Merge pull request #1 from Symexpo/add-docker-container

feat: add Docker and Apptainer containers

.github/workflows/docker-publish.yml

@@ -0,0 +1,99 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  # schedule:
+    # - cron: '35 8 * * *'
+  push:
+    branches: [ "develop" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "develop" ]
+  workflow_dispatch:
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
+        with:
+          cosign-release: 'v2.2.4'
+
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: ./containers
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

containers/Dockerfile

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+# Use an official Ubuntu as a parent image
+FROM ubuntu:24.04
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG env_path
+
+# Install dependencies
+RUN apt-get update && apt-get install -y \
+    openjdk-17-jdk \
+    maven \
+    python3 \
+    python3-pip \
+    wget \
+    unzip \
+    git \
+    && apt-get clean
+
+# Install Miniconda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh
+
+# Set path to conda
+ENV PATH /opt/conda/bin:$PATH
+
+# Install Osmosis
+RUN wget --quiet https://github.com/openstreetmap/osmosis/releases/download/0.48.3/osmosis-0.48.3.zip -O /tmp/osmosis.zip && \
+    unzip /tmp/osmosis.zip -d /opt/osmosis && \
+    rm /tmp/osmosis.zip && \
+    ln -s /opt/osmosis/bin/osmosis /usr/local/bin/osmosis
+
+# Verify installations
+RUN java -version && \
+    mvn -version && \
+    python3 --version && \
+    conda --version && \
+    which osmosis
+
+# Copy the environment.yml file into the container if env_path is set (else will create an empty directory)
+COPY ${env_path} /tmp/environment.yml.tmp
+
+# Check if env_path is set, if not use from the repo
+RUN if [ -z "$env_path" ]; then \
+        cp ./environment.yml /tmp/environment.yml; \
+    else \
+        mv /tmp/environment.yml.tmp /tmp/environment.yml; \
+    fi
+
+# Create the conda environment
+RUN conda env create -f /tmp/environment.yml -n eqasim
+
+# Activate the environment
+RUN echo "source activate eqasim" > ~/.bashrc

containers/apptainer.def

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+Bootstrap: docker
+From: ghcr.io/eqasim-org/ile-de-france:latest
+
+%environment
+    source /opt/conda/bin/activate eqasim
+
+%runscript
+    exec python -m synpp "$@"

docs/containers.md

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+# Containers
+
+Containers for running the Eqasim pipeline are located in the `containers` folder
+
+## Docker container
+
+To build the container :
+`docker build -t eqasim .`
+
+This will pull the conda environment from the current repo.
+
+To build using your own environment.yml file :
+`docker build --build-arg env_path=/path/to/my/environment.yml -t eqasim .`
+
+To run the pipeline : 
+```bash
+docker run --rm -it \
+    --mount type=bind,src=/path/to/eqasim-ile-de-france,target=/usr/local/eqasim \
+    --mount type=bind,src=/path/to/eqasim-data,target=/usr/local/eqasim-data \
+    ghcr.io/eqasim-org/ile-de-france:latest /bin/bash -l -c "cd /usr/local/eqasim && python -m synpp"`
+```
+
+where :
+
+- `/path/to/eqasim-ile-de-france` is the path of the [eqasim pipline](https://github.com/eqasim-org/ile-de-france) on your *host* machine.
+- `/usr/local/eqasim` is going to be the path of the eqasim pipeline inside the container.
+- `/path/to/eqasim-data` is the path of the data (bdtopo, hts, sirene, etc.) folder on your *host* machine.
+- `/usr/local/eqasim-data` is the path of the data folder in the container. **This is the path you need to put in your `congif.yml` file**
+
+## Apptainer 
+
+To build the container : 
+`apptainer -v -d build eqasim.sif apptainer.def`
+
+To run the pipeline : 
+`apptainer run eqasim.sif`