Added Torch and Integration tools to Singularity Sandbox#5
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Pull Request Overview
This PR introduces enhancements to the benchmarking suite by adding a force‑refresh option for sandbox environments, reorganizing dependency listings in the requirements file, and updating the .gitignore to exclude Singularity image files.
- Added a user prompt and corresponding force‑refresh logic for refreshing both Docker and Singularity sandboxes in InteractiveAgentTester.py.
- Restructured the requirements.txt file into logical sections and added new dependencies.
- Updated .gitignore to ignore Singularity image files.
Reviewed Changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| benchmarking/sandbox/requirements.txt | Reorganized dependency groups and added new dependencies. |
| benchmarking/InteractiveAgentTester.py | Introduced force‑refresh functionality for Docker and Singularity sandboxes. |
| benchmarking/.gitignore | Added exclusion entry for Singularity image files (*.sif). |
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This pull request introduces enhancements to the benchmarking suite, focusing on sandbox management, user interactivity, and dependency organization. Key changes include adding optional force-refresh functionality for sandbox environments, restructuring the
requirements.txtfile for clarity, and updating the.gitignorefile to exclude Singularity image files.Sandbox Management Enhancements:
benchmarking/InteractiveAgentTester.py: Introduced aforce_refreshoption to allow users to force-update sandbox environments. For Docker, this removes the container and image; for Singularity, it deletes the SIF file if it exists. [1] [2] [3] [4]Dependency Organization:
benchmarking/sandbox/requirements.txt: Restructured the file to group dependencies by functionality (e.g., core stack, visualization, single-cell analysis, dimensionality reduction, notebook support, utilities). Added new dependencies likezarr,h5netcdf, and tools for batch correction and integration.File Exclusion Updates:
benchmarking/.gitignore: Added*.sifto exclude Singularity image files from version control.