template update

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/vscode/devcontainers/python:3.9-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
 
 ENV PYTHONUNBUFFERED 1
 
@@ -8,7 +8,7 @@ ARG USER_GID=$USER_UID
 RUN if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then groupmod --gid $USER_GID vscode && usermod --uid $USER_UID --gid $USER_GID vscode; fi
 
 # [Option] Install Node.js
-ARG INSTALL_NODE="true"
+ARG INSTALL_NODE="false"
 ARG NODE_VERSION="lts/*"
 RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
 

.devcontainer/license_header.txt

@@ -1,4 +1,4 @@
-Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)
 
 Licensed under the Apache License, Version 2.0 (the "License");

.github/workflows/check_template_files.yaml

@@ -4,14 +4,23 @@ on: push
 
 jobs:
   check-template-files:
+    name: Check template files
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        id: setup-python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.12'
+
       - name: Check template files
+        id: check-template-files
         run: |
           if [ "${{ github.event.repository.name }}" == "microservice-repository-template" ]
           then

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 prof/
 
 # Translations
@@ -132,6 +133,12 @@ dmypy.json
 # ignore VS Code settings:
 .vscode/
 
+# key stores
+*.key
+*.rnd
+.keystore
+.ssl/
+
 # desktop settings and thumbnails
 .DS_Store
 desktop.ini

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+   Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
    for the German Human Genome-Phenome Archive (GHGA)
 
    Licensed under the Apache License, Version 2.0 (the "License");

scripts/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

scripts/script_utils/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

scripts/script_utils/cli.py

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -26,6 +26,13 @@ def echo_success(message: str):
     typer.echo(styled_message)
 
 
+def echo_warning(message: str):
+    """Print a warning message."""
+
+    styled_message = typer.style(text=message, fg=typer.colors.YELLOW)
+    typer.echo(styled_message)
+
+
 def echo_failure(message: str):
     """Print a failure message."""
 

scripts/update_all.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,33 +19,57 @@
 """Run all update scripts that are present in the repository in the correct order"""
 
 try:
-    from scripts.update_template_files import main as update_template
+    from update_template_files import main as update_template
 except ImportError:
-    pass
+    print("update_template_files script not found")
 else:
     print("Pulling in updates from template repository")
     update_template()
 
 try:
-    from scripts.update_config_docs import main as update_config
+    from update_pyproject import main as update_pyproject
 except ImportError:
-    pass
+    print("update_pyproject script not found")
+else:
+    print("Updating pyproject.toml file")
+    update_pyproject()
+
+try:
+    from update_lock import main as update_lock
+except ImportError:
+    print("update_lock script not found")
+else:
+    print("Upgrading the lock file")
+    update_lock(upgrade=True)
+
+try:
+    from update_hook_revs import main as update_hook_revs
+except ImportError:
+    print("update_hook_revs script not found")
+else:
+    print("Updating config docs")
+    update_hook_revs()
+
+try:
+    from update_config_docs import main as update_config
+except ImportError:
+    print("update_config_docs script not found")
 else:
     print("Updating config docs")
     update_config()
 
 try:
-    from scripts.update_openapi_docs import main as update_openapi
+    from update_openapi_docs import main as update_openapi
 except ImportError:
-    pass
+    print("update_openapi_docs script not found")
 else:
     print("Updating OpenAPI docs")
     update_openapi()
 
 try:
-    from scripts.update_readme import main as update_readme
+    from update_readme import main as update_readme
 except ImportError:
-    pass
+    print("update_readme script not found")
 else:
     print("Updating README")
     update_readme()

scripts/update_template_files.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -40,12 +40,20 @@ def run(main_fn):
         main_fn(check="--check" in sys.argv[1:])
 
 
-REPO_ROOT_DIR = Path(__file__).parent.parent.resolve()
+REPO_ROOT_DIR = Path(__file__).parent.parent.absolute()
+
+FILE_LIST_DIR_NAME = ".template"
+DEPRECATED_FILES = "deprecated_files"
+MANDATORY_FILES = "mandatory_files"
+STATIC_FILES = "static_files"
 
-DEPRECATED_FILES = ".deprecated_files"
-MANDATORY_FILES = ".mandatory_files"
-STATIC_FILES = ".static_files"
 IGNORE_SUFFIX = "_ignore"
+
+TEMPLATE_LIST_REL_PATHS = [
+    f"{FILE_LIST_DIR_NAME}/{list_name}.txt"
+    for list_name in [STATIC_FILES, MANDATORY_FILES, DEPRECATED_FILES]
+]
+
 RAW_TEMPLATE_URL = (
     "https://raw.githubusercontent.com/ghga-de/microservice-repository-template/main/"
 )
@@ -55,10 +63,15 @@ class ValidationError(RuntimeError):
     """Raised when files need to be updated."""
 
 
+def get_file_list_path(list_name: str, relative: bool = False) -> Path:
+    """Get the path to the file list of the given name."""
+    return Path(REPO_ROOT_DIR / FILE_LIST_DIR_NAME / f"{list_name}.txt")
+
+
 def get_file_list(list_name: str) -> list[str]:
     """Return a list of all file names specified in a given list file."""
-    list_path = REPO_ROOT_DIR / list_name
-    with open(list_path, "r", encoding="utf8") as list_file:
+    list_path = get_file_list_path(list_name)
+    with open(list_path, encoding="utf8") as list_file:
         file_list = [
             clean_line
             for clean_line in (
@@ -127,7 +140,7 @@ def check_file(relative_file_path: str, diff: bool = False) -> bool:
             print(f"  - {local_file_path}: cannot check, remote is missing")
             return True
 
-        with open(local_file_path, "r", encoding="utf8") as file:
+        with open(local_file_path, encoding="utf8") as file:
             return diff_content(local_file_path, file.read(), template_file_content)
 
     return False
@@ -153,7 +166,7 @@ def update_file(relative_file_path: str, diff: bool = False) -> bool:
             return True
 
         if diff and local_file_path.exists():
-            with open(local_file_path, "r", encoding="utf8") as file:
+            with open(local_file_path, encoding="utf8") as file:
                 if file.read() == template_file_content:
                     return False
 
@@ -212,14 +225,13 @@ def remove_files(files: list[str], check: bool = False) -> bool:
 def main(check: bool = False):
     """Update the static files in the service template."""
     updated = False
-    if not check:
-        update_files([STATIC_FILES], diff=True, check=False)
+
+    print("Template lists...")
+    if update_files(TEMPLATE_LIST_REL_PATHS, diff=True, check=False):
+        updated = True
 
     print("Static files...")
     files_to_update = get_file_list(STATIC_FILES)
-    if check:
-        files_to_update.append(STATIC_FILES)
-    files_to_update.extend((MANDATORY_FILES, DEPRECATED_FILES))
     if update_files(files_to_update, diff=True, check=check):
         updated = True