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explicitly install numkit and cpython with GROMACS
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- work around some weird installation issues that are probably due to
  the fact that we need to pull GROMACS from bioconda in some instances
- (1) For macOS Python 2.7, numkit gets uninstalled: need to keep it
  explicitly.
- (2) For Python 3.9, mamba wants to replace cpython with pypy and that
  leads to all kinds of problems (similar to what was reported in
  mamba-org/mamba#658 ). We explicitly request
  the cpython version of Python 3.9 when installing GROMACS.
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orbeckst committed Sep 15, 2023
1 parent 3b3a616 commit bb640ec
Showing 1 changed file with 6 additions and 2 deletions.
8 changes: 6 additions & 2 deletions .github/workflows/ci.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ jobs:
cache-downloads: true
cache-environment: true
create-args: >-
python=${{ matrix.python-version }}
python=${{ matrix.python-version }}.*=*_cpython
- name: Python version information ${{ matrix.python-version }}
run: |
Expand All @@ -97,8 +97,12 @@ jobs:
micromamba install pytest pytest-pep8 pytest-cov codecov
- name: Install GROMACS (${{ matrix.gromacs-version }})
# UGLY HACK/FIX (probably to issues with bioconda packages)
# - For 3.9, micromamba insists on using pypy 3.9 (and --py-pin does not help).
# - For 2.7 macOS, numkit would get uninstalled.
# We can't freeze because then it's not possible to install older GROMACS versions from bioconda.
run: |
micromamba install --py-pin 'gromacs==${{ matrix.gromacs-version }}' pocl
micromamba install 'gromacs==${{ matrix.gromacs-version }}' pocl numkit python=${{ matrix.python-version }}.*=*_cpython
- name: Install package (with no dependencies)
run: |
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