Merge pull request #2458 from mashehu/add-retry-functionality

switch to safe_get for github requests

.github/workflows/create-test-lint-wf-template.yml

@@ -16,6 +16,7 @@ concurrency:
 
 env:
   NXF_ANSI_LOG: false
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   RunTestWorkflow:

nf_core/utils.py

@@ -480,6 +480,8 @@ def __call__(self, r):
         if os.environ.get("GITHUB_TOKEN") is not None and self.auth is None:
             self.auth_mode = "Bearer token with GITHUB_TOKEN"
             self.auth = BearerAuth(os.environ["GITHUB_TOKEN"])
+        else:
+            log.warning("Could not find GitHub authentication token. Some API requests may fail.")
 
         log.debug(f"Using GitHub auth: {self.auth_mode}")
 
@@ -833,7 +835,7 @@ def prompt_remote_pipeline_name(wfs):
     # Non nf-core repo on GitHub
     if pipeline.count("/") == 1:
         try:
-            gh_api.get(f"https://api.github.com/repos/{pipeline}")
+            gh_api.safe_get(f"https://api.github.com/repos/{pipeline}")
         except Exception:
             # No repo found - pass and raise error at the end
             pass