Speed up (using mamba) and fix the CI; better installation documentation #69
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
should be a lot faster, based on experiences with it in wotplot
i thiiiink this should address the mamba-takes-forever-on-github- actions crap -- at least, it worked locally. but double-check; i may need to do the thing of creating an empty env and then updating that from the yaml (see mamba-org/mamba#633 (comment))
Codecov Report
@@ Coverage Diff @@
## main #69 +/- ##
=======================================
Coverage 80.49% 80.49%
=======================================
Files 20 20
Lines 2466 2466
Branches 555 555
=======================================
Hits 1985 1985
Misses 455 455
Partials 26 26 |
- mention mamba (close #50) - mention install-from-source as backup option
fedarko
changed the title
fedarko
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Closes #68.
Switched to mamba and replaced the
defaultschannel in the environment YAML withnodefaults, since mixingdefaultsandconda-forgecauses problems for mamba (https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#mixing-the-defaults-and-conda-forge-channels). This combination of changes fixed and sped up the build.I also updated the dev documentation (to mention using mamba instead of conda) and updated the environment YAML's upper limit on Python from
<= 3.7to< 3.8(I think this is a more accurate way of writing this out, plus it matches what I already had in thesetup.pyand bioconda recipe files...)