chore: publish docker image on release (#112)

.github/workflows/dockerize.yaml

@@ -0,0 +1,83 @@
+name: dockerize
+run-name: dockerize
+on:
+  push:
+    # only build+push docker on release-please tags
+    tags: ["v*"]
+    paths:
+    - ".github/actions/**"
+    - ".github/workflows/**"
+    - "conda-recipe/**"
+    - "genome_kit/**"
+    - "setup.py"
+    - "setup/**"
+    - "src/**"
+    - "tests/**"
+
+jobs:
+  docker-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: ./.github/actions/build-gk
+        with:
+          platform: linux-64
+
+      - name: restore mamba env
+        id: restore_mamba_cache
+        uses: actions/cache/restore@v4
+        with:
+          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**') }}
+          path: |
+            ~/micromamba
+            ~/.condarc
+            ~/bin/micromamba
+          fail-on-cache-miss: true
+
+      - name: restore the gk package tarballs
+        id: restore_gk_pkg
+        uses: actions/cache/restore@v4
+        with:
+          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/meta.yaml', 'src/**', 'genome_kit/**', 'tests/**') }}
+          path: |
+            ~/conda-bld
+          fail-on-cache-miss: true
+
+      - name: create gk env
+        id: create-gk-env
+        shell: bash -l -e {0}
+        run: |
+          set -x
+          # explicitly select py310
+          pgk_file_path=$(eval ls -1 ~/conda-bld/linux-64/*py310*.tar.bz2 | head -1)
+          pkg_file=$(basename ${pgk_file_path})
+          pkg_version=$(echo $pkg_file | grep -Eo '[0-9]+\.[0-9]+\.[0-9]+')
+          echo "PKG_VERSION=${pkg_version}" >> $GITHUB_OUTPUT
+          micromamba activate build
+          conda index ~/conda-bld
+          mamba create -n genomekit -c file://${HOME}/conda-bld genomekit=${pkg_version}
+          set +x
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          context: /home/runner/micromamba/envs/build/envs
+          file: Dockerfile
+          push: true
+          tags: |
+            deepgenomicsinc/genomekit:latest
+            deepgenomicsinc/genomekit:latest-py310
+            deepgenomicsinc/genomekit:${{ steps.create-gk-env.outputs.PKG_VERSION }}-py310

.github/workflows/publish-docs.yaml

@@ -49,14 +49,13 @@ jobs:
         shell: bash -l -e {0}
         run: |
           set -x
-          pkg_name=$(eval ls -1 ~/conda-bld/*/*.tar.bz2 | head -1)
-          pkg_name=$(basename ${pkg_name})
-          pkg_version=$(echo $pkg_name | grep -Eo '[0-9]+\.[0-9]+\.[0-9]+')
-          pkg_name=${pkg_name%%-[0-9]*}
+          pgk_file_path=$(eval ls -1 ~/conda-bld/*/*.tar.bz2 | head -1)
+          pkg_file=$(basename ${pgk_file_path})
+          pkg_version=$(echo $pkg_file | grep -Eo '[0-9]+\.[0-9]+\.[0-9]+')
           micromamba activate build
           conda index ~/conda-bld
           mamba create -n doc-build -c file://${HOME}/conda-bld \
-            ${pkg_name}=${pkg_version} \
+            genomekit=${pkg_version} \
             m2r2 \
             make \
             myst-parser \

Dockerfile

@@ -0,0 +1,3 @@
+FROM ubuntu:22.04
+COPY genomekit /opt/conda/envs/
+ENV PATH=/opt/conda/envs/genomekit/bin:$PATH

docs-src/quickstart.rst

@@ -20,6 +20,14 @@ You can install GenomeKit with::
     conda install -c conda-forge genomekit
 
 
+Use with docker
+~~~~~~~~~~~~~~~~~
+
+Alternatively you can use GenomeKit with docker::
+
+    $ docker run -it --rm deepgenomicsinc/genomekit:latest python
+    >>> import genome_kit
+
 Basics
 ------