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

[d33bs]

Description

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.

A first step towards addressing #214 .

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

Please ensure that all boxes are checked before indicating that a pull request is ready for review.

• I have read the CONTRIBUTING.md guidelines.
• My code follows the style guidelines of this project.
• I have performed a self-review of my own code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• New and existing unit tests pass locally with my changes.
• I have added tests that prove my fix is effective or that my feature works.
• I have deleted all non-relevant text in this pull request template.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.96%. Comparing base (2cd5ad5) to head (bc093ef).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #362   +/-   ##
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  Coverage   94.96%   94.96%           
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  Files          56       56           
  Lines        3136     3136           
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  Hits         2978     2978           
  Misses        158      158           

Flag	Coverage Δ
unittests	94.96% <ø> (ø)

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[kenibrewer]

Will get around to reviewing this in detail tomorrow. My main suggestions will be focused on seeing if we can find a way to avoid including the entire git history of our repo in the image. I think there's a path forward using poetry-dynamic-versioning[plugin] and relying and built versions of our codebase instead of copied versions.

[gwaybio]

@kenibrewer - let us know if you're able to give this a look. Thanks!

(it is beyond my skill set)

[kenibrewer]

Sorry for the delay in the review @d33bs . Have had some major projects going on at work. Here is some feedback focused primarily on reducing bloat within the docker image which I expect to be quite unwieldy in the current approach.

I tiered my recommendations based on the potential impact and complexity of implementation,

Strongly recommended fixes

• Do not use poetry virtual environments in the docker image and instead install dependencies directly into base python.
• Do not install docs dependency group within docker image.

Recommended fixes

• Avoid copying the entire git history of pycytominer into the image, potentially by implementing the feature in FeatureRequest: Add build artifacts for CI/CD pipeline #369 .

Discretionary fixes

• Remove dev dependencies from final build image using a multi-stage build.

Here's a pseudo dockerfile for the last item:

FROM python:latest AS build
COPY pycytominer requirements.txt ./
RUN pip install requirements.txt

FROM build as test
COPY tests requirements-dev.txt ./
RUN pip install requirements-dev.txt

Then use this https://docs.docker.com/build/building/multi-stage/#stop-at-a-specific-build-stage to tag one image as pycytominer-test and other other as pycytominer. Run pytest in the test image and then push the build image to dockerhub.

[d33bs]

I've added some updates here based on your suggestions @kenibrewer, thanks a bunch for your assistance with the adjacent work in #373! I believe current test failures with the Docker image test revolve around those which I plan to address as part of the changed s3 data locations mentioned in #374 . I'm working on resolving the data issues in #374 before running a full test workflow check here.

[kenibrewer]

Looks great! A few minor suggestions for adding clarity to the github actions at your discretion.

[kenibrewer]

Looks like the extract should probably target '--directory.'

Or maybe we just create the pycytominer directory first

[d33bs]

Thanks again @kenibrewer for your review and continued comments! I feel good about where things now stand and will merge this in now.