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sync: Keep automated template update PRs open #3851

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ae22b17
don't close open template update PRs
mashehu Oct 28, 2025
8d07eec
Merge branch 'dev' into keep-sync-pr-open
ningyuxin1999 Oct 28, 2025
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69 changes: 0 additions & 69 deletions nf_core/pipelines/sync.py
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,6 @@ def sync(self) -> None:
self.create_merge_base_branch()
self.push_merge_branch()
self.make_pull_request()
self.close_open_template_merge_prs()
except PullRequestExceptionError as e:
self.reset_target_dir()
raise PullRequestExceptionError(e)
Expand Down Expand Up @@ -410,74 +409,6 @@ def make_pull_request(self):
log.debug(f"GitHub API PR worked, return code {r.status_code}")
log.info(f"GitHub PR created: {self.gh_pr_returned_data['html_url']}")

def close_open_template_merge_prs(self):
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I wouldn't remove this functions, maybe we want to reimplement this in the future? But we could deprecate them for now, maybe add a TODO comment or something similar?

"""Get all template merging branches (starting with 'nf-core-template-merge-')
and check for any open PRs from these branches to the self.from_branch
If open PRs are found, add a comment and close them
"""
log.info("Checking for open PRs from template merge branches")

# Look for existing pull-requests
list_prs_url = f"https://api.github.com/repos/{self.gh_repo}/pulls"
with self.gh_api.cache_disabled():
list_prs_request = self.gh_api.get(list_prs_url)

list_prs_json, list_prs_pp = self._parse_json_response(list_prs_request)

log.debug(f"GitHub API listing existing PRs:\n{list_prs_url}\n{list_prs_pp}")
if list_prs_request.status_code != 200:
log.warning(f"Could not list open PRs ('{list_prs_request.status_code}')\n{list_prs_url}\n{list_prs_pp}")
return False

for pr in list_prs_json:
if isinstance(pr, int):
log.debug(f"Incorrect PR format: {pr}")
else:
log.debug(f"Looking at PR from '{pr['head']['ref']}': {pr['html_url']}")
# Ignore closed PRs
if pr["state"] != "open":
log.debug(f"Ignoring PR as state not open ({pr['state']}): {pr['html_url']}")
continue

# Don't close the new PR that we just opened
if pr["head"]["ref"] == self.merge_branch:
continue

# PR is from an automated branch and goes to our target base
if pr["head"]["ref"].startswith("nf-core-template-merge-") and pr["base"]["ref"] == self.from_branch:
self.close_open_pr(pr)

def close_open_pr(self, pr) -> bool:
"""Given a PR API response, add a comment and close."""
log.debug(f"Attempting to close PR: '{pr['html_url']}'")

# Make a new comment explaining why the PR is being closed
comment_text = (
f"Version `{nf_core.__version__}` of the [nf-core/tools](https://github.com/nf-core/tools) pipeline template has just been released. "
f"This pull-request is now outdated and has been closed in favour of {self.pr_url}\n\n"
f"Please use {self.pr_url} to merge in the new changes from the nf-core template as soon as possible."
)
with self.gh_api.cache_disabled():
self.gh_api.post(url=pr["comments_url"], data=json.dumps({"body": comment_text}))

# Update the PR status to be closed
with self.gh_api.cache_disabled():
pr_request = self.gh_api.patch(url=pr["url"], data=json.dumps({"state": "closed"}))

pr_request_json, pr_request_pp = self._parse_json_response(pr_request)

# PR update worked
if pr_request.status_code == 200:
log.debug(f"GitHub API PR-update worked:\n{pr_request_pp}")
log.info(
f"Closed GitHub PR from '{pr['head']['ref']}' to '{pr['base']['ref']}': {pr_request_json['html_url']}"
)
return True
# Something went wrong
else:
log.warning(f"Could not close PR ('{pr_request.status_code}'):\n{pr['url']}\n{pr_request_pp}")
return False

@staticmethod
def _parse_json_response(response) -> tuple[Any, str]:
"""Helper method to parse JSON response and create pretty-printed string.
Expand Down
65 changes: 0 additions & 65 deletions tests/pipelines/test_sync.py
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Original file line number Diff line number Diff line change
Expand Up @@ -311,71 +311,6 @@ def test_make_pull_request_bad_response(self, mock_post, mock_get):
"Something went badly wrong - GitHub API PR failed - got return code 404"
)

@mock.patch("nf_core.utils.gh_api.get", side_effect=mocked_requests_get)
def test_close_open_template_merge_prs(self, mock_get):
"""Try closing all open prs"""
psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
psync.inspect_sync_dir()
psync.get_wf_config()
psync.gh_api.get = mock_get
psync.gh_username = "list_prs"
psync.gh_repo = "list_prs/response"
os.environ["GITHUB_AUTH_TOKEN"] = "test"

with mock.patch("nf_core.pipelines.sync.PipelineSync.close_open_pr") as mock_close_open_pr:
psync.close_open_template_merge_prs()

prs = mock_get(f"https://api.github.com/repos/{psync.gh_repo}/pulls").data
for pr in prs:
if pr.get("state", None) == "open":
mock_close_open_pr.assert_any_call(pr)

@mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post)
@mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch)
def test_close_open_pr(self, mock_patch, mock_post) -> None:
psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
psync.inspect_sync_dir()
psync.get_wf_config()
psync.gh_api.post = mock_post
psync.gh_api.patch = mock_patch
psync.gh_username = "bad_url"
psync.gh_repo = "bad_url/response"
os.environ["GITHUB_AUTH_TOKEN"] = "test"
pr: dict[str, str | dict[str, str]] = {
"state": "open",
"head": {"ref": "nf-core-template-merge-3"},
"base": {"ref": "main"},
"html_url": "pr_html_url",
"url": "url_to_update_pr",
"comments_url": "pr_comments_url",
}

assert psync.close_open_pr(pr)
mock_patch.assert_called_once_with(url="url_to_update_pr", data='{"state": "closed"}')

@mock.patch("nf_core.utils.gh_api.post", side_effect=mocked_requests_post)
@mock.patch("nf_core.utils.gh_api.patch", side_effect=mocked_requests_patch)
def test_close_open_pr_fail(self, mock_patch, mock_post):
psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
psync.inspect_sync_dir()
psync.get_wf_config()
psync.gh_api.post = mock_post
psync.gh_api.patch = mock_patch
psync.gh_username = "bad_url"
psync.gh_repo = "bad_url/response"
os.environ["GITHUB_AUTH_TOKEN"] = "test"
pr = {
"state": "open",
"head": {"ref": "nf-core-template-merge-3"},
"base": {"ref": "main"},
"html_url": "pr_html_url",
"url": "bad_url_to_update_pr",
"comments_url": "pr_comments_url",
}

assert not psync.close_open_pr(pr)
mock_patch.assert_called_once_with(url="bad_url_to_update_pr", data='{"state": "closed"}')

def test_reset_target_dir(self):
"""Try resetting target pipeline directory"""
psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
Expand Down