Log error when multiple remotes have the same org name

CHANGELOG.md

@@ -33,6 +33,7 @@
 - Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
+- Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([#2228](https://github.com/nf-core/tools/pull/2228)).
 
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 

nf_core/components/install.py

@@ -58,6 +58,9 @@ def install(self, component, silent=False):
  if not silent:
  modules_json.check_up_to_date()
 
+ # Verify that the remote repo's org_path does not match the org_path of any alternate repo among the installed modules
+ self.check_alternate_remotes(modules_json)
+
  # Verify SHA
  if not self.modules_repo.verify_sha(self.prompt, self.sha):
  return False
@@ -264,3 +267,25 @@ def clean_modules_json(self, component, modules_repo, modules_json):
  self.component_type, component, repo_to_remove, modules_repo.repo_path
  )
  return component_values["installed_by"]
+
+ def check_alternate_remotes(self, modules_json):
+ """
+ Check whether there are previously installed components with the same org_path but different remote urls
+ Log warning if multiple remotes exist.
+
+ Return:
+ True: if problematic components are found
+ False: if problematic components are not found
+ """
+ alternate_remotes = False
+ modules_json.load()
+ for repo_url, repo_content in modules_json.modules_json.get("repos", dict()).items():
+ for dir in repo_content.get(self.component_type, dict()).keys():
+ if dir == self.org and repo_url != self.modules_repo.remote_url:
+ alternate_remotes = True
+ if alternate_remotes:
+ warn_msg = f"Multiple module remotes are used with the same org_path '{self.org}': {', '.join(alternate_remotes)}. This may result in reinstalled modules from the wrong remote."
+ log.warning(warn_msg)
+ return True
+ else:
+ return False