Create a dockerfile for running the model code locally or in azure (#107

)

* Adding image-build

* Adding docker file

* Dockerfile builds pyrenew correctly

* Adding action to build image

* Adding triggers for the container image

* Pushing to the ghcr

* Update container-image.yml

* Tagging and adding read access [skip ci]

* Adding login action via redhat-actions [skip ci]

* Hardcoding image_registry [skip ci]

* Direct login without the action [skip ci]

* Direct login without the action [skip ci] 3

* Cleaning up before undrafting PR

* Correcting the instructions to install pyrenew

* Wrong address to image

.github/workflows/container_image.yml

@@ -0,0 +1,35 @@
+name: Build container image
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+permissions:
+  packages: write
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Installs podman
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y --no-install-recommends podman
+
+      - name: Log in to ghcr.io
+        run: |
+          podman login \
+            -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} \
+            ghcr.io/cdcgov
+
+      - name: Build container image
+        run: |
+          make image-build
+          podman tag pyrenew:latest ghcr.io/cdcgov/pyrenew:latest
+          podman push ghcr.io/cdcgov/pyrenew:latest
+        working-directory: model

model/Dockerfile

@@ -0,0 +1,32 @@
+FROM ubuntu:24.04
+
+LABEL org.opencontainers.image.description="Image of PyRenew python package"
+LABEL org.opencontainers.image.source="https://github.com/CDCgov/multisignal-epi-inference"
+LABEL org.opencontainers.image.authors="CDC's Center for Forecasting Analytics"
+LABEL org.opencontainers.image.license="Apache-2.0"
+
+# Installing python3-11.0
+RUN apt-get update && apt install -y python3.12
+
+# Adding the alias python3 for python3.12
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.12 1
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.12 1
+
+# Installing poetry
+RUN apt install -y pipx && \
+    pipx install poetry
+
+RUN echo "export PATH=$PATH:/root/.local/bin" >> ~/.bashrc
+
+ENV PATH="${PATH}:/root/.local/bin"
+
+# Copying the project files
+COPY src/ poetry.lock pyproject.toml Makefile LICENSE README.md /pyrenew/
+
+# Setting the working directory
+WORKDIR /pyrenew
+
+# Installing the dependencies
+RUN poetry install
+
+CMD ["bash"]

model/Makefile

@@ -1,3 +1,24 @@
+CONTAINER=podman
+# Pass as environment variables
+# CONTAINER_REGISTRY=
+# CONTAINER_URL=
+
+
+# Help target listing the available targets
+help:
+	@echo "Available targets"
+	@echo "================="
+	@echo "  help           : Show this help message"
+	@echo "  install        : Install the project dependencies"
+	@echo "  test           : Run the tests"
+	@echo "  docs           : Render the documentation"
+	@echo "  clean          : Clean the generated files"
+	@echo "  docs/notebooks : Convert the Quarto files to Jupyter notebooks"
+	@echo "  test_images    : Generate reference images for tests"
+	@echo "  image-build    : Build the podman/Docker image"
+	@echo "  image-run      : Run the podman/Docker image"
+	@echo "  image-push     : Push the podman/Docker image to the registry"
+
 install:
 	poetry install
 
@@ -39,4 +60,26 @@ clean:
 		rm -f docs/example-with-datasets.$$i; \
 	done
 
-.PHONY: install test docs clean docs/notebooks docs/py test_images
+image-build: Dockerfile
+	$(CONTAINER) build -t pyrenew:latest .
+
+image-run:
+	$(CONTAINER) run -it --rm -v $(PWD):/mnt pyrenew:latest
+
+image-az-login:
+	if [ -z $(CONTAINER_REGISTRY) ]; then \
+		echo "Please set the CONTAINER_REGISTRY environment variable"; \
+		exit 1; \
+	fi
+	az login
+	az acr login --name $(CONTAINER_REGISTRY)
+
+image-push:
+	if [ -z $(CONTAINER_URL) ]; then \
+		echo "Please set the CONTAINER_URL environment variable"; \
+		exit 1; \
+	fi
+	$(CONTAINER) push pyrenew:latest $(CONTAINER_URL)/pyrenew:latest
+
+.PHONY: install test docs clean docs/notebooks docs/py test_images image-build \
+	image-run

model/README.md

@@ -7,7 +7,15 @@
 Install via pip with
 
 ```bash
-pip install git+https://github.com/cdcent/cfa-pyrenew.git
+pip install git+https://github.com/CDCgov/multisignal-epi-inference@main#subdirectory=model
+```
+
+## Container image
+
+A container image is available at `ghcr.io/CDCgov/pyrenew:latest`. You can pull it with
+
+```bash
+docker pull ghcr.io/CDCgov/pyrenew:latest
 ```
 
 ## Demo