feat: Allow the environment variable SNAKEMAKE_CONDA_PREFIX to be present without --use-conda #2263
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
…thout use_conda. Instead of exiting warn, and then set conda_prefix to None and continue without conda.
|
Kudos, SonarCloud Quality Gate passed!
|
|
@johanneskoester could you approve the CI tests for this PR? Thanks! |
johanneskoester
approved these changes
Jun 5, 2023
johanneskoester
pushed a commit
that referenced
this pull request
Jun 9, 2023
🤖 I have created a release *beep* *boop* --- ## [7.27.0](v7.26.0...v7.27.0) (2023-06-07) ### Features * Allow the environment variable SNAKEMAKE_CONDA_PREFIX to be present without --use-conda ([#2263](#2263)) ([e4eba8d](e4eba8d)) ### Bug Fixes * adapt linting rule to Python 3.11 ([a3a5c58](a3a5c58)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Outdated suggestions cannot be applied.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.
Description
SNAKEMAKE_CONDA_PREFIX is a great tool for shared computing environments and I am encouraging everyone in our lab to set it in their
.bashrcit to help with the number of conda builds we have and reduce file usage. However, there is one downside and that is it becomes impossible to run a non conda snakemake without clearing the environment variable because the lack of--use-condawill force snakemake to exit.In this PR I suggest a quality of life improvement. Instead of having snakemake error out, it will instead warn that the environment variable is set but conda environments will not be used or built because
--use-condais not set. Note, this will only happen when the environment variable is set and not when it is passed as a command line argument.Thanks for considering!
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).