Upgrading versions and adding Continuous Integration and Delivery

.dockerignore

@@ -0,0 +1,8 @@
+.github
+.ruff_cache/
+.venv/
+data/
+dist/
+docs/
+example/
+oncodrivefml.egg-info/

.github/workflows/build.yaml

@@ -0,0 +1,207 @@
+name: Build and Publish
+
+on:
+  push:
+    tags:
+      - "**"
+    branches:
+      - "**"
+
+permissions:
+  contents: read
+
+env:
+  TERM: xterm
+
+jobs:
+  packages-build:
+    name: Build packages
+    runs-on: ubuntu-latest
+    env:
+      RUFF_FORMAT: github
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+
+      - name: Prepare virtual environment
+        run: make create-env
+
+      - name: Check format
+        run: |
+          make check-format || true
+          BOLDRED=$(tput bold && tput setaf 1)
+          RESET=$(tput sgr0)
+          echo "${BOLDRED}==> We won't fail on formatting errors for the time being, but we will in the future.${RESET}"
+      
+      - name: Check lint
+        run: |
+          make check-lint || true
+          BOLDRED=$(tput bold && tput setaf 1)
+          RESET=$(tput sgr0)
+          echo "${BOLDRED}==> We won't fail on lint errors for the time being, but we will in the future.${RESET}"
+
+      - name: Build packages
+        run: make build-dist
+
+      - name: Upload packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-packages
+          path: dist
+
+  docker-build:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+
+      - name: Prepare virtual environment
+        run: make create-env
+
+      - name: Check Dockerfile
+        run: make check-docker
+
+      - name: Build Docker image
+        run: make build-image
+
+      # TODO: Enable this when we figure out how to run it without having to download several Gigabytes of data.
+      # - name: Test Docker image
+      #   run: make run-example
+
+  docs-build:
+    name: Build documentation
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+
+      - name: Prepare virtual environment
+        run: make create-env
+
+      - name: Check version matching the tag
+        shell: bash
+        run: make docs
+
+      - name: Upload documentation
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build
+
+  check-version:
+    name: Check version
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - packages-build
+      - docker-build
+      - docs-build
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+
+      - name: Prepare virtual environment
+        run: make create-env
+
+      - name: Check version matching the tag
+        run: make check-version
+
+  packages-publish:
+    name: Publish packages
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    env:
+      PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
+    needs:
+      - check-version
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+
+      - name: Prepare virtual environment
+        run: make create-env
+
+      - name: Download packages
+        uses: actions/download-artifact@v4
+        with:
+          name: python-packages
+
+      - name: Publish to PyPI
+        if: ${{ env.PYPI_USERNAME != '' }}
+        env:
+          PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: make publish-dist
+
+  docker-push:
+    name: Push Docker image
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+    needs:
+      - check-version
+
+    steps:
+      - if: ${{ env.DOCKER_USERNAME != '' }}
+        uses: actions/checkout@v3
+
+      - name: Login to DockerHub
+        if: ${{ env.DOCKER_USERNAME != '' }}
+        run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
+
+      - name: Push Docker image
+        if: ${{ env.DOCKER_USERNAME != '' }}
+        run: make push-image
+
+  docs-publish:
+    name: Publish documentation
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    env:
+      RTD_USERNAME: ${{ secrets.RTD_USERNAME }}
+    needs:
+      - check-version
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+
+      - name: Prepare virtual environment
+        run: make create-env
+
+      - name: Download documentation
+        uses: actions/download-artifact@v4
+        with:
+          name: documentation
+
+      # TODO: Add a step to publish the docs to ReadTheDocs

.gitignore

@@ -36,4 +36,8 @@ example/cdsOriginal
 docs/build
 
 # External users tests
-external_checks
+external_checks
+
+.ruff_cache/
+.venv
+data/

.hadolint.yaml

@@ -0,0 +1,2 @@
+ignored:
+  - DL3003

.python-version

@@ -0,0 +1 @@
+3.8

Dockerfile

@@ -0,0 +1,20 @@
+FROM python:3.8-slim
+
+# hadolint ignore=DL3013
+RUN pip install --no-cache-dir --upgrade pip
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends --no-install-suggests \
+        build-essential=12.9 \
+        zlib1g-dev=1:1.2.13.dfsg-1 && \
+    rm -rf /var/lib/apt/lists/*
+
+# hadolint ignore=DL3042
+RUN --mount=type=cache,target=/root/.cache/pip \
+    --mount=type=bind,target=/project,rw \
+    cd /project && \
+    pip install .
+
+ENTRYPOINT [ "/usr/local/bin/oncodrivefml" ]