Template update

.devcontainer/dev_install

@@ -7,7 +7,7 @@ cd /workspace
 python -m pip install --upgrade pip
 
 # install or upgrade dependencies for development and testing
-pip install --no-deps -r requirements-dev.txt
+pip install --no-deps -r ./lock/requirements-dev.txt
 
 # install the package itself in edit mode:
 pip install --no-deps -e .

.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

@@ -0,0 +1,19 @@
+# This file is only needed, if your repository uses FastAPI
+name: Check if openapi.yaml is up to date
+
+on: push
+
+jobs:
+  static-code-analysis:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - id: common
+        uses: ghga-de/gh-action-common@v4
+
+      - name: Check if openapi.yaml is up to date
+        run: |
+          export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
+
+          ./scripts/update_openapi_docs.py --check

.github/workflows/check_pyproject.yaml

@@ -0,0 +1,16 @@
+name: Check if the config schema and the example are up to date.
+
+on: push
+
+jobs:
+  static-code-analysis:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - id: common
+        uses: ghga-de/gh-action-common@v4
+
+      - name: Check pyproject.toml
+        run: |
+          ./scripts/update_pyproject.py --check

.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: |

.pyproject_generation/README.md

@@ -0,0 +1,29 @@
+<!--
+ 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.
+
+-->
+
+# Generating the pyproject.toml
+
+The pyproject.toml of the service is generated by combining static configuration
+captured in [`./pyproject_template.toml`](./pyproject_template.toml) and custom
+package metadata specified in [`./pyproject_custom.toml`](./pyproject_custom.toml).
+
+The `./pyproject_template.toml` is managed by the template, please do not edit manually.
+
+You may specify properties in the `./pyproject_custom.toml` which are already specified
+in the `./pyproject_template.toml`. In that case, the `./pyproject_custom.toml` takes
+priority.

.pyproject_generation/pyproject_custom.toml

@@ -0,0 +1,17 @@
+[project]
+name = "ghga_connector"
+version = "1.2.0"
+description = "GHGA Connector - A CLI client application for interacting with the GHGA system."
+dependencies = [
+    "typer~=0.9.0",
+    "crypt4gh>=1.6, <2",
+    "ghga-service-commons[api, crypt]~=2.0.0",
+    "hexkit[s3]~=2.0.0",
+]
+
+
+[project.urls]
+Repository = "https://github.com/ghga-de/ghga-connector"
+
+[project.scripts]
+ghga-connector = "ghga_connector.__main__:run"

.ruff.toml → .pyproject_generation/pyproject_template.toml

@@ -1,11 +1,37 @@
+[build-system]
+requires = ["setuptools>=67.7.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+readme = "README.md"
+authors = [
+    { name = "German Human Genome Phenome Archive (GHGA)", email = "[email protected]" },
+]
+requires-python = ">=3.9"
+license = { text = "Apache 2.0" }
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
+    "Topic :: Software Development :: Libraries",
+    "Intended Audience :: Developers",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
 exclude = [
     ".git",
     ".devcontainer",
     "__pycache__",
     "build",
     "dist",
 ]
-
 ignore = [
     "E", # pycodestyle errors
     "W", # pycodestyle warnings - pycodestyle covered by black
@@ -23,9 +49,7 @@ ignore = [
     "D206", # indent-with-spaces (ignored for formatter)
     "D300", # triple-single-quotes (ignored for formatter)
 ]
-
 line-length = 88
-
 select = [
     "C90", # McCabe Complexity
     "F", # pyflakes codes
@@ -39,26 +63,45 @@ select = [
     "SIM", # flake8-simplify
     "D", # pydocstyle
 ]
-
 fixable = [
     "UP", # e.g. List -> list
     "I", # sort imports
     "D", # pydocstyle
 ]
-
 src = ["src", "tests", "examples", "scripts"]
-
 target-version = "py39"
 
-[mccabe]
+[tool.ruff.mccabe]
 max-complexity = 10
 
-[per-file-ignores]
+[tool.ruff.per-file-ignores]
 "scripts/*" = ["PL", "S", "SIM", "D"]
 "tests/*" = ["S", "SIM", "PLR", "B011"]
 ".devcontainer/*" = ["S", "SIM", "D"]
 "examples/*" = ["S", "D"]
 "__init__.py" = ["D"]
 
-[pydocstyle]
+[tool.ruff.pydocstyle]
 convention = "pep257"
+
+[tool.mypy]
+disable_error_code = "import"
+show_error_codes = true
+exclude = [
+    'build/lib/',
+]
+warn_redundant_casts = true
+warn_unused_ignores = true
+check_untyped_defs = true
+no_site_packages = false
+
+[tool.pytest.ini_options]
+minversion = "7.1"
+asyncio_mode = "strict"
+
+[tool.coverage.paths]
+source = [
+  "src",
+  "/workspace/src",
+  "**/lib/python*/site-packages",
+]

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.

.description.md → .readme_generation/description.md

@@ -1,9 +1,9 @@
-<!-- Please provide a short overview of the features of this service.-->
-
 The GHGA Connector is a command line client facilitating interaction with the file storage infrastructure of GHGA.
-To this end, it provides commands for the up- and download of files that interact with the RESTful APIs exposed by the Upload Controller Service (https://github.com/ghga-de/upload-controller-service) and Download Controller Service (https://github.com/ghga-de/download-controller-service), respectively.
+To this end, it provides commands for the up- and download of files that interact with the RESTful APIs exposed
+by the Upload Controller Service (https://github.com/ghga-de/upload-controller-service) and Download Controller Service (https://github.com/ghga-de/download-controller-service), respectively.
 
-When uploading, the Connector expects an unencrypted file that is subsequently encrypted according to the Crypt4GH standard (https://www.ga4gh.org/news_item/crypt4gh-a-secure-method-for-sharing-human-genetic-data/) and only afterwards uploaded to the GHGA storage infrastructure.
+When uploading, the Connector expects an unencrypted file that is subsequently encrypted according to the Crypt4
+GH standard (https://www.ga4gh.org/news_item/crypt4gh-a-secure-method-for-sharing-human-genetic-data/) and only afterwards uploaded to the GHGA storage infrastructure.
 
 When downloading, the resulting file is still encrypted in this manner and can be decrypted using the Connector's decrypt command.
 As the user is expected to download multiple files, this command takes a directory location as input and an optional output directory location can be provided, creating the directory if it does not yet exist (defaulting to the current working directory, if none is provided).

.design.md → .readme_generation/design.md

@@ -1,7 +1,3 @@
-<!-- Please provide an overview of the architecture and design of the code base.
-Mention anything that deviates from the standard triple hexagonal architecture and
-the corresponding structure. -->
-
 This is a Python-based client enabling interaction with GHGA's file services.
 Contrary to the design of the actual services, the client does not follow the triple-hexagonal architecture.
 The client is roughly structured into three parts:

.readme_template.md → .readme_generation/readme_template.md

@@ -1,6 +1,5 @@
-
-[![tests](https://github.com/ghga-de/$name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/tests.yaml)
-[![Coverage Status](https://coveralls.io/repos/github/ghga-de/$name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$name?branch=main)
+[![tests](https://github.com/ghga-de/$repo_name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$repo_name/actions/workflows/tests.yaml)
+[![Coverage Status](https://coveralls.io/repos/github/ghga-de/$repo_name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$repo_name?branch=main)
 
 # $title
 

.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 +19,26 @@ docs
 
 setup.py
 setup.cfg
+requirements-dev-common.in
+requirements-dev.in
+requirements-dev.txt
+requirements.txt
+pytest.ini
+readme_generation.md
 
 .pylintrc
 .flake8
+.mypy.ini
+.ruff.toml
+.coveragerc
 .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