From 72fe1e4ed221f86886990cb624adc5b304a08af5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Rahn?= <1529364+rrahn@users.noreply.github.com>
Date: Tue, 11 Nov 2025 13:09:37 +0100
Subject: [PATCH 1/3] Fix GH API rate limits.

---
 .github/workflows/pytest.yml                    |  2 ++
 tests/test_datasets/test_test_datasets_utils.py | 15 +++++++++++++--
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index fed3698f36..e7b43be2c3 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -101,6 +101,8 @@ jobs:
 
       - name: Test with pytest
         id: pytest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.coveragerc --durations=0 -n auto && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py
diff --git a/tests/test_datasets/test_test_datasets_utils.py b/tests/test_datasets/test_test_datasets_utils.py
index 3a58765752..628ae67852 100644
--- a/tests/test_datasets/test_test_datasets_utils.py
+++ b/tests/test_datasets/test_test_datasets_utils.py
@@ -1,3 +1,4 @@
+import os
 import unittest
 
 import requests
@@ -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)
 
@@ -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

From b13a03ca7049e5e65a3b6d288a5de42debe537f8 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Wed, 12 Nov 2025 10:19:00 +0000
Subject: [PATCH 2/3] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a04aea7af9..d65e93264b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -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

From 0fa71ea9d6c586cc769a17065dcb6bb3720ac9af Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Rahn?= <1529364+rrahn@users.noreply.github.com>
Date: Wed, 12 Nov 2025 12:24:05 +0100
Subject: [PATCH 3/3] Remove GITHUB_TOKEN from pytest workflow

Removed GITHUB_TOKEN from pytest environment since it is already present on workflow level.
---
 .github/workflows/pytest.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index e7b43be2c3..fed3698f36 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -101,8 +101,6 @@ jobs:
 
       - name: Test with pytest
         id: pytest
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           python3 -m pytest tests/${{matrix.test}} --color=yes --cov --cov-config=.coveragerc --durations=0 -n auto && exit_code=0|| exit_code=$?
           # don't fail if no tests were collected, e.g. for test_licence.py