build(docker): add Dockerfile and container image build tests (#362)

* build(docker): add Dockerfile and tests

This change adds a Dockerfile for pycytominer along with associated checks and tests to ensure the image is prepared for use on distribution platforms like Docker Hub.

* exclude docs from dockerfile deps install

Co-Authored-By: Ken Brewer <[email protected]>

* build(docker): refine docker image and build tests

* build(docker): refine docker build tests

Co-Authored-By: Ken Brewer <[email protected]>

---------

Co-authored-by: Ken Brewer <[email protected]>

.github/workflows/integration-test.yml

@@ -144,3 +144,52 @@ jobs:
           path: dist/*.tar.gz
           if-no-files-found: error
           retention-days: 90
+  docker-image-test:
+    runs-on: ubuntu-latest
+    # set a dependency sequence to occur after build job completion
+    needs: build
+    env:
+      version: ${{ needs.build.outputs.version }}
+      sdist_filename: pycytominer-${{ needs.build.outputs.version}}.tar.gz
+      sdist_extracted_name: pycytominer-${{ needs.build.outputs.version}}
+    steps:
+      # checks out selected files for docker image build testing
+      - name: Checkout selected files
+        uses: actions/checkout@v4
+        with:
+          sparse-checkout: |
+            build/docker/Dockerfile
+            tests
+          sparse-checkout-cone-mode: false
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+      # gather the sdist tar.gz name (which varies)
+      # unzips the sdist
+      - name: Extract sdist
+        run: |
+          tar -xzvf "${{ env.sdist_filename}}"
+      # note: roughly follows Docker documentation on GitHub Actions usage
+      # found on the following https://github.com/docker/build-push-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      # attempts to build a test image for observing test behavior
+      # and modeling a production image build. Version label
+      # assumes pwd of, for example: pycytominer-1.0.1.post37.dev0+55690e4,
+      # where we attempt to use 1.0.1.post37.dev0+55690e4 as a version label.
+      - name: Build docker image for testing
+        run: |
+          cd "${{ env.sdist_extracted_name }}" && \
+          cp -r ../tests . && \
+          docker build -f ../build/docker/Dockerfile \
+            -t pycytominer:testing \
+            --label version="${{ env.version }}" \
+            --target testing \
+            .
+      # runs pytest for pycytominer within a docker container based on the image above
+      - name: Run tests through docker image
+        run: |
+          docker run pycytominer:testing pytest

.pre-commit-config.yaml

@@ -18,3 +18,7 @@ repos:
     rev: v1.6.26
     hooks:
       - id: actionlint
+  - repo: https://github.com/hadolint/hadolint
+    rev: v2.12.1-beta
+    hooks:
+      - id: hadolint-docker

Makefile

@@ -18,3 +18,8 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+# note: presumes the existence of docker daemon to receive docker commands
+test_docker_build:
+	docker build -f build/docker/Dockerfile -t pycytominer:latest . && \
+	docker run pycytominer:latest poetry run pytest

build/docker/Dockerfile

@@ -0,0 +1,37 @@
+FROM python:3.11 as base
+
+# set various metadata, loosely following biocontainers standards from:
+# https://biocontainers-edu.readthedocs.io/en/latest/what_is_biocontainers.html
+LABEL base_image="python:3.11"
+LABEL software="pycytominer"
+LABEL about.summary="Python package for processing image-based profiling data"
+LABEL about.home="https://github.com/cytomining/pycytominer"
+LABEL about.documentation="https://pycytominer.readthedocs.io/en/stable/"
+LABEL about.license_file="https://github.com/cytomining/pycytominer/blob/main/LICENSE.md"
+LABEL about.license="SPDX:BSD-3-Clause"
+
+# set the workdir to /app
+WORKDIR /app
+
+# configures poetry to install dependencies without virtualenvs
+# see: https://python-poetry.org/docs/configuration/#virtualenvscreate
+ENV POETRY_VIRTUALENVS_CREATE=false
+
+# install poetry and poetry dynamic versioning
+# hadolint ignore=DL3013
+RUN pip install --no-cache-dir poetry
+
+# create stage for production build (no dev or non-essential deps)
+FROM base as production
+
+# copy the pycytominer source into image
+COPY . .
+
+# install pycytominer using poetry root dependencies and all extras
+RUN poetry install --all-extras -v --no-interaction
+
+# create stage for production build (no dev or non-essential deps)
+FROM production as testing
+
+# install pycytominer from poetry with group deps and all extras for testing
+RUN poetry install --with dev --all-extras -v --no-interaction

pyproject.toml

@@ -39,6 +39,7 @@ license = "BSD-3-Clause"
 readme = "README.md"
 homepage = "https://pycytominer.readthedocs.io/"
 repository = "https://github.com/cytomining/pycytominer"
+include = [{ path = "poetry.lock", format = "sdist" }]
 
 [tool.poetry.dependencies]
 python          = ">=3.8,<4.0"