Fix 2.4 sync

CHANGELOG.md

@@ -1,5 +1,9 @@
 # nf-core/tools: Changelog
 
+## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
+
+- Patch release to try to fix the template sync ([#1585](https://github.com/nf-core/tools/pull/1585)).
+
 ## [v2.4 - Cobolt Koala](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 
 ### Template

nf_core/sync.py

@@ -76,11 +76,14 @@ def __init__(
  self.gh_repo = gh_repo
  self.pr_url = ""
 
+ # Set up the API auth if supplied on the command line
  self.gh_api = nf_core.utils.gh_api
- if self.gh_username and "GITHUB_AUTH_TOKEN" in os.environ:
- self.gh_api.auth = requests.auth.HTTPBasicAuth(self.gh_username, os.environ["GITHUB_AUTH_TOKEN"])
- self.gh_api.return_ok = [200, 201]
  self.gh_api.lazy_init()
+ if self.gh_username and "GITHUB_AUTH_TOKEN" in os.environ:
+ log.debug(f"Authenticating sync as {self.gh_username}")
+ self.gh_api.setup_github_auth(
+ requests.auth.HTTPBasicAuth(self.gh_username, os.environ["GITHUB_AUTH_TOKEN"])
+ )
 
  def sync(self):
  """Find workflow attributes, create a new template pipeline on TEMPLATE"""
@@ -320,7 +323,6 @@ def make_pull_request(self):
 
  # Make new pull-request
  stderr = rich.console.Console(stderr=True, force_terminal=nf_core.utils.rich_force_colors())
- log.debug("Submitting PR to GitHub API")
  with self.gh_api.cache_disabled():
  try:
  r = self.gh_api.request_retry(

nf_core/utils.py

@@ -454,21 +454,25 @@ def __call__(self, r):
 
  log.debug(f"Using GitHub auth: {self.auth_mode}")
 
- def log_content_headers(self, request):
+ def log_content_headers(self, request, post_data=None):
  """
  Try to dump everything to the console, useful when things go wrong.
  """
  log.debug(f"Requested URL: {request.url}")
  log.debug(f"From requests cache: {request.from_cache}")
  log.debug(f"Request status code: {request.status_code}")
  log.debug(f"Request reason: {request.reason}")
+ if post_data is None:
+ post_data = {}
  try:
  log.debug(json.dumps(dict(request.headers), indent=4))
  log.debug(json.dumps(request.json(), indent=4))
+ log.debug(json.dumps(post_data, indent=4))
  except Exception as e:
  log.debug(f"Could not parse JSON response from GitHub API! {e}")
  log.debug(request.headers)
  log.debug(request.content)
+ log.debug(post_data)
 
  def safe_get(self, url):
  """
@@ -504,14 +508,16 @@ def request_retry(self, url, post_data=None):
  while True:
  # GET request
  if post_data is None:
+ log.debug(f"Seding GET request to {url}")
  r = self.get(url=url)
  # POST request
  else:
+ log.debug(f"Seding POST request to {url}")
  r = self.post(url=url, json=post_data)
 
  # Failed but expected - try again
  if r.status_code in self.return_retry:
- self.log_content_headers(r)
+ self.log_content_headers(r, post_data)
  log.debug(f"GitHub API PR failed - got return code {r.status_code}")
  wait_time = float(re.sub("[^0-9]", "", str(r.headers.get("Retry-After", 0))))
  if wait_time == 0:
@@ -522,8 +528,8 @@ def request_retry(self, url, post_data=None):
 
  # Unexpected error - raise
  elif r.status_code not in self.return_ok:
- self.log_content_headers(r)
- raise AssertionError(f"GitHub API PR failed - got return code {r.status_code} from {url}")
+ self.log_content_headers(r, post_data)
+ raise RuntimeError(f"GitHub API PR failed - got return code {r.status_code} from {url}")
 
  # Success!
  else:

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = "2.4"
+version = "2.4.1"
 
 with open("README.md") as f:
  readme = f.read()