Fix #161 - Automation for Docker publish and mkdocs githubio (#163)

* Fix #161 - Automation for Docker publish and mkdocs githubio

* add venv to path

Author: dnil

.github/workflows/build_and_publish.yml

@@ -16,3 +16,48 @@ jobs:
       - uses: astral-sh/setup-uv@v3
       - run: uv build
       - run: uv publish --trusted-publishing always
+
+ docker-image-CI:
+   name: Docker Image CI
+   runs-on: ubuntu-latest
+   steps:
+
+    - name: Check out git repository
+      uses: actions/checkout@v4
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Set up Docker Buildx
+      id: buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Publish server image (Dockerfile-server) to Registry
+      uses: docker/build-push-action@v6
+      with:
+        context: ./
+        file: ./Dockerfile
+        push: true
+        provenance: mode=max
+        sbom: true
+        tags: "clinicalgenomics/genmod:latest, clinicalgenomics/genmod:${{ github.event.release.tag_name }}"
+
+
+ deploy-docs:
+    name: Deploy Docs to GitHubIO
+    runs-on: ubuntu-latest
+    steps:
+     - name: Checkout repo
+       uses: actions/checkout@v4
+     - name: Setup environment for docs deployment
+       uses: actions/setup-python@v5
+       with:
+         python-version: 3.x
+     - name: Install mkdocs
+       run: pip install mkdocs mkdocs-material markdown-include
+     - name: Deploy documentation
+       run: mkdocs gh-deploy --force
+

CHANGELOG.md

@@ -9,14 +9,16 @@ Please add a new candidate release at the top after changing the latest one. Fee
 Try to use the following format:
 
 ## [unreleased]
+### Changed
+- Use `uv` with `hatchling` to build and publish ([#104](https://github.com/Clinical-Genomics/genmod/issues/143))
+- Automation for Docker publish and mkdocs githubio ([#161](https://github.com/Clinical-Genomics/genmod/issues/161))
 ### Fixed
 - The optional fields Source and Version are allowed in the VCF header([#106](https://github.com/Clinical-Genomics/genmod/pull/106))
 - Released the constraint on Python 3.8 (collections, pkg_resources to importlib, tests) ([#142](https://github.com/Clinical-Genomics/genmod/pull/142))
 - Update annotation examples ([#144](https://github.com/Clinical-Genomics/genmod/pull/144))
 - Updated documentation with warning about compounds only being scored within the first family in the VCF ([#151](https://github.com/Clinical-Genomics/genmod/pull/151))
 - Fixed sorting of variants ([#152](https://github.com/Clinical-Genomics/genmod/pull/152))
 - genmod annotate for mitochondrial variants when using the `chrM` notation ([#157](https://github.com/Clinical-Genomics/genmod/pull/157))
-- Use `uv` with `hatchling` to build and publish ([#104](https://github.com/Clinical-Genomics/genmod/issues/143))
 - Fix linting issues ([#154](https://github.com/Clinical-Genomics/genmod/issues/154))
 - genmod models adds headers to VCF even if it contains no variants ([#160](https://github.com/Clinical-Genomics/genmod/pull/160)) 
 

Dockerfile

@@ -7,8 +7,11 @@ RUN apk update & apk add build-base zlib-dev
 # Copy the project into the image
 ADD . /app
 
-# Sync the project into a new environment, using the frozen lockfile
+# Sync the project into a new virtual environment, using the frozen lockfile
 WORKDIR /app
 RUN uv sync --frozen
 
-ENTRYPOINT ["uv", "run", "genmod"]
+# Add the project venv to PATH to be able to run genmod without changing to the environment
+ENV PATH="/app/.venv/bin:$PATH"
+
+ENTRYPOINT ["genmod"]