Use pip-tools (GSI 334)

.deprecated_files

@@ -14,3 +14,6 @@ scripts/check_mandatory_and_static_files.py
 scripts/update_static_files.py
 
 docs
+
+setup.py
+setup.cfg

.devcontainer/dev_install

@@ -6,11 +6,11 @@ cd /workspace
 # upgrade pip
 python -m pip install --upgrade pip
 
-# install with all extras in editable mode
-pip install -e .[all]
-
 # install or upgrade dependencies for development and testing
-pip install -r requirements-dev.txt
+pip install --no-deps -r requirements-dev.txt
+
+# install the package itself in edit mode:
+pip install --no-deps -e .
 
 # install pre-commit hooks to git
 pre-commit install

.github/workflows/check_config_docs.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v2
+        uses: ghga-de/gh-action-common@v3
 
       - 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@v2
+        uses: ghga-de/gh-action-common@v3
 
       - 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@v2
+        uses: ghga-de/gh-action-common@v3
 
       - 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@v2
+        uses: ghga-de/gh-action-common@v3
 
       - uses: pre-commit/[email protected]
         env:

.github/workflows/unit_and_int_tests.yaml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v2
+        uses: ghga-de/gh-action-common@v3
 
       - name: Run pytest
         run: |

.mandatory_files

@@ -19,10 +19,11 @@ Dockerfile
 config_schema.json
 example_config.yaml
 LICENSE
+pyproject.toml
 README.md
-setup.py
-setup.cfg
+requirements-dev.in
 requirements-dev.txt
+requirements.txt
 
 .description.md
 .design.md

.readme_template.md

@@ -97,7 +97,7 @@ Moreover, inside the devcontainer, a convenience commands `dev_install` is avail
 It installs the service with all development dependencies, installs pre-commit.
 
 The installation is performed automatically when you build the devcontainer. However,
-if you update dependencies in the [`./setup.cfg`](./setup.cfg) or the
+if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the
 [`./requirements-dev.txt`](./requirements-dev.txt), please run it again.
 
 ## License

.static_files

@@ -45,8 +45,7 @@ example_data/README.md
 pytest.ini
 
 LICENSE
-requirements.txt
-requirements-dev-common.txt
+requirements-dev-common.in
 setup.py
 
 .readme_template.md

README.md

@@ -70,21 +70,21 @@ my_microservice --help
 ### Parameters
 
 The service requires the following configuration parameters:
-- **`host`** *(string)*: IP of the host. Default: `127.0.0.1`.
+- **`host`** *(string)*: IP of the host. Default: `"127.0.0.1"`.
 
 - **`port`** *(integer)*: Port to expose the server on the specified host. Default: `8080`.
 
-- **`log_level`** *(string)*: Controls the verbosity of the log. Must be one of: `['critical', 'error', 'warning', 'info', 'debug', 'trace']`. Default: `info`.
+- **`log_level`** *(string)*: Controls the verbosity of the log. Must be one of: `["critical", "error", "warning", "info", "debug", "trace"]`. Default: `"info"`.
 
-- **`auto_reload`** *(boolean)*: A development feature. Set to `True` to automatically reload the server upon code changes. Default: `False`.
+- **`auto_reload`** *(boolean)*: A development feature. Set to `True` to automatically reload the server upon code changes. Default: `false`.
 
 - **`workers`** *(integer)*: Number of workers processes to run. Default: `1`.
 
-- **`api_root_path`** *(string)*: Root path at which the API is reachable. This is relative to the specified host and port. Default: `/`.
+- **`api_root_path`** *(string)*: Root path at which the API is reachable. This is relative to the specified host and port. Default: `"/"`.
 
-- **`openapi_url`** *(string)*: Path to get the openapi specification in JSON format. This is relative to the specified host and port. Default: `/openapi.json`.
+- **`openapi_url`** *(string)*: Path to get the openapi specification in JSON format. This is relative to the specified host and port. Default: `"/openapi.json"`.
 
-- **`docs_url`** *(string)*: Path to host the swagger documentation. This is relative to the specified host and port. Default: `/docs`.
+- **`docs_url`** *(string)*: Path to host the swagger documentation. This is relative to the specified host and port. Default: `"/docs"`.
 
 - **`cors_allowed_origins`** *(array)*: A list of origins that should be permitted to make cross-origin requests. By default, cross-origin requests are not allowed. You can use ['*'] to allow any origin.
 
@@ -100,9 +100,9 @@ The service requires the following configuration parameters:
 
   - **Items** *(string)*
 
-- **`service_name`** *(string)*: Default: `my_microservice`.
+- **`service_name`** *(string)*: Default: `"my_microservice"`.
 
-- **`language`** *(string)*: Must be one of: `['Greek', 'Croatian', 'French', 'German']`. Default: `Croatian`.
+- **`language`** *(string)*: Must be one of: `["Greek", "Croatian", "French", "German"]`. Default: `"Croatian"`.
 
 
 ### Usage:
@@ -163,7 +163,7 @@ Moreover, inside the devcontainer, a convenience commands `dev_install` is avail
 It installs the service with all development dependencies, installs pre-commit.
 
 The installation is performed automatically when you build the devcontainer. However,
-if you update dependencies in the [`./setup.cfg`](./setup.cfg) or the
+if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the
 [`./requirements-dev.txt`](./requirements-dev.txt), please run it again.
 
 ## License

pyproject.toml

@@ -0,0 +1,37 @@
+[build-system]
+requires = ["setuptools>=67.7.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "my_microservice"
+version = "0.1.0"
+description = "My-Microservice - a short description"
+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",
+]
+dependencies = [
+    "typer ~= 0.7.0",
+    "ghga-service-commons[api] ~= 0.7.0",
+    "ghga-event-schemas ~= 0.13.0",
+    "hexkit[akafka,s3,mongodb] ~= 0.10.0"
+]
+
+[project.urls]
+Repository = "https://github.com/ghga-de/my-microservice"
+
+[tool.setuptools.packages.find]
+where = ["src"]

readme_generation.md

@@ -24,11 +24,11 @@ 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 [`./setup.cfg`](`./setup.cfg).
+  in the [`./pyproject.toml`](./pyproject.toml).
 - summary: A short 1-2 sentence summary derived from the description in the
-  [`./setup.cfg`](`./setup.cfg).
+  [`./pyproject.toml`](./pyproject.toml).
 - version: The package version derived from the version specified in the
-  [`./setup.cfg`](`./setup.cfg).
+  [`./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).
 - design_description: A markdown-formatted description of the overall architecture and

requirements-dev-common.in

@@ -0,0 +1,38 @@
+# common requirements for development and testing of services
+
+pytest>=7.2.0
+pytest-asyncio>=0.20.3
+pytest-cov>=4.0.0
+pytest-profiling>=1.7.0
+snakeviz>=2.2.0
+
+pre-commit>=3.1.1
+
+mypy>=1.0.0
+mypy-extensions>=1.0.0
+
+pylint>=2.16.4
+flake8>=6.0.0
+bandit>=1.7.4
+
+black>=23.1.0
+
+isort>=5.12.0
+
+click>=8.1.0
+typer>=0.7.0
+
+httpx>=0.23.3
+pytest-httpx>=0.21.3
+
+urllib3>=1.26.15
+requests>=2.28.2
+
+stringcase>=1.2.0
+jsonschema2md>=1.0.0
+setuptools>=67.7.2
+
+# required since switch to pyproject.toml and pip-tools
+pip-tools>=7.3.0
+tomli>=2.0.1
+tomli_w>=1.0.0

requirements-dev.in

@@ -0,0 +1,7 @@
+# requirements for development and testing this service
+
+# common requirements for development and testing
+-r requirements-dev-common.in
+
+# additional requirements can be listed here
+testcontainers[kafka,mongo]>=3.4.1