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Reorganize dependencies #3497

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merged 3 commits into from
Jan 6, 2022
Merged

Reorganize dependencies #3497

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a01c825
reorganize dependencies
lilyminium Jan 6, 2022
6d55ff4
remove repo checks
lilyminium Jan 6, 2022
50f34e7
Revert "remove repo checks"
lilyminium Jan 6, 2022
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61 changes: 37 additions & 24 deletions .github/actions/setup-deps/action.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -83,24 +83,36 @@ runs:
steps:
- name: conda_install
shell: bash -l {0}
run: |
# setup env variable for the minimum deps
CONDA_MIN_DEPS="${{ inputs.biopython }} ${{ inputs.codecov }} "
CONDA_MIN_DEPS+="${{ inputs.cython }} ${{ inputs.griddataformats }} "
CONDA_MIN_DEPS+="${{ inputs.gsd }} ${{ inputs.hypothesis }} "
CONDA_MIN_DEPS+="${{ inputs.matplotlib }} ${{ inputs.mmtf-python }} "
CONDA_MIN_DEPS+="${{ inputs.networkx }} ${{ inputs.numpy }} "
CONDA_MIN_DEPS+="${{ inputs.pip }} ${{ inputs.pytest }} "
CONDA_MIN_DEPS+="${{ inputs.scipy }} ${{ inputs.threadpoolctl }} "
CONDA_MIN_DEPS+="${{ inputs.tqdm }} "

# setup env variable for optional deps
CONDA_OPT_DEPS="${{ inputs.chemfiles-python }} ${{ inputs.clustalw }} "
CONDA_OPT_DEPS+="${{ inputs.h5py }} ${{ inputs.joblib }} "
CONDA_OPT_DEPS+="${{ inputs.netcdf4 }} ${{ inputs.openmm }} "
CONDA_OPT_DEPS+="${{ inputs.rdkit }} ${{ inputs.scikit-learn }} "
CONDA_OPT_DEPS+="${{ inputs.seaborn }} ${{ inputs.tidynamics }} "
env:
CONDA_MIN_DEPS: |
${{ inputs.biopython }}
${{ inputs.codecov }}
${{ inputs.cython }}
${{ inputs.griddataformats }}
${{ inputs.gsd }}
${{ inputs.hypothesis }}
${{ inputs.matplotlib }}
${{ inputs.mmtf-python }}
${{ inputs.networkx }}
${{ inputs.numpy }}
${{ inputs.pip }}
${{ inputs.pytest }}
${{ inputs.scipy }}
${{ inputs.threadpoolctl }}
${{ inputs.tqdm }}
CONDA_OPT_DEPS: |
${{ inputs.chemfiles-python }}
${{ inputs.clustalw }}
${{ inputs.h5py }}
${{ inputs.joblib }}
${{ inputs.netcdf4 }}
${{ inputs.openmm }}
${{ inputs.rdkit }}
${{ inputs.scikit-learn }}
${{ inputs.seaborn }}
${{ inputs.tidynamics }}

run: |
# setup full variable
if [ ${{ inputs.full-deps }} = "true" ]; then
CONDA_DEPS="${CONDA_MIN_DEPS} ${CONDA_OPT_DEPS} ${{ inputs.extra-conda-deps }}"
Expand All @@ -117,14 +129,15 @@ runs:

- name: pip_install
shell: bash -l {0}
env:
PIP_MIN_DEPS: |
${{ inputs.coverage }}
${{ inputs.pytest-cov }}
${{ inputs.pytest-xdist }}
PIP_OPT_DEPS: |
${{ inputs.duecredit }}
${{ inputs.parmed }}
run: |
# setup env variable for the minimum deps
PIP_MIN_DEPS="${{ inputs.coverage }} ${{ inputs.pytest-cov }} "
PIP_MIN_DEPS+="${{ inputs.pytest-xdist }} "

# setup env variable for optional deps
PIP_OPT_DEPS="${{ inputs.duecredit }} ${{ inputs.parmed }} "

# setup full variable
if [ ${{ inputs.full-deps }} = "true" ]; then
PIP_DEPS="${PIP_MIN_DEPS} ${PIP_OPT_DEPS} ${{ inputs.extra-pip-deps }}"
Expand Down