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fix: remove default packages from conda envs #2749

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timtroendle
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@timtroendle timtroendle commented Mar 12, 2024

Fixes #2748.

Description

Ensure that conda's default packages are not installed by Snakemake.

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (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).

@johanneskoester johanneskoester changed the title Remove default packages from conda envs fix: femove default packages from conda envs Mar 13, 2024
@johanneskoester johanneskoester changed the title fix: femove default packages from conda envs fix: remove default packages from conda envs Mar 13, 2024
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johanneskoester commented Mar 13, 2024

Good idea, I was not even aware of that possibility. May I ask you to mention the behavior you implemented here in the docs section about Snakemake's conda integration?

@timtroendle timtroendle force-pushed the feature-no-conda-default-packages branch from 9b3626d to 9ebb0e9 Compare March 15, 2024 14:56
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Sure. Done in the updated commit.

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sonarcloud bot commented Mar 15, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.4% Duplication on New Code

See analysis details on SonarCloud

@johanneskoester johanneskoester merged commit 027906c into snakemake:main Mar 26, 2024
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johanneskoester pushed a commit that referenced this pull request Mar 26, 2024
🤖 I have created a release *beep* *boop*
---


##
[8.10.2](v8.10.1...v8.10.2)
(2024-03-26)


### Bug Fixes

* remove default packages from conda envs
([#2749](#2749))
([027906c](027906c))
* use base64 encoding for passing default resources args to jobs
([#2780](#2780))
([4735bc3](4735bc3))

---
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>
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Snakemake should ignore conda's default pacakges
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