obtain module suggestions from installed modules

CHANGELOG.md

@@ -31,6 +31,7 @@
 - Update how we interface with git remotes. ([#1626](https://github.com/nf-core/tools/issues/1626))
 - Add prompt for module name to `nf-core modules info` ([#1644](https://github.com/nf-core/tools/issues/1644))
 - Update docs with example of custom git remote ([#1645](https://github.com/nf-core/tools/issues/1645))
+- Command `nf-core modules test` obtains module name suggestions from installed modules ([#1624](https://github.com/nf-core/tools/pull/1624))
 - Add `--base-path` flag to `nf-core modules` to specify the base path for the modules in a remote. Also refactored `modules.json` code. ([#1643](https://github.com/nf-core/tools/issues/1643))
 
 ## [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

@@ -13,14 +13,14 @@
 import questionary
 import rich
 
+import nf_core.modules.module_utils
 import nf_core.utils
-
-from .modules_repo import ModulesRepo
+from nf_core.modules.modules_command import ModuleCommand
 
 log = logging.getLogger(__name__)
 
 
-class ModulesTest(object):
+class ModulesTest(ModuleCommand):
     """
     Class to run module pytests.
 
@@ -52,11 +52,25 @@ def __init__(
         module_name=None,
         no_prompts=False,
         pytest_args="",
+        remote_url=None,
+        branch=None,
+        no_pull=False,
     ):
         self.module_name = module_name
         self.no_prompts = no_prompts
         self.pytest_args = pytest_args
 
+        # Check repository type
+        try:
+            pipeline_dir, repo_type = nf_core.modules.module_utils.get_repo_type(".", use_prompt=False)
+            log.debug(f"Found {repo_type} repo: {pipeline_dir}")
+        except UserWarning as e:
+            log.debug(f"Only showing remote info: {e}")
+            pipeline_dir = None
+
+        super().__init__(pipeline_dir, remote_url, branch, no_pull)
+        self.get_pipeline_modules(True)  # To change!
+
     def run(self):
         """Run test steps"""
         if not self.no_prompts:
@@ -71,25 +85,66 @@ def run(self):
     def _check_inputs(self):
         """Do more complex checks about supplied flags."""
 
+        # Retrieving installed modules
+        if self.repo_type == "modules":
+            local = False
+            installed_modules = self.module_names["modules"]
+        else:
+            local = questionary.confirm("Is the module local?", style=nf_core.utils.nfcore_question_style).unsafe_ask()
+            if local:
+                installed_modules = self.module_names.get("local/modules")
+            else:
+                installed_modules = self.module_names.get("nf-core/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()
+            if installed_modules is None:
+                raise UserWarning(
+                    "No installed modules were found from '{self.modules_repo.remote_url}'.\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.get_avail_modules(),
+                choices=installed_modules,
                 style=nf_core.utils.nfcore_question_style,
             ).unsafe_ask()
-        module_dir = Path("modules") / self.module_name
 
-        # First, sanity check that the module directory exists
-        if not module_dir.is_dir():
+        # Sanity check that the module directory exists
+        self._validate_folder_structure(local)
+
+    def _validate_folder_structure(self, local=False):
+        """Validate that the modules follow the correct folder structure to run the tests:
+        - modules/TOOL/SUBTOOL/
+        - tests/modules/TOOL/SUBTOOL/
+
+        local (bool): Testing local modules (True) or nf-core modules (False)
+        """
+        if local:
+            basedir = "modules/local"
+        else:
+            basedir = "modules/nf-core"
+
+        if self.repo_type == "modules":
+            module_path = Path("modules") / self.module_name
+            test_path = Path("tests/modules") / self.module_name
+        else:
+            module_path = Path(f"{basedir}/modules") / self.module_name
+            test_path = Path(f"{basedir}/tests/modules") / self.module_name
+
+        if not module_path.is_dir():
+            raise UserWarning(
+                f"Cannot find directory '{module_path}'. Should be TOOL/SUBTOOL or TOOL. Are you running the tests inside the nf-core/modules main directory?"
+            )
+        if not test_path.is_dir():
             raise UserWarning(
-                f"Cannot find directory '{module_dir}'. Should be TOOL/SUBTOOL or TOOL. Are you running the tests inside the nf-core/modules main directory?"
+                f"Cannot find directory '{test_path}'. Should be TOOL/SUBTOOL or TOOL."
+                "Are you running the tests inside the nf-core/modules main directory?"
+                "Do you have tests for the specified module?"
             )
 
     def _set_profile(self):

nf_core/modules/modules_command.py

@@ -34,7 +34,7 @@ def __init__(self, dir, remote_url=None, branch=None, no_pull=False, base_path=N
         except LookupError as e:
             raise UserWarning(e)
 
-    def get_pipeline_modules(self):
+    def get_pipeline_modules(self, retrieve_local=False):
         """
         Get the modules installed in the current directory.
 
@@ -44,14 +44,19 @@ def get_pipeline_modules(self):
         is a clone of nf-core/modules the filed is set to
         `{"modules": modules_in_dir}`
 
+        retrieve_local (bool): True if retrieving local modules
+
         """
 
         self.module_names = {}
 
         module_base_path = f"{self.dir}/modules/"
 
         if self.repo_type == "pipeline":
-            repo_owners = (owner for owner in os.listdir(module_base_path) if owner != "local")
+            if retrieve_local:
+                repo_owners = os.listdir(module_base_path)
+            else:
+                repo_owners = (owner for owner in os.listdir(module_base_path) if owner != "local")
             repo_names = (
                 f"{repo_owner}/{name}"
                 for repo_owner in repo_owners

tests/modules/module_test.py

@@ -26,3 +26,20 @@ 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_proper_path(self):
+    """Test the check_inputs() function - raise UserWarning because installed modules were not found"""
+    cwd = os.getcwd()
+    with pytest.raises(SystemError):
+        assert nf_core.modules.ModulesTest(".", False, "")
+
+
+def test_modules_test_all_modules_listed(self):
+    """Test the check_inputs() function - raise UserWarning because installed modules were not found"""
+    cwd = os.getcwd()
+    meta_builder = nf_core.modules.ModulesTest(".", 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

@@ -110,6 +110,7 @@ def test_modulesrepo_class(self):
     from .modules.module_test import (
         test_modules_test_check_inputs,
         test_modules_test_no_name_no_prompts,
+        test_modules_test_no_proper_path,
     )
     from .modules.remove import (
         test_modules_remove_trimgalore,