chore: checkout full history for formatting

[johanneskoester]

Description

Related Issue

Checklist

• [x] I've formatted the PR title in accordance with the structure of the conventional commit messages.
• [x] I've updated the code style using pre-commit if needed.
• [x] I've updated or supplemented the documentation as needed.
• [x] I've read the CODE_OF_CONDUCT.md document.
• [x] I've read the CONTRIBUTING.md guide.

[huzuner]

Conda command is not being found in some technology tests and in one benchmark test Could this also be about the recent conda change on snakemake?

[johanneskoester]

@alethomas unexpected failures here. Seems like a bug in pangolin's internal usage of the snakemake api.

[johanneskoester]

Ok, I think I found the problem. Seems to be fixed in the latest pangolin release.

[johanneskoester]

However, this is not yet merged: https://github.com/bioconda/bioconda-recipes/pull/42192

[huzuner]

curl: (28) Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 20000 ms: Timeout was reached I guess there were some connections issues there. Could you perhaps rerun the tests?

[huzuner]

And for the ModuleNotFoundError: No module named 'distutils' error, I guess spades should be updated as discussed here: https://github.com/ablab/spades/issues/1266

[alethomas]

I already made a PR for the spades update but I guess in order to get this one working I need to merge it

[huzuner]

One of the technology tests is failing with:

Error: Failed to CreateArtifact: Received non-retryable error: Failed request: (409) Conflict: an artifact with this name already exists on the workflow run

This also seems to be present in the master branch. Could that be because of using the same path in Upload logs for both benchmark and technology tests: https://github.com/IKIM-Essen/uncovar/blob/75bd2e7f1cc803f31e8bc36066ab813ee5dd5fb2/.github/workflows/main.yml#L185 and https://github.com/IKIM-Essen/uncovar/blob/75bd2e7f1cc803f31e8bc36066ab813ee5dd5fb2/.github/workflows/main.yml#L377