Merge pull request #3481 from edanielson-ginkgo/config_repos_from_env_vars

Configure the default module repository, branch, and path from environment variables.

Author: edanielson-ginkgo

CHANGELOG.md

@@ -19,6 +19,7 @@
 ### Modules
 
 - increase meta index for multiple input channels ([#3463](https://github.com/nf-core/tools/pull/3463))
+- Configure the default module repository, branch, and path from environment variables. ([#3481](https://github.com/nf-core/tools/pull/3481))
 
 ### Subworkflows
 

nf_core/components/components_utils.py

@@ -1,4 +1,5 @@
 import logging
+import os
 import re
 from pathlib import Path
 from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
@@ -15,9 +16,9 @@
 log = logging.getLogger(__name__)
 
 # Constants for the nf-core/modules repo used throughout the module files
-NF_CORE_MODULES_NAME = "nf-core"
-NF_CORE_MODULES_REMOTE = "https://github.com/nf-core/modules.git"
-NF_CORE_MODULES_DEFAULT_BRANCH = "master"
+NF_CORE_MODULES_NAME = os.environ.get("NF_CORE_MODULES_NAME", "nf-core")
+NF_CORE_MODULES_REMOTE = os.environ.get("NF_CORE_MODULES_REMOTE", "https://github.com/nf-core/modules.git")
+NF_CORE_MODULES_DEFAULT_BRANCH = os.environ.get("NF_CORE_MODULES_DEFAULT_BRANCH", "master")
 
 
 def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]:

tests/components/test_components_utils.py

@@ -1,3 +1,7 @@
+import importlib
+import os
+from unittest import mock
+
 import responses
 
 import nf_core.components.components_utils
@@ -55,3 +59,23 @@ def test_get_biotools_ch_info_warn(self):
             response = nf_core.components.components_utils.get_biotools_response("bpipe")
             nf_core.components.components_utils.get_channel_info_from_biotools(response, "test")
             assert "Could not find an EDAM ontology term for 'test'" in self.caplog.text
+
+    def test_environment_variables_override(self):
+        """Test environment variables override default values"""
+        mock_env = {
+            "NF_CORE_MODULES_NAME": "custom-name",
+            "NF_CORE_MODULES_REMOTE": "https://custom-repo.git",
+            "NF_CORE_MODULES_DEFAULT_BRANCH": "custom-branch",
+        }
+
+        try:
+            with mock.patch.dict(os.environ, mock_env):
+                importlib.reload(nf_core.components.components_utils)
+                assert nf_core.components.components_utils.NF_CORE_MODULES_NAME == mock_env["NF_CORE_MODULES_NAME"]
+                assert nf_core.components.components_utils.NF_CORE_MODULES_REMOTE == mock_env["NF_CORE_MODULES_REMOTE"]
+                assert (
+                    nf_core.components.components_utils.NF_CORE_MODULES_DEFAULT_BRANCH
+                    == mock_env["NF_CORE_MODULES_DEFAULT_BRANCH"]
+                )
+        finally:
+            importlib.reload(nf_core.components.components_utils)