chore: migrate to pyproject.toml

[JaeAeich]

Description

migrate to using pyproject instead of setuptools.

Fixes #232

Summary by Sourcery

Migrates the project to use pyproject.toml and Poetry for dependency management and build configuration. This includes updating the Dockerfile, CI workflow, and development scripts to use Poetry, as well as removing obsolete files and adding a Makefile for common development tasks.

Enhancements:

• Replaces resource_filename with files from importlib.resources for improved resource handling.

Build:

• Migrates the build system from setup.py and requirements.txt to pyproject.toml and Poetry for dependency management.
• Updates the Dockerfile to use multi-stage builds and Poetry for installing dependencies, resulting in a cleaner and more efficient image build process.

CI:

• Updates the CI workflow to use Poetry for dependency installation and running linters, type checkers, and tests.

Chores:

• Removes obsolete files such as requirements.txt, setup.py, setup.cfg, MANIFEST.in, requirements_dev.txt, and requirements_docs.txt.
• Adds a Makefile to provide convenient commands for development tasks such as installing dependencies, running tests, and performing code quality checks.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request migrates the project to use pyproject.toml and Poetry for dependency management, updates the Dockerfile to use multi-stage builds with Poetry, modifies the GitHub Actions workflow to use Poetry for running checks, and updates the Makefile to use Poetry for managing dependencies and running commands. It also includes minor fixes for line length issues and replaces deprecated resource_filename with files.

Sequence diagram for GitHub Actions CI workflow

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sequenceDiagram
    participant GH Actions
    participant Poetry
    participant flake8
    participant mypy
    participant pytest
    GH Actions->>Poetry: Install dependencies
    Poetry-->>GH Actions: Dependencies installed
    GH Actions->>flake8: Run linting
    flake8-->>GH Actions: Linting results
    GH Actions->>mypy: Run type checking
    mypy-->>GH Actions: Type checking results
    GH Actions->>pytest: Run tests
    pytest-->>GH Actions: Test results

Updated class diagram for project dependencies

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classDiagram
    class pyproject.toml {
        -build-system
        -tool.poetry
            -dependencies
                -python
                -addict
                -celery
                -connexion
                -cryptography
                -Flask
                -flask-authz
                -Flask-Cors
                -Flask-PyMongo
                -pydantic
                -PyJWT
                -pymongo
                -PyYAML
                -requests
                -swagger-ui-bundle
                -toml
                -typing
                -Werkzeug
            -group.code_quality.dependencies
                -flake8
                -Flake8-pyproject
                -mypy
                -mypy-extensions
                -pylint
            -group.docs.dependencies
                -Sphinx
                -readthedocs-sphinx-ext
                -sphinx-rtd-theme
            -group.test.dependencies
                -coverage
                -mongomock
                -pytest
            -group.types.dependencies
                -types-PyYAML
                -types-requests
                -types-setuptools
                -types-urllib3
                -typing_extensions
    }
    note for pyproject.toml "Replaces requirements.txt and setup.py for dependency management"

File-Level Changes

Change	Details	Files
Migrated the project to use pyproject.toml for dependency management and build configuration.	Replaced setup.py, setup.cfg, requirements.txt, requirements_dev.txt, and requirements_docs.txt with pyproject.toml. Configured build system using Poetry. Defined project metadata, dependencies, and development dependencies in pyproject.toml. Configured mypy and flake8 settings within pyproject.toml.	pyproject.toml setup.py setup.cfg requirements.txt requirements_dev.txt requirements_docs.txt
Updated the Dockerfile to use multi-stage builds with Poetry for managing dependencies.	Introduced a poetry stage to install Poetry. Used Poetry to install dependencies and build the project in a builder stage. Copied the built wheel file to the final image and installed it using pip. Removed the installation of development dependencies in the Dockerfile. Added labels to the final image.	docker/Dockerfile
Modified the GitHub Actions workflow to use Poetry for dependency management and running checks.	Installed Poetry in the workflow. Used poetry install to install dependencies with different groups (code_quality, docs, test, types). Used poetry run to execute linting, type checking, and testing commands. Removed the explicit installation of setuptools.	.github/workflows/checks.yml
Updated the Makefile to use Poetry for managing dependencies and running commands.	Replaced pip commands with poetry run for linting, type checking, and testing. Added a target to create a virtual environment using python -m venv. Added a target to install dependencies using poetry.	Makefile
Removed unused files.	Removed MANIFEST.in and .flake8 files.	MANIFEST.in .flake8
Fixed line length issues in test file.	Added noqa E501 to lines exceeding maximum length.	tests/api/test_register_openapi.py
Replaced deprecated resource_filename with files.	Replaced resource_filename with files from importlib.resources.	tests/security/access_control/test_access_control_server.py
Fixed line length issues in foca file.	Added noqa E501 to lines exceeding maximum length.	foca/api/register_openapi.py

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[sourcery-ai]

Hey @JaeAeich - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider adding a poetry.lock file to the repository to ensure consistent dependency versions across environments.
• The removal of setup.py and requirements.txt is expected, but double-check that all references to these files have been removed from other parts of the project.

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (d4d1632) to head (663efe9).
Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff            @@
##               dev      #251   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           20        20           
  Lines          966       969    +3     
=========================================
+ Hits           966       969    +3     

Flag	Coverage Δ
test_unit	100.00% <100.00%> (ø)

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