refact: Move constants to new file and use MRepo

Moves constants from component_utils to constants.py so that ModulesRepo can be used from inside of component_utils, thereby avoiding a circular import
sanger-tol · Dec 16, 2024 · c0a7a00 · c0a7a00
1 parent f4cc0fe
commit c0a7a00
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Showing 11 changed files with 22 additions and 27 deletions.
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -54,7 +54,7 @@
     subworkflows_test,
     subworkflows_update,
 )
-from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE
+from nf_core.components.constants import NF_CORE_MODULES_REMOTE
 from nf_core.pipelines.download import DownloadError
 from nf_core.utils import check_if_outdated, nfcore_logo, rich_force_colors, setup_nfcore_dir
 

diff --git a/nf_core/components/components_utils.py b/nf_core/components/components_utils.py
@@ -1,25 +1,18 @@
 import logging
 import re
 from pathlib import Path
-from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union
 
 import questionary
 import requests
 import rich.prompt
 import yaml
 
-if TYPE_CHECKING:
-    from nf_core.modules.modules_repo import ModulesRepo
-
 import nf_core.utils
+from nf_core.modules.modules_repo import ModulesRepo
 
 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"
-
 
 def get_repo_info(directory: Path, use_prompt: Optional[bool] = True) -> Tuple[Path, Optional[str], str]:
     """
@@ -181,14 +174,14 @@ def get_components_to_install(
                 for component in components:
                     if isinstance(component, dict):
                         component_name = list(component.keys())[0].lower()
-                        git_remote = component[component_name]["git_remote"]
-                        org_path = Path(subworkflow_dir).parent.stem
+                        branch = component[component_name].get("branch")
+                        modules_repo = ModulesRepo(component[component_name]["git_remote"], branch)
                         current_comp_dict = subworkflows if component_name in subworkflows else modules
 
                         component_dict = {
-                            "org_path": org_path,
-                            "git_remote": git_remote,
-                            "branch": component[component_name].get("branch"),
+                            "org_path": modules_repo.repo_path,
+                            "git_remote": modules_repo.remote_url,
+                            "branch": branch,
                         }
 
                         current_comp_dict[component_name].update(component_dict)

diff --git a/nf_core/components/constants.py b/nf_core/components/constants.py
@@ -0,0 +1,4 @@
+# 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"
diff --git a/nf_core/components/info.py b/nf_core/components/info.py
@@ -15,7 +15,7 @@
 
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-from nf_core.components.components_utils import NF_CORE_MODULES_REMOTE
+from nf_core.components.constants import NF_CORE_MODULES_REMOTE
 from nf_core.modules.modules_json import ModulesJson
 
 log = logging.getLogger(__name__)

diff --git a/nf_core/components/install.py b/nf_core/components/install.py
@@ -14,11 +14,8 @@
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
-from nf_core.components.components_utils import (
-    NF_CORE_MODULES_NAME,
-    get_components_to_install,
-    prompt_component_version_sha,
-)
+from nf_core.components.components_utils import get_components_to_install, prompt_component_version_sha
+from nf_core.components.constants import NF_CORE_MODULES_NAME
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import ModulesRepo
 

diff --git a/nf_core/modules/modules_json.py b/nf_core/modules/modules_json.py
@@ -15,7 +15,8 @@
 from typing_extensions import NotRequired, TypedDict  # for py<3.11
 
 import nf_core.utils
-from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE, get_components_to_install
+from nf_core.components.components_utils import get_components_to_install
+from nf_core.components.constants import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.modules_repo import ModulesRepo
 from nf_core.pipelines.lint_utils import dump_json_with_prettier
 

diff --git a/nf_core/modules/modules_repo.py b/nf_core/modules/modules_repo.py
@@ -12,7 +12,7 @@
 
 import nf_core.modules.modules_json
 import nf_core.modules.modules_utils
-from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
+from nf_core.components.constants import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.synced_repo import RemoteProgressbar, SyncedRepo
 from nf_core.utils import NFCORE_CACHE_DIR, NFCORE_DIR, load_tools_config
 

diff --git a/nf_core/synced_repo.py b/nf_core/synced_repo.py
@@ -9,7 +9,7 @@
 import git
 from git.exc import GitCommandError
 
-from nf_core.components.components_utils import (
+from nf_core.components.constants import (
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,
 )

diff --git a/tests/modules/test_modules_json.py b/tests/modules/test_modules_json.py
@@ -3,7 +3,7 @@
 import shutil
 from pathlib import Path
 
-from nf_core.components.components_utils import (
+from nf_core.components.constants import (
     NF_CORE_MODULES_DEFAULT_BRANCH,
     NF_CORE_MODULES_NAME,
     NF_CORE_MODULES_REMOTE,

diff --git a/tests/modules/test_update.py b/tests/modules/test_update.py
@@ -8,7 +8,7 @@
 import yaml
 
 import nf_core.utils
-from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
+from nf_core.components.constants import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.install import ModuleInstall
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.patch import ModulePatch

diff --git a/tests/subworkflows/test_update.py b/tests/subworkflows/test_update.py
@@ -8,7 +8,7 @@
 import yaml
 
 import nf_core.utils
-from nf_core.components.components_utils import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
+from nf_core.components.constants import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.update import ModuleUpdate
 from nf_core.subworkflows.install import SubworkflowInstall