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Fix GH API rate limits. #3895

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Merged
mashehu merged 3 commits into from
Nov 17, 2025
Merged

Fix GH API rate limits. #3895

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72fe1e4
Fix GH API rate limits.
rrahn Nov 11, 2025
b13a03c
[automated] Update CHANGELOG.md
nf-core-bot Nov 12, 2025
0fa71ea
Remove GITHUB_TOKEN from pytest workflow
rrahn Nov 12, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@
- chore(deps): update mcr.microsoft.com/devcontainers/miniconda docker digest to 19516ba ([#3890](https://github.com/nf-core/tools/pull/3890))
- Update dependency textual to v6.6.0 ([#3892](https://github.com/nf-core/tools/pull/3892))
- chore(deps): update mcr.microsoft.com/devcontainers/base:debian docker digest to 2e826a6 ([#3893](https://github.com/nf-core/tools/pull/3893))
- Fix GH API rate limits. ([#3895](https://github.com/nf-core/tools/pull/3895))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.5 ([#3900](https://github.com/nf-core/tools/pull/3900))

### Template
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15 changes: 13 additions & 2 deletions tests/test_datasets/test_test_datasets_utils.py
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@@ -1,3 +1,4 @@
import os
import unittest

import requests
Expand Down Expand Up @@ -92,7 +93,7 @@ def test_modules_branch_name_changed(self):

def test_modules_branch_exists(self):
url = self.gh_urls.get_remote_tree_url_for_branch(MODULES_BRANCH_NAME)
resp = requests.get(url)
resp = self._request_with_token(url)
self.assertTrue(resp.ok)
self.assertTrue(len(resp.json()) != 0)

Expand Down Expand Up @@ -143,9 +144,19 @@ def test_github_endpoints(self):
self.assertTrue(url_2 is not None)
self.assertTrue(url_3 is not None)

resp_1 = requests.get(url_1)
resp_1 = self._request_with_token(url_1)
resp_2 = requests.get(url_2)
resp_3 = requests.get(url_3)
self.assertTrue(resp_1.ok)
self.assertTrue(resp_2.ok)
self.assertFalse(resp_3.ok)

def _request_with_token(self, url):
"""Make a request with a GitHub token if available to mitigate issues with API rate limits."""
headers = {}
github_token = os.environ.get("GITHUB_TOKEN")
if github_token:
headers["authorization"] = f"Bearer {github_token}"

resp = requests.get(url, headers=headers)
return resp