chore/monorepos

[bwalsh]

Description

This PR refactors the monorepos test infrastructure to remove Git LFS dependencies and transition to using git-drs (Data Repository Service) for managing large files. The changes simplify the test setup and execution by eliminating Git LFS installation requirements and replacing Git LFS commands with their git-drs equivalents.

Changes

tests/monorepos/Makefile

• Added generate-large-fixtures-run to .PHONY target list
• Updated generate-fixtures-run echo message to clarify it generates a "small set of fixtures"
• Added new generate-large-fixtures-run target that generates a large dataset (25 TCGA projects with 100 files each in 3 subdirectories)

tests/monorepos/run-test.sh

• Removed Git LFS dependency checks (~30 lines): Eliminated the section that verified Git LFS installation and provided installation instructions for macOS/Homebrew
• Updated repository initialization:
  • Changed calypr_admin projects ls to calypr-cli auth --all for project verification
  • Added GIT_LFS_SKIP_SMUDGE=1 flag to initial git clone
  • Replaced git lfs pull with git drs pull
• Migrated from Git LFS to Git DRS commands:
  • git lfs track → git drs track
  • git lfs ls-files → git drs ls-files
  • git lfs push --dry-run calls removed (no longer needed)
  • git lfs status calls removed (no longer needed)
• Updated git-drs remote configuration: Changed git drs remote add syntax from "$PROFILE" "$PROGRAM/$PROJECT" to origin "$PROGRAM/$PROJECT"
• Enhanced git-drs initialization: Added --enable-data-client-logs flag to git drs init
• Improved git config validation: Changed from generic grep search to specific git config --local --get drs.enable-data-client-logs check
• Bug fixes:
  • Added head -n 1 to file search to handle multiple matches
  • Commented out break statement to enable full test execution across all directories (instead of just testing one directory)

Why

These changes:

1. Simplify test environment setup by removing Git LFS as a prerequisite
2. Improve test reliability by using the purpose-built DRS system for large file management
3. Support monorepo testing with the new generate-large-fixtures-run target for comprehensive testing scenarios
4. Reduce maintenance burden by removing platform-specific installation logic (Homebrew on macOS)

Testing

The refactored test suite should now:

• Successfully initialize repositories without requiring Git LFS installation
• Properly track and manage large files using git-drs
• Execute complete test cycles across all generated fixture directories
• Provide better logging and diagnostics with data client logs enabled

---

Type of change:

• Refactoring/Infrastructure
• Bug fix
• New feature

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Drop the branch argument from git drs pull

When --clone is used, this always exits before hydration because git drs pull does not accept the branch argument carried over from git lfs pull; I checked cmd/pull/main.go, which rejects more than one arg, and docs/commands.md documents git drs pull as hydration-only. Since this script has set -e, git drs pull origin main aborts the clone validation path instead of hydrating the pointers.

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[bwalsh]

@matthewpeterkort Can you confirm this behavior?