obtain module suggestions from installed modules

CHANGELOG.md

@@ -21,6 +21,7 @@
 
 - Add `--fix-version` flag to `nf-core modules lint` command to update modules to the latest version ([#1588](https://github.com/nf-core/tools/pull/1588))
 - Fix a bug in the regex extracting the version from biocontainers URLs [#1598](https://github.com/nf-core/tools/pull/1598)
+- Command `nf-core modules test` obtains module name suggestions from installed modules [#1624](https://github.com/nf-core/tools/pull/1624)
 
 ## [v2.4.1 - Cobolt Koala Patch](https://github.com/nf-core/tools/releases/tag/2.4) - [2022-05-16]
 

nf_core/modules/module_test.py

@@ -13,10 +13,9 @@
 import questionary
 import rich
 
+import nf_core.modules.module_utils
 import nf_core.utils
 
-from .modules_repo import ModulesRepo
-
 log = logging.getLogger(__name__)
 
 
@@ -34,6 +33,10 @@ class ModulesTest(object):
         flat indicating if prompts are used
     pytest_args : tuple
         additional arguments passed to pytest command
+    all_local_modules: list
+        List of all installed local modules
+    all_nfcore_modules: list
+        List of all installed nf-core modules
 
     Methods
     -------
@@ -56,6 +59,8 @@ def __init__(
         self.module_name = module_name
         self.no_prompts = no_prompts
         self.pytest_args = pytest_args
+        self.all_local_modules = ""
+        self.all_nfcore_modules = ""
 
     def run(self):
         """Run test steps"""
@@ -71,17 +76,27 @@ def run(self):
     def _check_inputs(self):
         """Do more complex checks about supplied flags."""
 
+        # Get installed modules
+        self.all_local_modules, self.all_nfcore_modules = nf_core.modules.module_utils.get_installed_modules(
+            ".", "modules"
+        )
+
         # Get the tool name if not specified
         if self.module_name is None:
             if self.no_prompts:
                 raise UserWarning(
                     "Tool name not provided and prompts deactivated. Please provide the tool name as TOOL/SUBTOOL or TOOL."
                 )
-            modules_repo = ModulesRepo()
-            modules_repo.get_modules_file_tree()
+            all_installed_modules = [m.module_name for m in self.all_nfcore_modules]
+            if len(all_installed_modules) == 0:
+                raise UserWarning(
+                    "No installed modules were found.\n"
+                    "Are you running the tests inside the nf-core/modules main directory?\n"
+                    "Otherwise, make sure that the directory structure is modules/TOOL/SUBTOOL/ and tests/modules/TOOLS/SUBTOOL/"
+                )
             self.module_name = questionary.autocomplete(
                 "Tool name:",
-                choices=modules_repo.modules_avail_module_names,
+                choices=all_installed_modules,
                 style=nf_core.utils.nfcore_question_style,
             ).ask()
         module_dir = Path("modules") / self.module_name

tests/modules/module_test.py

@@ -26,3 +26,13 @@ def test_modules_test_no_name_no_prompts(self):
         meta_builder._check_inputs()
     os.chdir(cwd)
     assert "Tool name not provided and prompts deactivated." in str(excinfo.value)
+
+
+def test_modules_test_no_installed_modules(self):
+    """Test the check_inputs() function - raise UserWarning because installed modules were not found"""
+    cwd = os.getcwd()
+    meta_builder = nf_core.modules.ModulesTest(None, False, "")
+    with pytest.raises(UserWarning) as excinfo:
+        meta_builder._check_inputs()
+    os.chdir(cwd)
+    assert "No installed modules were found." in str(excinfo.value)

tests/test_modules.py

@@ -109,6 +109,7 @@ def test_modulesrepo_class(self):
     )
     from .modules.module_test import (
         test_modules_test_check_inputs,
+        test_modules_test_no_installed_modules,
         test_modules_test_no_name_no_prompts,
     )
     from .modules.remove import (