added dockerfile (#177)

.github/workflows/docker.yml

@@ -0,0 +1,120 @@
+# This workflow will build two Docker image and push then to GitHub Packages Container registry:
+# - a base image with the dependencies
+# - a main image with the application code
+
+name: Docker
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'docker/**'
+      - '.github/workflows/docker-base.yml'
+      - 'conda/*.yml'
+      - 'pyproject.toml'
+  pull_request:
+    branches: [main]
+    paths:
+      - 'docker/**'
+      - '.github/workflows/docker-base.yml'
+      - 'conda/*.yml'
+      - 'pyproject.toml'
+  release:
+    types: [published]
+
+jobs:
+  build_docker_images:
+    strategy:
+      matrix:
+        RAPIDS_VER:
+          - 24.04
+    name: Build Docker images
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+    steps:
+      - name: Maximize build disk space
+        uses: easimon/maximize-build-space@v10
+        with:
+          remove-dotnet: true
+          remove-android: true
+          remove-haskell: true
+          remove-codeql: true
+          root-reserve-mb: 35840
+          swap-size-mb: 1048
+
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker base image
+        id: meta-base
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ghcr.io/${{ github.repository }}-deps
+
+      - name: create yaml file for conda environment
+        run: |
+          grep -v -- '- rapids-singlecell' conda/rsc_rapids_${{ matrix.RAPIDS_VER }}.yml > docker/rsc_rapids.yml
+        shell: bash
+
+      - name: Build and push Docker base images
+        id: push-base
+        uses: docker/build-push-action@v5
+        with:
+          context: ./docker/
+          file: ./docker/Dockerfile.deps
+          push: ${{ github.event_name == 'release' }}
+          tags: ${{ steps.meta-base.outputs.tags }}
+          labels: ${{ steps.meta-base.outputs.labels }}
+          #cache-from: type=registry,ref=ghcr.io/${{ github.repository }}-deps
+
+      - name: Generate artifact attestation for base image
+        if: github.event_name == 'release'
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push-base.outputs.digest }}
+          push-to-registry: true
+
+      - name: Extract metadata (tags, labels) for main Docker image
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ghcr.io/${{ github.repository }}
+
+      - name: Build and push main Docker images
+        id: push
+        uses: docker/build-push-action@v5
+        with:
+          context: ./docker/
+          file: ./docker/Dockerfile
+          push: ${{ github.event_name == 'release' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          #cache-from: type=registry,ref=ghcr.io/${{ github.repository }}
+          build-contexts: |
+            rapids-singlecell-deps=docker-image://${{ steps.meta-base.outputs.tags }}
+
+      - name: Generate artifact attestation for main image
+        if: github.event_name == 'release'
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true
+
+      - name: list docker images
+        run: |
+          docker image ls -a
+        shell: bash

docker/Dockerfile

@@ -0,0 +1,20 @@
+FROM rapids-singlecell-deps
+
+ARG GIT_ID=main
+
+SHELL ["/bin/bash", "-euo", "pipefail", "-c"]
+
+ENV PATH=/opt/conda/bin:$PATH
+
+RUN <<EOF
+# install rapids_singlecell from source
+set -x
+mkdir /src
+cd /src
+git clone https://github.com/scverse/rapids_singlecell.git
+cd rapids_singlecell
+git checkout ${GIT_ID}
+/opt/conda/bin/python -m pip install --no-cache-dir -e .
+EOF
+
+ENTRYPOINT ["/opt/conda/bin/ipython"]

docker/Dockerfile.deps

@@ -0,0 +1,40 @@
+ARG CUDA_VER=11.8.0
+ARG LINUX_VER=ubuntu22.04
+
+FROM nvidia/cuda:${CUDA_VER}-base-${LINUX_VER}
+
+SHELL ["/bin/bash", "-euo", "pipefail", "-c"]
+
+ARG PYTHON_VER=3.11
+
+ENV PATH=/opt/conda/bin:$PATH
+ENV PYTHON_VERSION=${PYTHON_VER}
+
+COPY --from=condaforge/miniforge3:24.3.0-0 /opt/conda /opt/conda
+
+COPY rsc_rapids.yml rsc_rapids.yml
+
+ARG GIT_ID=main
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN <<EOF
+# install conda environment
+set -x
+apt-get -qq update
+apt-get -q -o=Dpkg::Use-Pty=0 -y dist-upgrade
+apt-get -q install -y -o=Dpkg::Use-Pty=0 git
+apt-get -q clean -y
+mamba env update -n base -f rsc_rapids.yml
+mamba install -y -n base pytest -c conda-forge
+mamba clean -afy
+EOF
+
+RUN <<EOF
+# install rapids_singlecell dependencies
+set -x
+/opt/conda/bin/python -m pip install --no-cache-dir git+https://github.com/scverse/rapids_singlecell.git@${GIT_ID}
+/opt/conda/bin/python -m pip uninstall -y --no-cache-dir rapids-singlecell
+/opt/conda/bin/python -m pip cache purge
+EOF
+
+ENTRYPOINT ["/opt/conda/bin/ipython"]

docker/docker-push.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+set -euxo pipefail
+
+docker_account=scverse
+rapids_version=24.04
+grep -v -- '- rapids-singlecell' conda/rsc_rapids_${rapids_version}.yml > rsc_rapids.yml
+docker build -t rapids-singlecell-deps:latest -f docker/Dockerfile.deps .
+rm rsc_rapids.yml
+docker build -t rapids-singlecell:latest -f docker/Dockerfile .
+latest_id=$( docker images |grep -e "rapids-singlecell[ \t]*latest"|head -n1|awk '{print $3}' )
+#docker tag $latest_id $docker_account/rapids-singlecell:latest
+#docker push $docker_account/rapids-singlecell:latest

docs/release-notes/0.10.3.md

@@ -3,6 +3,7 @@
 ```{rubric} Features
 ```
 * adds the flavor `seurat_v3_paper` to `pp.highly_variable_genes` {pr}`170` {smaller}`S Dicks`
+* build docker images in github CI {pr}`177` {smaller}`T Korten (HZDR/Helmholtz AI)`
 
 ```{rubric} Performance
 ```
@@ -12,6 +13,7 @@
 * updates `pp.highly_variable_genes` for the flavors `seurat` and `cell_ranger` {pr}`183` {smaller}`S Dicks`
 * `pp.scale` now uses `RawKernels` for dense and csr {pr}`185` {smaller}`S Dicks`
 
+
 ```{rubric} Bug fixes
 ```
 * fixes a bug where the `pp.scale` would have issues with `int64` indexing {pr}`187` {smaller}`S Dicks`