diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml new file mode 100644 index 0000000..53502e8 --- /dev/null +++ b/.github/workflows/docker-publish.yml @@ -0,0 +1,106 @@ +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: '16 19 * * *' + push: + branches: [ "main" ] + # Publish semver tags as releases. + tags: [ 'v*.*.*' ] + pull_request: + branches: [ "main" ] + +env: + # Use docker.io for Docker Hub if empty + REGISTRY: ghcr.io + # github.repository as / + IMAGE_NAME: ${{ github.repository }} + + +jobs: + build: + +# runs-on: ubuntu-latest + runs-on: ubuntu-24.04 + 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 + + - name: Print tool versions + run: | + set -x + pwd + ls + find . + + # 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: . + 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 {}@${DIGEST} diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..f515471 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,108 @@ +FROM ubuntu:24.04 + +ENV LANG=C.UTF-8 +ENV LC_ALL=C.UTF-8 +ENV DEBIAN_FRONTEND=noninteractive +ENV PYTHONUNBUFFERED=1 +ENV PYTHONDONTWRITEBYTECODE=1 +ENV MAMBA_NO_BANNER=1 + +ARG MINIFORGE_VERSION="24.3.0-0" + +# base packages +RUN apt-get update && apt-get install --no-install-recommends -y \ + tini \ + gosu \ + curl \ + ca-certificates \ + tar \ + unzip \ + gzip \ + time \ + htop \ + less \ + lsof \ + strace \ + procps \ + neovim \ + micro \ + ninja-build \ + texlive-latex-base \ + texlive-latex-extra \ + texlive-fonts-extra \ + && echo "apt-get done" \ +# && rm -rf /var/lib/apt/lists/* \ + ; + + +# create base conda environment using mambaforge +RUN set -x && \ + pwd && \ + MINIFORGE_FILENAME="Mambaforge-$(uname)-$(uname -m).sh" && \ + MINIFORGE_DOWNLOAD_URL="https://github.com/conda-forge/miniforge/releases/download/${MINIFORGE_VERSION}/${MINIFORGE_FILENAME}" && \ + curl -L -o "Miniforge3.sh" "$MINIFORGE_DOWNLOAD_URL" && \ + bash "./Miniforge3.sh" -b -p /opt/mambaforge && \ + /opt/mambaforge/bin/python --version && \ + /opt/mambaforge/condabin/mamba clean --all && \ + rm "./Miniforge3.sh" && \ + echo "done"; + + +# add base conda utils to path +ENV PATH="/opt/mambaforge/condabin:$PATH" + +RUN set -x && \ + conda config --file /opt/mambaforge/.condarc --add envs_dirs /opt/envs; + +RUN set -x && \ + mamba install conda-tree -n base && \ + mamba clean --all && \ + echo "done"; + +## + +RUN mkdir /app-build +RUN mkdir /app + +## + +COPY environment.yml /app-build +#COPY environment-pinned-linux.yml /app-build/environment.yml + +# create new conda environment named "main" +RUN set -x && \ + mamba env create -n main --file=/app-build/environment.yml && \ + /opt/envs/main/bin/python --version && \ + mamba clean --all && \ + echo "done"; + +RUN set -x && \ + conda env export -n main && \ + echo "done"; + + + + +# "activate" "main" conda environment +ENV CONDA_PREFIX="/opt/envs/main" +ENV PATH="$CONDA_PREFIX/bin:$PATH" + + +RUN set -x && \ + conda env export -n main > /app-build/environment-final.yml && \ + cat /app-build/environment-final.yml && \ + echo "done"; + +RUN set -x && \ + /opt/mambaforge/bin/conda-tree -n main deptree --small > /app-build/deptree.txt && \ + cat /app-build/deptree.txt && \ + echo "done"; + +WORKDIR /app +COPY . /app + +ENTRYPOINT ["tini", "-g", "--"] + +#CMD ["/bin/bash"] +CMD ["bash"] +#CMD ["/app/run_app.sh"] diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..d689499 --- /dev/null +++ b/environment.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge +dependencies: + - python=3.12 + - fastapi + - uvicorn + - sqlalchemy + - zstandard + - zstd + - jinja2 + - tabulate + - importlib_resources + - click + - libblas=*=*openblas + # linux-only + - _openmp_mutex=*=*_llvm \ No newline at end of file