Revert "Docker"

[jlee733]

-This PR is being reverted to keep this repo in sync with the Ando Lab's mdx2 repo
-The files being deleted will be moved to the 'mdx2-workflows' repo
-Reverts #38

Summary by CodeRabbit

• Chores
  • Updated Docker build configuration to support multiple architectures.
  • Modified development environment containerization approach.

[coderabbitai]

Walkthrough

The PR updates the GitHub Actions Docker build workflow to reference a new Dockerfile location at .github/Dockerfile, adds QEMU setup for multi-platform builds, removes cache configuration, and deletes the old root Dockerfile that previously orchestrated a multi-stage Python/Jupyter environment setup.

Changes

Cohort / File(s)	Summary
CI Workflow Configuration .github/workflows/docker.yml	Added QEMU setup step, updated Dockerfile reference to .github/Dockerfile, and removed cache-from/cache-to configuration.
Root Dockerfile dockerfile	Removed multi-stage Dockerfile that configured Python 3.10 environment with micromamba, conda packages (nexpy, jupyterlab, dials, xia2), and JupyterHub stack for port 8888.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Added Dockerfile and accessing mdx2 through Docker container #57: Introduces .github/Dockerfile and creates the new docker workflow structure that this PR references.
• Docker #38: Appears to revert these changes and re-introduce the original root Dockerfile configuration.

Suggested reviewers

• spmeisburger

Poem

🐇 A Dockerfile moves to a hidden place,
.github/ becomes its new space,
QEMU steps in to help build wide,
With cache swept clean, we let it glide,
Multi-platform dreams come true! 🐳

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Revert "Docker"' clearly and specifically summarizes the main change: reverting a previous Docker-related PR. It is concise, directly related to the changeset (which removes Docker configuration files), and provides meaningful context.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch revert-38-jlee-docker

📝 Coding Plan

• Generate coding plan for human review comments

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[coderabbitai]

🧹 Nitpick comments (2)

.github/workflows/docker.yml (2)

37-43: Restore Buildx cache to avoid expensive layer rebuilds on each CI run.

The workflow is missing cache-from and cache-to settings. The .github/Dockerfile has multiple expensive operations (apt-get install, micromamba environment creation, pip installs of external packages and the dev package) that rebuild from scratch on every run without caching. Add GitHub Actions cache:

Suggested cache settings

       - name: Build and push
         uses: docker/build-push-action@v6
         with:
           context: .
           file: .github/Dockerfile
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
           push: ${{ github.ref == 'refs/heads/main' }}
           tags: ${{ steps.tags.outputs.tags }}

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In @.github/workflows/docker.yml around lines 37 - 43, The Build and push step
using docker/build-push-action@v6 lacks Buildx layer caching; update the step
(the "Build and push" action) to add the cache-from and cache-to inputs and
enable loading/pushing of the cache so expensive layers in .github/Dockerfile
(apt installs, micromamba, pip installs) are reused across runs; specifically,
add cache-from: type=gha,scope=${{ github.ref }} and cache-to:
type=gha,mode=max,scope=${{ github.ref }} (or equivalent buildx cache settings)
and ensure push: ${{ github.ref == 'refs/heads/main' }} remains so cache is
uploaded on main.

---

22-24: QEMU setup is unused without declaring build platforms.

Line 22-23 adds QEMU emulation, but the build step at line 37-43 does not specify platforms. QEMU is only beneficial when building for multiple architectures. Either remove the QEMU setup or add explicit multi-arch platforms to the build configuration.

Suggested adjustment (if multi-arch is intended)

       - name: Build and push
         uses: docker/build-push-action@v6
         with:
           context: .
           file: .github/Dockerfile
+          platforms: linux/amd64,linux/arm64
           push: ${{ github.ref == 'refs/heads/main' }}
           tags: ${{ steps.tags.outputs.tags }}

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In @.github/workflows/docker.yml around lines 22 - 24, The QEMU setup step using
docker/setup-qemu-action@v3 is unused because the Docker build step (the
docker/build-push-action step) does not declare `platforms`; either remove the
"Set up QEMU" step entirely or update the Docker build step to enable multi-arch
builds by adding a `platforms:` input (e.g. platforms: linux/amd64,linux/arm64)
to the docker/build-push-action invocation so QEMU emulation is actually
required and used.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Nitpick comments:
In @.github/workflows/docker.yml:
- Around line 37-43: The Build and push step using docker/build-push-action@v6
lacks Buildx layer caching; update the step (the "Build and push" action) to add
the cache-from and cache-to inputs and enable loading/pushing of the cache so
expensive layers in .github/Dockerfile (apt installs, micromamba, pip installs)
are reused across runs; specifically, add cache-from: type=gha,scope=${{
github.ref }} and cache-to: type=gha,mode=max,scope=${{ github.ref }} (or
equivalent buildx cache settings) and ensure push: ${{ github.ref ==
'refs/heads/main' }} remains so cache is uploaded on main.
- Around line 22-24: The QEMU setup step using docker/setup-qemu-action@v3 is
unused because the Docker build step (the docker/build-push-action step) does
not declare `platforms`; either remove the "Set up QEMU" step entirely or update
the Docker build step to enable multi-arch builds by adding a `platforms:` input
(e.g. platforms: linux/amd64,linux/arm64) to the docker/build-push-action
invocation so QEMU emulation is actually required and used.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: d7b7547f-2303-4e6d-9a14-a15df13ad0dd

📥 Commits

Reviewing files that changed from the base of the PR and between a71f2f3 and ada3095.

📒 Files selected for processing (2)

• .github/workflows/docker.yml
• dockerfile

💤 Files with no reviewable changes (1)

• dockerfile