7 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, macos-12] + os: [ubuntu-latest, macos-latest] python-version: ["3.10"] rdkit: [true, false] openeye: [true, false] @@ -37,8 +37,8 @@ jobs: env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt PACKAGE: openff - PYTEST_ARGS: -r fE -v -x --tb=short -nauto - NB_ARGS: --nbval-lax --dist loadscope --ignore=examples/deprecated + PYTEST_ARGS: -r fE -v -x --tb=short -nauto --durations=10 + NB_ARGS: --nbval-lax --dist loadscope --ignore=examples/deprecated --ignore=examples/external steps: - uses: actions/checkout@v4 @@ -65,10 +65,6 @@ jobs: environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.yaml create-args: >- python=${{ matrix.python-version }} - # default - will pull down 2.0 which we don't want! - # micromamba-version: latest - # pin to latest 1.x release - micromamba-version: "1.5.10-0" - name: Additional info about the build run: | @@ -96,19 +92,10 @@ jobs: # so don't remove it. if [ ! -z "${{ env.PACKAGES_TO_REMOVE }}" ]; then for cpkg in ${{ env.PACKAGES_TO_REMOVE }}; do - if [[ $(conda list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi + if [[ $(micromamba list | grep $cpkg) ]]; then micromamba remove --force $cpkg --yes ; fi done fi - - name: Reinstall ParmEd - if: ${{ matrix.rdkit == false }} - run: | - micromamba remove --force parmed --yes - # See #1531, #1532, eventually this should work with 4 or 3 and 4 - micromamba install "parmed =3" -c conda-forge -yq - # Needed for other examples to run, but were removed incidentally alongside AmberTools - micromamba install h5py -c conda-forge -yq - - name: Check installed toolkits run: | for tk in ${{ env.TOOLKIT_CHECKS }}; do @@ -125,8 +112,9 @@ jobs: fi - name: Environment Information run: | - conda info - conda list + micromamba info + micromamba list + pip list - name: Run example scripts run: | diff --git a/devtools/conda-envs/openeye-examples.yaml b/devtools/conda-envs/openeye-examples.yaml index 691f77542..1b9a4d71f 100644 --- a/devtools/conda-envs/openeye-examples.yaml +++ b/devtools/conda-envs/openeye-examples.yaml @@ -38,7 +38,6 @@ dependencies: - qcportal >=0.50 - qcengine - mdtraj - - parmed =3 - nbval - pdbfixer - openmmforcefields >=0.11.2 diff --git a/devtools/conda-envs/rdkit-examples.yaml b/devtools/conda-envs/rdkit-examples.yaml index 4f903df78..3b7340bc7 100644 --- a/devtools/conda-envs/rdkit-examples.yaml +++ b/devtools/conda-envs/rdkit-examples.yaml @@ -26,9 +26,9 @@ dependencies: # Toolkit-specific # AmberTools 23 brings in ParmEd 4, which doesn't yet work with examples # https://github.com/openforcefield/openff-toolkit/issues/1532 - - ambertools =22.4 + - ambertools # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583 - - rdkit !=2024.03.6,!=2024.03.5 + - rdkit =2024 # Test-only/optional/dev/typing/examples - pytest - pytest-xdist