Make reprostim the default repronim-reprostim container entrypoint

[vmdocua]

Refactor repronim-reprostim container to be more "native" in usage.

Tasks:

• Update container entry point from python3 to reprostim shim.
• Include PsychoPy venv bin into system PATH env variable.
• Update helper bash scripts around container.
• Make sure GitHub container workflow actions and test passed well.
• Update RTD documentation with applied changes.
• Test container on local dev machine and typhon (will be completed after the PR is merged and released).

Closes #217.

[gemini-code-assist]

Summary of Changes

Hello, 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 comprehensive task list and plan to configure the repronim-reprostim container, establishing reprostim as its default entrypoint. This change aims to simplify container execution by allowing direct invocation of the reprostim command without requiring explicit python3 -m reprostim calls, thereby improving user experience and streamlining container workflows. The PR itself adds the documentation for this plan.

Highlights

• New Task Document Added: A new markdown document, .ai/task-container.md, has been added to detail the implementation plan for making reprostim the default container entrypoint for repronim-reprostim.
• Entrypoint Simplification Goal: The primary goal outlined in the new document is to enable direct invocation of reprostim <args> when running the container (e.g., singularity run <container.sif> <args> or docker run <image> <args>), eliminating the need for python3 -m reprostim.
• Planned Script Modifications: The task list specifies planned modifications to setup_container.sh, generate_container.sh, run_reprostim.sh, and run_reprostim_ci.sh to achieve the default entrypoint functionality and ensure compatibility across different container run modes.

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Changelog

• .ai/task-container.md
  • Added a new document outlining the tasks required to make reprostim the default container entrypoint.

Activity

• No human activity (comments, reviews, etc.) has been recorded for this pull request yet.

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[gemini-code-assist]

Code Review

This pull request adds a markdown file, .ai/task-container.md, which outlines a plan to make reprostim the default container entrypoint. However, the PR does not contain the actual code changes to implement this plan. The title, 'Make reprostim the default repronim-reprostim container entrypoint', is therefore misleading as it implies the work is completed. A pull request should ideally contain the code to be merged. This task list might be better suited as a comment on issue #217 or as part of a draft pull request description while the changes are being developed. I've also pointed out a potential contradiction in the planned tasks within the new file.

_{Note: Security Review has been skipped due to the limited scope of the PR.}

[gemini-code-assist]

There seems to be a contradiction between the first two tasks for setup_container.sh. The first task aims to make reprostim accessible by adding its directory to the system PATH, explicitly stating it's to avoid individual wrappers. The second task, however, proposes creating exactly such a wrapper script for reprostim. These appear to be two alternative solutions. Could you clarify if both are needed, or if one is preferred? If the PATH is correctly extended, a separate wrapper script should be unnecessary.

[github-actions]

🚀 PR was released in 0.7.27 🚀