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Fix GH API rate limits.#3895

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mashehu merged 3 commits into
nf-core:devfrom
rrahn:fix/gh_api_rate_limit
Nov 17, 2025
Merged

Fix GH API rate limits.#3895
mashehu merged 3 commits into
nf-core:devfrom
rrahn:fix/gh_api_rate_limit

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@rrahn

@rrahn rrahn commented Nov 12, 2025

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These tests do a direct request of a github API call, for which we receive API rate limit errors due to running on self-hosted runners.
This fixes this by populating the GITHUB_TOKEN to the test cases.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

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codecov Bot commented Nov 12, 2025

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.46%. Comparing base (eae5c97) to head (0fa71ea).
⚠️ Report is 25 commits behind head on dev.

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Comment thread .github/workflows/pytest.yml Outdated
- name: Test with pytest
id: pytest
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

@rrahn rrahn Nov 12, 2025

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I just saw, that GITHUB_TOKEN is already set on workflow level. I guess, this is then not needed.

@rrahn

rrahn commented Nov 14, 2025

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@mashehu I removed the github token in the step env.

rrahn and others added 3 commits November 14, 2025 15:15
Removed GITHUB_TOKEN from pytest environment since it is already present on workflow level.
@rrahn rrahn force-pushed the fix/gh_api_rate_limit branch from 40901c1 to 0fa71ea Compare November 14, 2025 14:17
@mashehu mashehu merged commit 3619d80 into nf-core:dev Nov 17, 2025
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3 participants