Merge pull request #2767 from mashehu/nf-test-profiles

Modules: Add `--profile` parameter to nf-test command

CHANGELOG.md

@@ -19,6 +19,7 @@
 ### Modules
 
 - Handle dirty local module repos by force checkout of commits and branches if needed ([#2734](https://github.com/nf-core/tools/pull/2734))
+- Add `--profile` parameter to nf-test command ([#2767](https://github.com/nf-core/tools/pull/2767))
 
 ### General
 

nf_core/__main__.py

@@ -1134,7 +1134,13 @@ def create_module(
     default=False,
     help="Run tests only once. Don't check snapshot stability",
 )
-def test_module(ctx, tool, dir, no_prompts, update, once):
+@click.option(
+    "--profile",
+    type=click.Choice(["docker", "singularity", "conda"]),
+    default=None,
+    help="Run tests with a specific profile",
+)
+def test_module(ctx, tool, dir, no_prompts, update, once, profile):
     """
     Run nf-test for a module.
 
@@ -1153,6 +1159,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once):
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
             verbose=ctx.obj["verbose"],
+            profile=profile,
         )
         module_tester.run()
     except (UserWarning, LookupError) as e:
@@ -1398,7 +1405,13 @@ def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest):
     default=False,
     help="Run tests only once. Don't check snapshot stability",
 )
-def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once):
+@click.option(
+    "--profile",
+    type=click.Choice(["none", "singularity"]),
+    default=None,
+    help="Run tests with a specific profile",
+)
+def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once, profile):
     """
     Run nf-test for a subworkflow.
 
@@ -1417,6 +1430,7 @@ def test_subworkflow(ctx, subworkflow, dir, no_prompts, update, once):
             remote_url=ctx.obj["modules_repo_url"],
             branch=ctx.obj["modules_repo_branch"],
             verbose=ctx.obj["verbose"],
+            profile=profile,
         )
         sw_tester.run()
     except (UserWarning, LookupError) as e:

nf_core/components/components_test.py

@@ -48,6 +48,8 @@ class ComponentsTest(ComponentCommand):  # type: ignore[misc]
         flag indicating if the existing snapshot should be updated
     once : bool
         flag indicating if the test should be run only once
+    profile : str
+        container software to use (docker, singularity or conda)
 
     Methods
     -------
@@ -72,6 +74,7 @@ def __init__(
         verbose: bool = False,
         update: bool = False,
         once: bool = False,
+        profile: Optional[str] = None,
     ):
         super().__init__(component_type, directory, remote_url, branch, no_prompts=no_prompts)
         self.component_name = component_name
@@ -82,6 +85,7 @@ def __init__(
         self.obsolete_snapshots: bool = False
         self.update = update
         self.once = once
+        self.profile = profile
 
     def run(self) -> None:
         """Run build steps"""
@@ -129,7 +133,7 @@ def check_inputs(self) -> None:
             )
 
         # Check container software to use
-        if os.environ.get("PROFILE") is None:
+        if os.environ.get("PROFILE") is None and self.profile is None:
             os.environ["PROFILE"] = ""
             if self.no_prompts:
                 log.info(
@@ -190,10 +194,11 @@ def generate_snapshot(self) -> bool:
         update = "--update-snapshot" if self.update else ""
         self.update = False  # reset self.update to False to test if the new snapshot is stable
         tag = f"subworkflows/{self.component_name}" if self.component_type == "subworkflows" else self.component_name
+        profile = self.profile if self.profile else os.environ["PROFILE"]
 
         result = nf_core.utils.run_cmd(
             "nf-test",
-            f"test --tag {tag} --profile {os.environ['PROFILE']} {verbose} {update}",
+            f"test --tag {tag} --profile {profile} {verbose} {update}",
         )
         if result is not None:
             nftest_out, nftest_err = result
@@ -232,16 +237,18 @@ def check_snapshot_stability(self) -> bool:
             log.error("nf-test snapshot is not stable")
             self.errors.append("nf-test snapshot is not stable")
             return False
+
         else:
             if self.obsolete_snapshots:
                 # ask if the user wants to remove obsolete snapshots using nf-test --clean-snapshot
                 if self.no_prompts or Confirm.ask(
                     "nf-test found obsolete snapshots. Do you want to remove them?", default=True
                 ):
+                    profile = self.profile if self.profile else os.environ["PROFILE"]
                     log.info("Removing obsolete snapshots")
                     nf_core.utils.run_cmd(
                         "nf-test",
-                        f"test --tag {self.component_name} --profile {os.environ['PROFILE']} --clean-snapshot",
+                        f"test --tag {self.component_name} --profile {profile} --clean-snapshot",
                     )
                 else:
                     log.debug("Obsolete snapshots not removed")