Harmonize/refactor reprostim container build and PsychoPy

[yarikoptic]

Tasks:

• Ensure we have correct permissions under /opt.
• Merge all --run commands into the single layer.
• Cleanup uv cache, use latest psychopy_linux_installer and try new feature they provided (replace --uninstall-build-packages with --cleanup to include uv cache wieluk/psychopy_linux_installer#91).
• Reduce container image size more and cleanup other possible locations like:
  • psychopy_linux_installer under /opt/psychopy-installer
  • unused reprostim folders/files when installed from worktree in CI mode
• Make PsychoPy GUI/tools to be working when executed directly from container .
• Create CI test to check PsychoPy GUI can be executed from container
  • Add to docker build script a test for psychopy to be executable from within under xvfb #189.
• Make sure that command-line tools used by reprostim package explicitly installed in the container and can be executed:
  • ffmpeg / ffprobe
  • v4l-utils
  • mediainfo

Closes #188
Closes #189

[gemini-code-assist]

Summary of Changes

Hello @yarikoptic, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request introduces a crucial step in the container build process to explicitly manage file permissions within the /opt directory. By adding a chmod command, it ensures that all users within the generated container have appropriate read and execute access to the software and resources located under /opt, thereby preventing potential permission-related issues and enhancing the container's overall usability.

Highlights

• Permissions for /opt: A new --run command has been added to the container generation script to recursively set read and execute permissions (a+rX) for the /opt directory.
• Container Build Process: The permission setting is now an explicit step within the generate_container.sh script, ensuring that /opt and its contents have consistent access rights upon container creation.

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[gemini-code-assist]

Code Review

This pull request adds a chmod command to set permissions for the /opt directory within the generated container. My review focuses on improving the implementation. I've identified a bug where shell variables were not being expanded correctly due to improper quoting. My suggestion fixes this bug and also merges the new chmod command with the preceding one, which aligns with your TODO in the description to consolidate --run commands. This will make the Dockerfile generation more efficient by reducing layers.

[gemini-code-assist]

There's a potential bug here. The variable $REPROSTIM_CAPTURE_CLEAN is inside single quotes, so it will not be expanded by the shell. The literal string $REPROSTIM_CAPTURE_CLEAN will be passed to bash -c inside the container, which is likely not what you intend. The same issue exists on the line above for $REPROSTIM_CAPTURE_BUILD.

As you noted in the PR description, it's good practice to merge multiple --run commands to reduce image layers. You can fix the variable expansion and merge the commands at the same time.

Suggested change

	--run "bash -c '$REPROSTIM_CAPTURE_CLEAN'" \
	--run "chmod a+rX -R /opt"
	--run "${REPROSTIM_CAPTURE_CLEAN} && chmod a+rX -R /opt"

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 3.25%. Comparing base (58c366f) to head (a0c4c87).
⚠️ Report is 41 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff            @@
##           master    #193      +/-   ##
=========================================
- Coverage    3.57%   3.25%   -0.33%     
=========================================
  Files          22      22              
  Lines        2407    2645     +238     
  Branches      338     371      +33     
=========================================
  Hits           86      86              
- Misses       2321    2559     +238     

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