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chore: work around setuptools 76 hash mismatch from March 9, 2025 #3370

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chore/setuptools-workaround
Mar 11, 2025
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chore: work around setuptools 76 hash mismatch from March 9, 2025 #3370
johanneskoester merged 3 commits intomainfrom
chore/setuptools-workaround

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@johanneskoester johanneskoester commented Mar 11, 2025 •
edited by coderabbitai bot
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Description

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).

Summary by CodeRabbit

  • Chores
    • Streamlined dependency management to consolidate package installations for a more consistent and reliable setup process.

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coderabbitai bot commented Mar 11, 2025 •
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📝 Walkthrough

Walkthrough

The test-environment.yml file has been updated to change how dependencies are managed. Specifically, the dependencies for cwltool and cwl-utils have been moved from the pip section to the main dependencies list, meaning they will now be installed via conda instead of pip.

Changes

File Change Summary
test-environment.yml Removed cwltool and cwl-utils from the pip section and added them to the main dependencies list.
📜 Recent review details

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Reviewing files that changed from the base of the PR and between d1c369b and 663ccb9.

⛔ Files ignored due to path filters (1)
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📒 Files selected for processing (2)
  • test-environment.yml (1 hunks)
  • test-environment.yml (1 hunks)
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🔇 Additional comments (1)
test-environment.yml (1)

61-62:

Details

❓ Verification inconclusive

Dependency Update: Installing cwltool and cwl-utils via Conda

Moving these two dependencies from the pip section to the main dependencies list ensures that they are now installed via conda. This change should help work around the setuptools 76 hash mismatch issues that can occur with pip. Please verify that both packages are available and up-to-date in your specified conda channels (e.g., conda-forge or bioconda), so that the installation remains stable and consistent.

Based on the snippet in test-environment.yml (lines 61–62) showing the dependencies:

  - cwltool
  - cwl-utils

the changes correctly reflect that these dependencies are now listed in the main dependencies (thus to be installed via conda) as opposed to being in the pip section. This update is intended to work around setuptools 76 hash mismatch issues associated with pip.

Please verify on your side that:

  • Both cwltool and cwl-utils are available in the intended conda channels (e.g., conda-forge or bioconda).
  • The packages are up-to-date in these channels to ensure stable installation.

Dependency Update Verified: Confirm Conda Package Availability

  • Verify lines 61–62 in test-environment.yml reflect the changes.
  • Confirm cwltool and cwl-utils are current in your conda channels.

🏁 Script executed:

#!/bin/bash
# Display lines 60 to 70 of test-environment.yml to verify that the cwltool and cwl-utils changes are in place
sed -n '60,70p' test-environment.yml

Length of output: 318

Dependency Update Verified:
The output from test-environment.yml confirms that the dependencies are now correctly listed under the conda dependencies section:

  • - cwltool
  • - cwl-utils

Please ensure that these packages are also available and kept up-to-date in your preferred conda channels (e.g., conda-forge or bioconda) to maintain a stable installation and work around the setuptools 76 hash mismatch issues.

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@johanneskoester johanneskoester changed the title Chore/setuptools-workaround chore: work around setuptools 76 hash mismatch from March 9, 2025 Mar 11, 2025
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sonarqubecloud bot commented Mar 11, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@johanneskoester johanneskoester merged commit 477e5f8 into main Mar 11, 2025
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@johanneskoester johanneskoester deleted the chore/setuptools-workaround branch March 11, 2025 10:19
This was referenced Mar 11, 2025
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kjohnsen pushed a commit to kjohnsen/snakemake that referenced this pull request Dec 15, 2025
@johanneskoester @kjohnsen
chore: work around setuptools 76 hash mismatch from March 9, 2025 (sn…
bfa95bf 
…akemake#3370)

### Description

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] 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).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Chores**
- Streamlined dependency management to consolidate package installations
for a more consistent and reliable setup process.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->
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