warn instead of fail when no components are installed from the repo

nf-core · Jan 22, 2024 · c07afe1 · c07afe1
1 parent faf8529
commit c07afe1
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -600,7 +600,7 @@ def lint(
 
     # Run the lint tests!
     try:
-        lint_obj, module_lint_obj = run_linting(
+        lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(
             dir,
             release,
             fix,
@@ -613,7 +613,7 @@ def lint(
             json,
             ctx.obj["hide_progress"],
         )
-        if len(lint_obj.failed) + len(module_lint_obj.failed) > 0:
+        if len(lint_obj.failed) + len(module_lint_obj.failed) + len(subworkflow_lint_obj.failed) > 0:
             sys.exit(1)
     except AssertionError as e:
         log.critical(e)

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
@@ -97,9 +97,7 @@ def __init__(
                         )
                     )
             if not self.all_remote_components:
-                raise LookupError(
-                    f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline."
-                )
+                log.warning(f"No {self.component_type} from {self.modules_repo.remote_url} installed in pipeline.")
             local_component_dir = Path(self.dir, self.component_type, "local")
             self.all_local_components = []
             if local_component_dir.exists():

diff --git a/nf_core/lint_utils.py b/nf_core/lint_utils.py
@@ -18,7 +18,7 @@
 
 def print_joint_summary(lint_obj, module_lint_obj, subworkflow_lint_obj):
     """Print a joint summary of the general pipe lint tests and the module and subworkflow lint tests"""
-    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + len(subworkflow_lint_obj.passed)
+    nbr_passed = len(lint_obj.passed) + len(module_lint_obj.passed) + len(subworkflow_lint_obj.passed or 0)
     nbr_ignored = len(lint_obj.ignored)
     nbr_fixed = len(lint_obj.fixed)
     nbr_warned = len(lint_obj.warned) + len(module_lint_obj.warned) + len(subworkflow_lint_obj.warned)