Merge pull request #2218 from NovakApis/feature/python-typing/modules…

…_utils.py

python-typing/modules_utils.py

nf_core/modules/modules_utils.py

@@ -1,7 +1,8 @@
 import logging
 import os
-import urllib
 from pathlib import Path
+from typing import List, Optional, Tuple
+from urllib.parse import urlparse
 
 from ..components.nfcore_component import NFCoreComponent
 
@@ -14,31 +15,29 @@ class ModuleException(Exception):
     pass
 
 
-def repo_full_name_from_remote(remote_url):
+def repo_full_name_from_remote(remote_url: str) -> str:
     """
     Extracts the path from the remote URL
     See https://mirrors.edge.kernel.org/pub/software/scm/git/docs/git-clone.html#URLS for the possible URL patterns
     """
     # Check whether we have a https or ssh url
     if remote_url.startswith("https"):
-        path = urllib.parse.urlparse(remote_url)
-        path = path.path
+        path = urlparse(remote_url).path
         # Remove the intial '/'
         path = path[1:]
         # Remove extension
         path = os.path.splitext(path)[0]
     else:
         # Remove the initial `git@``
-        path = remote_url.split("@")
-        path = path[-1] if len(path) > 1 else path[0]
-        path = urllib.parse.urlparse(path)
-        path = path.path
+        split_path: list = remote_url.split("@")
+        path = split_path[-1] if len(split_path) > 1 else split_path[0]
+        path = urlparse(path).path
         # Remove extension
         path = os.path.splitext(path)[0]
     return path
 
 
-def get_installed_modules(dir, repo_type="modules"):
+def get_installed_modules(dir: str, repo_type="modules") -> Tuple[List[str], List[str]]:
     """
     Make a list of all modules installed in this repository
 
@@ -52,9 +51,9 @@ def get_installed_modules(dir, repo_type="modules"):
     returns (local_modules, nfcore_modules)
     """
     # initialize lists
-    local_modules = []
-    nfcore_modules = []
-    local_modules_dir = None
+    local_modules: List[str] = []
+    nfcore_modules: List[str] = []
+    local_modules_dir: Optional[str] = None
     nfcore_modules_dir = os.path.join(dir, "modules", "nf-core")
 
     # Get local modules
@@ -82,7 +81,9 @@ def get_installed_modules(dir, repo_type="modules"):
                 nfcore_modules.append(m)
 
     # Make full (relative) file paths and create NFCoreComponent objects
-    local_modules = [os.path.join(local_modules_dir, m) for m in local_modules]
+    if local_modules_dir:
+        local_modules = [os.path.join(local_modules_dir, m) for m in local_modules]
+
     nfcore_modules = [
         NFCoreComponent(
             m,