tidy up root dir (GSI-540)

.github/workflows/check_config_docs.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check config docs
         run: |

.github/workflows/check_openapi_spec.yaml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check if openapi.yaml is up to date
         run: |

.github/workflows/check_readme.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check readme
         run: |

.github/workflows/static_code_analysis.yaml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - uses: pre-commit/[email protected]
         env:

.github/workflows/tests.yaml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - id: pytest
         run: |

readme_generation.md → .readme_generation/README.md

@@ -18,30 +18,30 @@
 
 # Readme Generation
 
-The README file is generated by collecting information from different sources as
+The Repository README is generated by collecting information from different sources as
 outlined in the following.
 
 - name: The full name of the package is derived from the remote origin Git repository.
 - title: A title case representation of the name.
 - shortname: An abbreviation of the full name. This is derived from the name mentioned
-  in the [`./pyproject.toml`](./pyproject.toml).
+  in the [`../pyproject.toml`](../pyproject.toml).
 - summary: A short 1-2 sentence summary derived from the description in the
-  [`./pyproject.toml`](./pyproject.toml).
+  [`../pyproject.toml`](../pyproject.toml).
 - version: The package version derived from the version specified in the
-  [`./pyproject.toml`](./pyproject.toml).
+  [`../pyproject.toml`](../pyproject.toml).
 - description: A markdown-formatted description of the features and use cases of this
-  service or package. Obtained from the [`./.description.md`](./.description.md).
+  service or package. Obtained from the [`./description.md`](./description.md).
 - design_description: A markdown-formatted description of the overall architecture and
-  design of the package. Obtained from the [`./.design.md`](./.design.md).
+  design of the package. Obtained from the [`./design.md`](./design.md).
 - config_description: A markdown-formatted description of all config parameters.
-  This is autogenerated from the [`./config_schema.json`](./config_schema.json).
+  This is autogenerated from the [`../config_schema.json`](../config_schema.json).
 - openapi_doc: A markdown-formatted description of the HTTP API. This is autogenerated
-  and links to the [`./openapi.yaml`](./openapi.yaml). If the openapi.yaml is not
+  and links to the [`../openapi.yaml`](../openapi.yaml). If the openapi.yaml is not
   this documentation is empty.
 
-The [`./.readme_template.md`](./.readme_template.md) serves as a template where the
+The [`./readme_template.md`](./readme_template.md) serves as a template where the
 above variable can be filled in using Pythons `string.Template` utility from the
 standard library.
 
-The [`./scripts/update_readme.py`] script can be used to collect all information and
-fill it into the template to generate the README file.
+The [`../scripts/update_readme.py`](../scripts/update_readme.py) script can be used to
+collect all information and fill it into the template to generate the README file.

.template/README.md

@@ -0,0 +1,47 @@
+<!--
+ Copyright 2021 - 2023 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");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+-->
+
+# Template File Lists
+
+This directory contains multiple text files that are listing paths to other files
+of this repository. The listed files are affected in different ways by template updates
+as explained in the following.
+
+## `static_files.txt`
+The files listed here are synced with their counterparts in the template. They should
+never be modified manually.
+
+## `static_files_ignore.txt`
+To opt out of template updates just for individual files declared as static
+(e.g. because you would like manually modify them), you may add them to this list.
+
+## `mandatory_files.txt`
+The contents of the files listed here are not synced with the template, however, upon
+every template update it is checked that the files exist. You should modify them
+manually to the needs of your repository.
+
+## `mandatory_files_ignore.txt`
+To opt out of existence checks for individual files declared as mandatory, you may add
+them to this list.
+
+## `deprecated_files.txt`
+Files listed here must not exist in your repository and are automatically deleted upon
+a template update.
+
+## `deprecated_files_ignore.txt`
+If you would like to keep files declared as deprecated, you may add them to this list.

.deprecated_files → .template/deprecated_files.txt

@@ -19,7 +19,21 @@ docs
 
 setup.py
 setup.cfg
+requirements-dev-common.in
+requirements-dev.in
+requirements-dev.txt
+requirements.txt
 
 .pylintrc
 .flake8
 .editorconfig
+.deprecated_files
+.deprecated_files_ignore
+.mandatory_files
+.mandatory_files_ignore
+.static_files
+.static_files_ignore
+.description.md
+.design.md
+.readme_template.md
+.readme_generation.md

.mandatory_files → .template/mandatory_files.txt

@@ -13,16 +13,18 @@ tests/fixtures/__init__.py
 
 scripts/script_utils/fastapi_app_location.py
 
+.readme_generation/description.md
+.readme_generation/design.md
+
+lock/requirements-dev.in
+lock/requirements-dev.txt
+lock/requirements.txt
+
 Dockerfile
 config_schema.json
 example_config.yaml
 LICENSE
 pyproject.toml
 README.md
-requirements-dev.in
-requirements-dev.txt
-requirements.txt
 
-.description.md
-.design.md
 .pre-commit-config.yaml

.static_files → .template/static_files.txt

@@ -40,6 +40,14 @@ scripts/README.md
 
 example_data/README.md
 
+.template/README.md
+
+.readme_generation/.readme_template.md
+.readme_generation/README.md
+
+lock/requirements-dev-template.in
+lock/README.md
+
 .coveragerc
 .gitattributes
 .gitignore
@@ -48,7 +56,3 @@ example_data/README.md
 pytest.ini
 
 LICENSE
-requirements-dev-common.in
-
-.readme_template.md
-readme_generation.md

lock/README.md

@@ -0,0 +1,56 @@
+<!--
+ Copyright 2021 - 2023 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");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+
+-->
+
+# Lock Files
+
+This directory contains two lock files locking the dependencies of this microservice:
+
+The [`./requirements.txt`](./requirements.txt) contains production dependencies.
+
+The [`./requirements-dev.txt`](./requirements-dev.txt) additionally contains development
+dependencies.
+
+## Sources
+
+For generating the production lock file, only the dependencies specified in the
+[`../pyproject.toml`](../pyproject.toml) are considered as input.
+
+For generating the development lock file, additionally, the
+[`./requirements-dev-template.in`](./requirements-dev-template.in) as well as
+the [`./requirements-dev.in`](./requirements-dev.in) are considered.
+
+The `./requirements-dev-template.in` is automatically updated from the template
+repository and should not be manually modified.
+
+If you require additional dev dependencies not part of the
+`./requirements-dev-template.in`, you can add them to the
+`./requirements-dev.in`.
+
+## Update and Upgrade
+
+The lock files can be updated running the
+[`../scripts/update_lock.py`](../scripts/update_lock.py) script. This will keep the
+dependency versions in the lockfile unchanged unless they are in conflict with the
+the input sources. In that case, the affected dependencies are updated to the latest
+versions compatible with the input.
+
+If you would like to upgrade all dependencies in the lock file to the latest versions
+compatible with the input, you can run `../scripts/update_lock.py --upgrade`.
+
+If you just want to check if the script would do update, you can run
+`../scripts/update_lock.py --check`.

requirements-dev.in → lock/requirements-dev.in

@@ -1,7 +1,7 @@
 # requirements for development and testing this service
 
-# common requirements for development and testing
--r requirements-dev-common.in
+# template requirements for development and testing
+-r requirements-dev-template.in
 
 # additional requirements can be listed here
 testcontainers[kafka,mongo]>=3.4.1

scripts/license_checker.py

@@ -64,12 +64,12 @@
     ".mypy.ini",
     ".pytest_cache",
     ".editorconfig",
-    ".static_files",
-    ".static_files_ignore",
-    ".mandatory_files",
-    ".mandatory_files_ignore",
-    ".deprecated_files",
-    ".deprecated_files_ignore",
+    ".template/.static_files.txt",
+    ".template/.static_files_ignore.txt",
+    ".template/.mandatory_files.txt",
+    ".template/.mandatory_files_ignore.txt",
+    ".template/.deprecated_files.txt",
+    ".template/.deprecated_files_ignore.txt",
 ]
 
 # exclude file by file ending from license header check:

scripts/update_hook_revs.py

@@ -27,7 +27,7 @@
 
 REPO_ROOT_DIR = Path(__file__).parent.parent.resolve()
 PRE_COMMIT_CFG_PATH = REPO_ROOT_DIR / ".pre-commit-config.yaml"
-LOCK_FILE_PATH = REPO_ROOT_DIR / "requirements-dev.txt"
+LOCK_FILE_PATH = REPO_ROOT_DIR / "lock" / "requirements-dev.txt"
 
 
 def make_dependency_dict(requirements: list[Requirement]) -> dict[str, str]:

scripts/update_lock.py

@@ -31,11 +31,12 @@
 from script_utils import cli, deps
 
 REPO_ROOT_DIR = Path(__file__).parent.parent.resolve()
+LOCK_DIR = REPO_ROOT_DIR / "lock"
 
 PYPROJECT_TOML_PATH = REPO_ROOT_DIR / "pyproject.toml"
-DEV_DEPS_PATH = REPO_ROOT_DIR / "requirements-dev.in"
-OUTPUT_LOCK_PATH = REPO_ROOT_DIR / "requirements.txt"
-OUTPUT_DEV_LOCK_PATH = REPO_ROOT_DIR / "requirements-dev.txt"
+DEV_DEPS_PATH = LOCK_DIR / "requirements-dev.in"
+OUTPUT_LOCK_PATH = LOCK_DIR / "requirements.txt"
+OUTPUT_DEV_LOCK_PATH = LOCK_DIR / "requirements-dev.txt"
 
 
 def fix_temp_dir_comments(file_path: Path):

scripts/update_readme.py

@@ -32,9 +32,10 @@
 
 ROOT_DIR = Path(__file__).parent.parent.resolve()
 PYPROJECT_TOML_PATH = ROOT_DIR / "pyproject.toml"
-DESCRIPTION_PATH = ROOT_DIR / ".description.md"
-DESIGN_PATH = ROOT_DIR / ".design.md"
-README_TEMPLATE_PATH = ROOT_DIR / ".readme_template.md"
+README_GENERATION_DIR = ROOT_DIR / ".readme_generation"
+DESCRIPTION_PATH = README_GENERATION_DIR / "description.md"
+DESIGN_PATH = README_GENERATION_DIR / "design.md"
+README_TEMPLATE_PATH = README_GENERATION_DIR / "readme_template.md"
 CONFIG_SCHEMA_PATH = ROOT_DIR / "config_schema.json"
 OPENAPI_YAML_REL_PATH = "./openapi.yaml"
 README_PATH = ROOT_DIR / "README.md"

scripts/update_template_files.py

@@ -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/"
 )
@@ -55,9 +63,14 @@ 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
+    list_path = get_file_list_path(list_name)
     with open(list_path, encoding="utf8") as list_file:
         file_list = [
             clean_line
@@ -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