Merge pull request #3085 from mashehu/tool-fairy

Add `--migrate_pytest` option to `nf-core test` command

CHANGELOG.md

@@ -61,6 +61,7 @@
 - Update python:3.12-slim Docker digest to f11725a ([#3071](https://github.com/nf-core/tools/pull/3071))
 - Fix number of arguments for pipelines_create within the command_create function ([#3074](https://github.com/nf-core/tools/pull/3074))
 - Update python:3.12-slim Docker digest to 740d94a ([#3079](https://github.com/nf-core/tools/pull/3079))
+- Add `--migrate_pytest` option to `nf-core <modules|subworkflows> test` command ([#3085](https://github.com/nf-core/tools/pull/3085))
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 ([#3091](https://github.com/nf-core/tools/pull/3091))
 - Pipelines: allow numbers in custom pipeline name ([#3094](https://github.com/nf-core/tools/pull/3094))
 - Add bot action to update textual snapshots and write bot documentation ([#3102](https://github.com/nf-core/tools/pull/3102))

nf_core/__main__.py

@@ -1154,11 +1154,17 @@ def command_modules_create(
     default=None,
     help="Run tests with a specific profile",
 )
-def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile):
+@click.option(
+    "--migrate-pytest",
+    is_flag=True,
+    default=False,
+    help="Migrate a module with pytest tests to nf-test",
+)
+def command_modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a module.
     """
-    modules_test(ctx, tool, dir, no_prompts, update, once, profile)
+    modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest)
 
 
 # nf-core modules lint
@@ -1352,11 +1358,17 @@ def command_subworkflows_create(ctx, subworkflow, dir, author, force, migrate_py
     default=None,
     help="Run tests with a specific profile",
 )
-def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
+@click.option(
+    "--migrate-pytest",
+    is_flag=True,
+    default=False,
+    help="Migrate a subworkflow with pytest tests to nf-test",
+)
+def command_subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a subworkflow.
     """
-    subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile)
+    subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest)
 
 
 # nf-core subworkflows list subcommands

nf_core/commands_modules.py

@@ -219,14 +219,29 @@ def modules_create(
         sys.exit(1)
 
 
-def modules_test(ctx, tool, dir, no_prompts, update, once, profile):
+def modules_test(ctx, tool, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a module.
 
     Given the name of a module, runs the nf-test command to test the module and generate snapshots.
     """
     from nf_core.components.components_test import ComponentsTest
 
+    if migrate_pytest:
+        modules_create(
+            ctx,
+            tool,
+            dir,
+            author="",
+            label="",
+            meta=True,
+            no_meta=False,
+            force=False,
+            conda_name=None,
+            conda_package_version=None,
+            empty_template=False,
+            migrate_pytest=migrate_pytest,
+        )
     try:
         module_tester = ComponentsTest(
             component_type="modules",

nf_core/commands_subworkflows.py

@@ -34,14 +34,16 @@ def subworkflows_create(ctx, subworkflow, dir, author, force, migrate_pytest):
         sys.exit(1)
 
 
-def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile):
+def subworkflows_test(ctx, subworkflow, dir, no_prompts, update, once, profile, migrate_pytest):
     """
     Run nf-test for a subworkflow.
 
     Given the name of a subworkflow, runs the nf-test command to test the subworkflow and generate snapshots.
     """
     from nf_core.components.components_test import ComponentsTest
 
+    if migrate_pytest:
+        subworkflows_create(ctx, subworkflow, dir, None, False, True)
     try:
         sw_tester = ComponentsTest(
             component_type="subworkflows",