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Improve usage of setup-miniconda #249
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Based on the input description in action.yml¹, the default value is "flexible", and "true" is just an alias to "flexible". ¹ https://github.com/conda-incubator/setup-miniconda/blob/7e642bb2e4ca56ff706818a0febf72bb226d348d/action.yml#L173-L186
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Hmm, there are a few failing jobs:
The first 3 all fail on this step: cli/.github/actions/setup-integration-tests/action.yaml Lines 60 to 71 in 2b53cd4
I don't understand why they are failing, since the outputs of The failure on the 4th job is a known issue with the |
I looked into the Python 3.6 failures a bit more by splitting the step up to see where it's failing: victorlin@7171b90 Running CI on that commit makes it apparent that |
Mystery solved! The output of Plus, only the 3.6 version of Python from the default wget https://anaconda.org/anaconda/python/3.6.13/download/linux-64/python-3.6.13-h12debd9_1.tar.bz2
tar -xf python-3.6.13-h12debd9_1.tar.bz2 --one-top-level
./python-3.6.13-h12debd9_1/bin/python --version 2> stderr 1> stdout
cat stderr
# Python 3.6.13 :: Anaconda, Inc.
cat stdout
wget https://anaconda.org/anaconda/python/3.7.15/download/linux-64/python-3.7.15-h7a1cb2a_1.tar.bz2
tar -xf python-3.7.15-h7a1cb2a_1.tar.bz2 --one-top-level
./python-3.7.15-h7a1cb2a_1/bin/python --version 2> stderr 1> stdout
cat stderr
cat stdout
# Python 3.7.15 Currently CI passes outside of this PR because it is pulling Python from |
Python from the default anaconda channel can be unreliable¹. Use conda-forge which worked previously. ¹ #249 (comment)
Nod. It'd probably be useful to add (Also, debugging that sort of failure is right up the alley of our new "debugging runner" workflow. 🙃) |
Good sleuthing. Agreed we probably want the conda-forge build instead of the Anaconda build. In addition, I guess we could also change:
to:
to grep both stdout and stderr. (Or maybe only grepping stdout is a feature, e.g. it caught this unintentional change.) Although |
Based on the input description in action.yml¹, the default value is already "test" which means it should be auto-activated. ¹ https://github.com/conda-incubator/setup-miniconda/blob/7e642bb2e4ca56ff706818a0febf72bb226d348d/action.yml#L79-L91
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After comparing the workarounds in conda-incubator/setup-miniconda#274, I replaced e1036f6...06150f7 with 5239f4b which is a simpler way of accomplishing the same thing. |
Oh, I'll keep that in mind for next time!
Yeah, it was good to have here. I'll plan to leave it as-is. |
Ahh, I like this a lot more. Less change, less weirdness around setting an alternative solver, and avoids the Windows DLL issue. |
Hmm, but looks like |
Looked into that a little more, and it seems like the
which subsequent
|
(I'm particularly interested in this issue because I think it will resolve the CI failures in my recently-opened #250. :-) |
The option to use mamba-version in this action is still marked as experimental and has shown to be problematic with transient failures. An alternative is to use Mambaforge, which is a Miniforge variant that comes with Mamba in the base environment. It uses the conda-forge channel as the only default channel¹. However, conda-forge must be added to the channels input to the setup-miniconda action, since it creates and uses a separate condarc file which contains the specified channels along with defaults², and defaults should be avoided at least for the Python version³. ¹ https://github.com/conda-forge/miniforge/blob/871e98647a95b99a769dd9f40669d06c44514bca/README.md ² #249 (comment) ³ #249 (comment)
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Looks like there's an open issue for this: conda-incubator/setup-miniconda#207 |
🙌
We could also set |
There's lots of ways to reliably get away from
I'll think about which one to use and make another PR. |
Also ok by me to leave things as-is for now. |
Description of proposed changes
See commit messages.
Related issue(s)
Adapted from nextstrain/augur#1126.
Testing