Fix failing tests

nf_core/modules/lint/__init__.py

@@ -96,9 +96,12 @@ def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull
  else:
  raise LookupError(f"No modules from {self.modules_repo.remote_url} installed in pipeline.")
  else:
+ module_dir = Path(self.dir, "modules")
  self.all_remote_modules = [
- NFCoreModule(module_dir / m, self.repo_type, Path(self.dir)) for m in self.module_names["modules"]
+ NFCoreModule(m, None, module_dir / m, self.repo_type, Path(self.dir))
+ for m in self.module_names["modules"]
  ]
+ self.all_local_modules = []
 
  self.lint_config = None
  self.modules_json = None

nf_core/modules/lint/meta_yml.py

@@ -28,7 +28,7 @@ def meta_yml(module_lint_object, module):
  if module.is_patched:
  lines = ModulesDiffer.try_apply_patch(
  module.module_name,
- "nf-core/modules",
+ module_lint_object.modules_repo.fullname,
  module.patch_path,
  Path(module.module_dir).relative_to(module.base_dir),
  reverse=True,

tests/modules/lint.py

@@ -1,5 +1,9 @@
+import pytest
+
 import nf_core.modules
 
+from ..utils import GITLAB_URL
+
 
 def test_modules_lint_trimgalore(self):
  """Test linting the TrimGalore! module"""
@@ -16,11 +20,8 @@ def test_modules_lint_empty(self):
  self.mods_remove.remove("fastqc")
  self.mods_remove.remove("multiqc")
  self.mods_remove.remove("custom/dumpsoftwareversions")
- module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
- module_lint.lint(print_results=False, all_modules=True)
- assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
- assert len(module_lint.passed) == 0
- assert len(module_lint.warned) == 0
+ with pytest.raises(LookupError):
+ nf_core.modules.ModuleLint(dir=self.pipeline_dir)
 
 
 def test_modules_lint_new_modules(self):
@@ -30,3 +31,20 @@ def test_modules_lint_new_modules(self):
  assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
  assert len(module_lint.passed) > 0
  assert len(module_lint.warned) >= 0
+
+
+def test_modules_lint_no_gitlab(self):
+ """Test linting a pipeline with no modules installed"""
+ with pytest.raises(LookupError):
+ nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+
+
+def test_modules_lint_gitlab_modules(self):
+ """Lint modules from a different remote"""
+ self.mods_install_gitlab.install("fastqc")
+ self.mods_install_gitlab.install("multiqc")
+ module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+ module_lint.lint(print_results=False, all_modules=True)
+ assert len(module_lint.failed) == 0
+ assert len(module_lint.passed) > 0
+ assert len(module_lint.warned) >= 0

tests/test_modules.py

@@ -110,7 +110,9 @@ def test_modulesrepo_class(self):
  )
  from .modules.lint import (
  test_modules_lint_empty,
+ test_modules_lint_gitlab_modules,
  test_modules_lint_new_modules,
+ test_modules_lint_no_gitlab,
  test_modules_lint_trimgalore,
  )
  from .modules.list import (