Merge pull request #2870 from nf-core/task_1763/short_sha

fix: adds a short sha representation to modules list command pointing to the repo specific commit

CHANGELOG.md

@@ -79,6 +79,8 @@
 - Patch: handle file not found when it is an added file to a module ([#2771](https://github.com/nf-core/tools/pull/2771))
 - Handle symlinks when migrating pytest ([#2770](https://github.com/nf-core/tools/pull/2770))
 - Add `--profile` parameter to nf-test command ([#2767](https://github.com/nf-core/tools/pull/2767))
+- Reduce the sha length in the `nf-core modules list local` and add links to the specific commit ([#2870](https://github.com/nf-core/tools/pull/2870))
+- Add links the nf-core module page and to open the local file in VSCode for module lint results ([#2870](https://github.com/nf-core/tools/pull/2870))
 
 ### General
 

nf_core/components/lint/__init__.py

@@ -11,6 +11,7 @@
 import rich.box
 import rich.console
 import rich.panel
+import rich.repr
 from rich.markdown import Markdown
 from rich.table import Table
 
@@ -31,6 +32,7 @@ class LintExceptionError(Exception):
     pass
 
 
+@rich.repr.auto
 class LintResult:
     """An object to hold the results of a lint test"""
 
@@ -42,6 +44,7 @@ def __init__(self, component, lint_test, message, file_path):
         self.component_name = component.component_name
 
 
+@rich.repr.auto
 class ComponentLint(ComponentCommand):
     """
     An object for linting modules and subworkflows either in a clone of the 'nf-core/modules'
@@ -231,9 +234,21 @@ def format_result(test_results, table):
                 if last_modname and lint_result.component_name != last_modname:
                     even_row = not even_row
                 last_modname = lint_result.component_name
+
+                # If this is an nf-core module, link to the nf-core webpage
+                if lint_result.component.repo_url == "https://github.com/nf-core/modules.git":
+                    module_url = "https://nf-co.re/modules/" + lint_result.component_name.replace("/", "_")
+                    module_name = f"[link={module_url}]{lint_result.component_name}[/link]"
+                else:
+                    module_name = lint_result.component_name
+
+                # Make the filename clickable to open in VSCode
+                file_path = os.path.relpath(lint_result.file_path, self.dir)
+                file_path_link = f"[link=vscode://file/{os.path.abspath(file_path)}]{file_path}[/link]"
+
                 table.add_row(
-                    Markdown(f"{lint_result.component_name}"),
-                    os.path.relpath(lint_result.file_path, self.dir),
+                    module_name,
+                    file_path_link,
                     Markdown(f"{lint_result.message}"),
                     style="dim" if even_row else None,
                 )

nf_core/components/list.py

@@ -70,7 +70,7 @@ def pattern_msg(keywords: List[str]) -> str:
         # We have a pipeline - list what's installed
         else:
             # Check that we are in a pipeline directory
-            print(f"{self.repo_type=}")
+            log.info(f"Repository type: [blue]{self.repo_type}")
             try:
                 if self.repo_type != "pipeline":
                     raise UserWarning(
@@ -125,10 +125,11 @@ def pattern_msg(keywords: List[str]) -> str:
                             version_sha = component_entry["git_sha"]
                             try:
                                 # pass repo_name to get info on modules even outside nf-core/modules
-                                message, date = ModulesRepo(
+                                module = ModulesRepo(
                                     remote_url=repo_url,
                                     branch=component_entry["branch"],
-                                ).get_commit_info(version_sha)
+                                )
+                                message, date = module.get_commit_info(version_sha)
                             except LookupError as e:
                                 log.warning(e)
                                 date = "[red]Not Available"
@@ -140,7 +141,14 @@ def pattern_msg(keywords: List[str]) -> str:
                             version_sha = "[red]Not Available"
                             date = "[red]Not Available"
                             message = "[red]Not Available"
-                        table.add_row(component, repo_url, version_sha, message, date)
+                        nice_repo_name = repo_url.replace("https://github.com/", "").replace(".git", "")
+                        table.add_row(
+                            component,
+                            f"[link={repo_url}]{nice_repo_name}[/link]",
+                            f"[link={module.gitless_repo()}/commit/{version_sha}]{version_sha[:7]}[/link]",
+                            message,
+                            date,
+                        )
                         components.append(component)
 
         if print_json:

nf_core/modules/modules_repo.py

@@ -69,6 +69,12 @@ def __init__(self, remote_url=None, branch=None, no_pull=False, hide_progress=Fa
 
         self.avail_module_names = None
 
+    def gitless_repo(self):
+        gitless_repo_url = self.remote_url
+        if self.remote_url and ".git" in self.remote_url:
+            gitless_repo_url = gitless_repo_url[:-4]
+        return gitless_repo_url
+
     def setup_local_repo(self, remote, branch, hide_progress=True, in_cache=False):
         """
         Sets up the local git repository. If the repository has been cloned previously, it