chore: migrate to pyproject.toml

.github/workflows/checks.yml

@@ -36,21 +36,21 @@ jobs:
           python-version: ${{ matrix.py-version-img[0] }}
       - name: Install requirements
         run: |
-          pip install -e .[dev]
-          pip install setuptools
+          pip install poetry
+          poetry install --with=code_quality,docs,test,types
       - name: Lint with flake8
-        run: flake8
+        run: poetry run flake8
       - name: Run mypy
-        run: mypy foca
+        run: poetry run mypy foca
       - name: Start MongoDB
         uses: supercharge/mongodb-github-action@1.7.0
         with:
           mongodb-version: ${{ matrix.mongodb-version }}
           mongodb-port: ${{ matrix.mongodb-port }}
       - name: Calculate unit test coverage
         run: |
-          coverage run --source foca -m pytest -W ignore::DeprecationWarning
-          coverage xml
+          poetry run coverage run --source foca -m pytest -W ignore::DeprecationWarning
+          poetry run coverage xml
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
@@ -72,10 +72,10 @@ jobs:
               --build-arg PY_IMAGE=${PY_IMAGE} \
               .
           cd ./examples/petstore
-          docker-compose up --build -d
+          docker compose up --build -d
           cd ../..
           sleep 10
-          pytest ./tests/integration_tests.py
+          poetry run pytest ./tests/integration_tests.py
 
   Docker:
     runs-on: ubuntu-latest

.readthedocs.yaml

@@ -9,6 +9,11 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
+  jobs:
+    post_create_environment:
+      - python -m pip install poetry
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
     # You can also specify other tool versions:
     # nodejs: "20"
     # rust: "1.70"
@@ -26,11 +31,3 @@ sphinx:
 # formats:
 #    - pdf
 #    - epub
-
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
-        - dev

Makefile

@@ -0,0 +1,74 @@
+# NOTE: This Makefile assumes that dependencies are installed and, if a virtual
+# environment is used, it is activated.
+
+## Variables ##################################################################
+# NOTE: Define any variables here if needed in the future
+
+## Documentation ##############################################################
+# NOTE: Keep all the targets in alphabetical order for better readability.
+
+default: help
+
+.PHONY: help
+help:
+	@echo "\nUsage: make [target] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+	@echo "Available targets:\n"
+
+	@echo "Code Quality ------------------------------------------------------------------"
+	@echo "  \033[1m\033[35mformat-lint\033[0m \033[37m(fl)\033[0m: \033[36mRun linter, formatter, spellcheck.\033[0m"
+	@echo "  \033[1m\033[35mtype-check\033[0m \033[37m(tc)\033[0m: \033[36mPerform type checking.\033[0m\n"
+
+	@echo "Environment Management --------------------------------------------------------"
+	@echo "  \033[1m\033[35mclean-venv\033[0m \033[37m(cv)\033[0m: \033[36mRemove virtual environment.\033[0m"
+	@echo "  \033[1m\033[35minstall\033[0m \033[37m(i)\033[0m: \033[36mInstall app and dependencies.\033[0m"
+	@echo "  \033[1m\033[35mvenv\033[0m \033[37m(v)\033[0m: \033[36mCreate virtual environment.\033[0m\n"
+
+	@echo "Testing -----------------------------------------------------------------------"
+	@echo "  \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n"
+
+.PHONY: clean-venv cv
+clean-venv:
+	@echo "\nRemoving the virtual environment ++++++++++++++++++++++++++++++++++++++++++++++\n"
+	@rm -rf .venv
+
+cv: clean-venv
+
+.PHONY: format-lint fl
+format-lint:
+	@echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n"
+	@poetry run flake8
+	@typos .
+
+fl: format-lint
+
+.PHONY: install i
+install:
+	@echo "\nInstalling this package its dependencies +++++++++++++++++++++++++++++++++\n"
+	@poetry install --with=code_quality,docs,test,types
+
+i: install
+
+.PHONY: test t
+test:
+	@echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+	@poetry run pytest tests/
+
+t: test
+
+.PHONY: type-check tc
+type-check:
+	@echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n"
+	@poetry run mypy foca
+
+tc: type-check
+
+.PHONY: venv v
+venv:
+	@echo "\nCreating a virtual environment ++++++++++++++++++++++++++++++++++++++++++++++++\n"
+	@python -m venv .venv
+	@echo "\nSummary +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+	@echo "Virtual environment created successfully."
+	@echo "To activate the environment for this shell session, run:"
+	@echo "source .venv/bin/activate"
+
+v: venv

docker/Dockerfile

@@ -1,52 +1,50 @@
+###################################################
+#   Stage 1: Get poetry                           #
+###################################################
 ARG PY_IMAGE=3.12-slim-bookworm
-FROM python:$PY_IMAGE as base
-
-# Metadata
-LABEL software="FOCA"
-LABEL software.description="Kickstart OpenAPI-based microservice development with Flask & Connexion"
-LABEL software.website="https://github.com/elixir-cloud-aai/foca"
-LABEL software.license="https://spdx.org/licenses/Apache-2.0"
-LABEL maintainer="alexander.kanitz@alumni.ethz.ch"
-LABEL maintainer.organisation="ELIXIR Cloud & AAI"
-
-# Build image
-FROM base as builder
-
-# Install general dependencies
-ENV PACKAGES openssl git build-essential python3-dev curl jq
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    rm -rf /var/lib/apt/lists/*
+FROM python:$PY_IMAGE AS poetry
+
+ENV PYTHONDONTWRITEBYTECODE=1 \
+PYTHONUNBUFFERED=1 
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        curl \
+        && rm -rf /var/lib/apt/lists/*
+
+RUN curl -sSL https://install.python-poetry.org | python3 - && \
+        ln -s /root/.local/bin/poetry /usr/local/bin/poetry
+
+###################################################
+#   Stage 2: Get deps                             #
+###################################################
+FROM poetry AS builder
+
 WORKDIR /app
 
-# Install Python dependencies
-COPY requirements.txt ./
-RUN pip install \
-        --no-warn-script-location \
-        --prefix="/install" \
-        -r requirements.txt
+COPY . /app/
 
-# Install FOCA
-COPY setup.py README.md ./
-COPY foca/ ./foca/
-RUN pip install --upgrade pkginfo && \
-    pip install . \
-        --no-warn-script-location \
-        --prefix="/install"
+RUN poetry config virtualenvs.create false \
+    && poetry build
 
-# Final image
-FROM base
+# ###################################################
+# #   Stage 3: Add Metadata and install wheel       #
+# ###################################################
+FROM python:$PY_IMAGE
+
+COPY --from=builder /app/dist /app/dist
+
+RUN pip install /app/dist/*.whl
+
+LABEL org.opencontainers.image.title="FOCA"
+LABEL org.opencontainers.image.description="Kickstart OpenAPI-based microservice development with Flask & Connexion"
+LABEL org.opencontainers.image.source="https://github.com/elixir-cloud-aai/foca"
+LABEL org.opencontainers.image.licenses="Apache-2.0"
+LABEL org.opencontainers.image.authors="alexander.kanitz@alumni.ethz.ch"
+LABEL org.opencontainers.image.vendor="ELIXIR Cloud & AAI"
 
 # Python UserID workaround for OpenShift/K8S
 ENV LOGNAME=ipython
 ENV USER=ipython
 ENV HOME=/tmp/user
 
-# Install general dependencies
-ENV PACKAGES openssl git build-essential python3-dev curl jq
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends ${PACKAGES} && \
-    rm -rf /var/lib/apt/lists/*
-
-# Copy Python packages
-COPY --from=builder /install /usr/local
+WORKDIR /app

foca/api/register_openapi.py

@@ -57,7 +57,7 @@ def register_openapi(
         if spec.add_operation_fields is not None:
             for key, val in spec.add_operation_fields.items():
                 for path_item_object in spec_parsed.get('paths', {}).values():
-                    for operation, operation_object in path_item_object.items():
+                    for operation, operation_object in path_item_object.items():  # noqa: E501
                         if operation not in _OPERATION_OBJECT_FIELDS:
                             continue
                         operation_object[key] = val