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 +58,11 @@ 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
+        if self.check_alternate_remotes(modules_json):
+            err_msg = f"You are trying to install {self.component_type} from different repositories with the same organization name '{self.org}' (set in the `.nf-core.yml` file in the `org_path` field).\nThis is not supported, and will likely cause problems. org_path should be set to the github account/organization name."
+            log.err(err_msg)
+
         # Verify SHA
         if not self.modules_repo.verify_sha(self.prompt, self.sha):
             return False
@@ -264,3 +269,19 @@ 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 error if multiple remotes exist.
+
+        Return:
+            True: if problematic components are found
+            False: if problematic components are not found
+        """
+        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:
+                    return True
+        return False