From 67a84e6e4f5bbe21ee36204e39f2a9f67487c0dd Mon Sep 17 00:00:00 2001
From: Adam Talbot <adam.talbot@seqera.io>
Date: Mon, 14 Aug 2023 14:39:26 +0100
Subject: [PATCH] fix: Drop container error to warning

Changes:
 - Container registries do not have a consistent API, so calling them
   for container presence doesn't seem to work on GHCR or NVCR.
 - This drops the error to a warning so we don't fail tests.

Relates to https://github.com/nf-core/modules/issues/3693 and https://github.com/nf-core/tools/issues/2393
---
 CHANGELOG.md                    | 4 ++++
 nf_core/modules/lint/main_nf.py | 7 ++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf5a0627ab..07e3bd4b3b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,7 +9,11 @@
 - Add module MULTIQC to modules.config ([#2377](https://github.com/nf-core/tools/pull/2377))
 - Update the Code of Conduct ([#2381](https://github.com/nf-core/tools/pull/2381))
 - Save template information to `.nf-core.yml` and deprecate argument `--template-yaml` for `nf-core sync` ([#2388](https://github.com/nf-core/tools/pull/2388) and [#2389](https://github.com/nf-core/tools/pull/2389))
+<<<<<<< HEAD
 - Remove fixed Ubuntu test and added to standard testing matrix
+=======
+- Reduce container finding error to warning since the registries are not consistent.
+>>>>>>> 4e7fd2f3 (fix: Drop container error to warning)
 
 ### Download
 
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 617e53c069..deb47b5799 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -346,8 +346,9 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
         if url is None:
             continue
         try:
+            container_url = "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url)
             response = requests.head(
-                "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url),
+                container_url,
                 stream=True,
                 allow_redirects=True,
             )
@@ -360,10 +361,10 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
             self.failed.append(("container_links", "Unable to connect to container URL", self.main_nf))
             continue
         if not response.ok:
-            self.failed.append(
+            self.warned.append(
                 (
                     "container_links",
-                    f"Unable to connect to {response.url}, status code: {response.status_code}",
+                    f"Unable to connect to container registry, code:  {response.status_code}, url: {response.url}",
                     self.main_nf,
                 )
             )