modernized CI workflow #254
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orbeckst
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Sep 15, 2023
orbeckst
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- fix mamba installation fails on macOS GH runner #253
- use micromamba instead of mamba
- use CODECOV_TOKEN for codecov
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- use micromamba instead of mamba - use separate ci/conda-envs/test_env.yaml for conda env - use CODECOV_TOKEN for codecov
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Codecov Report
@@ Coverage Diff @@
## main #254 +/- ##
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Coverage 66.49% 66.49%
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Files 23 23
Lines 4325 4325
Branches 739 739
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Hits 2876 2876
Misses 1256 1256
Partials 193 193
📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
- install matplotlib instead of matplotlib-base for Python 2.7 (also works in 3) - used same version pins in setup.py and test_env.yaml - removed numpy from testing dep in setup.py as it is a package dep
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Remaining issue is that for Python 3.9, the installation of GROMACS (from bioconda) changes python==3.9 to pypy==3.9, somewhat reminiscent of mamba-org/mamba#658. Things to try
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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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