[python] Consolidation and vacuuming are now platform configuration options #1690
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Commit and fragment_metadata consolidation and vacuuming can improve the opening and query performance of SOMA experiments. Vacuuming requires slight coordination though and should not happen by default. Instead a platform config allows the user to control these operations based. This will be expanded to defaults for top-level `io` packages where its more likely a user is doing a one-shot ingestion and will want automatic handling. A new platform config, `consolidate_and_vacuum` has been added which is a boolean to handle this behavior.
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eddelbuettel
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bkmartinjr
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Sep 17, 2023
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CI fails are orthogonal and are tracked by the still-open #1692. Merging this PR and monitoring its post-merge |
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…ptions (#1690) * Consolidation and vacuuming are now platform configuration options Commit and fragment_metadata consolidation and vacuuming can improve the opening and query performance of SOMA experiments. Vacuuming requires slight coordination though and should not happen by default. Instead a platform config allows the user to control these operations based. This will be expanded to defaults for top-level `io` packages where its more likely a user is doing a one-shot ingestion and will want automatic handling. A new platform config, `consolidate_and_vacuum` has been added which is a boolean to handle this behavior. * set is_mac for ci-minimal workflow
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…ptions (#1690) (#1696) * Consolidation and vacuuming are now platform configuration options Commit and fragment_metadata consolidation and vacuuming can improve the opening and query performance of SOMA experiments. Vacuuming requires slight coordination though and should not happen by default. Instead a platform config allows the user to control these operations based. This will be expanded to defaults for top-level `io` packages where its more likely a user is doing a one-shot ingestion and will want automatic handling. A new platform config, `consolidate_and_vacuum` has been added which is a boolean to handle this behavior. * set is_mac for ci-minimal workflow Co-authored-by: Seth Shelnutt <Shelnutt2@gmail.com>
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The backport to To backport manually, run these commands in your terminal: # Fetch latest updates from GitHub
git fetch
# Create a new working tree
git worktree add .worktrees/backport-release-1.4 release-1.4
# Navigate to the new working tree
cd .worktrees/backport-release-1.4
# Create a new branch
git switch --create backport-1690-to-release-1.4
# Cherry-pick the merged commit of this pull request and resolve the conflicts
git cherry-pick --mainline 1 25f5a27f459501c32605734dca9a44ccf8aa0325
# Push it to GitHub
git push --set-upstream origin backport-1690-to-release-1.4
# Go back to the original working tree
cd ../..
# Delete the working tree
git worktree remove .worktrees/backport-release-1.4Then, create a pull request where the |
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Issue and/or context:
Consolidation and vacuuming need to be controllable by the user, and should default at the low level to off. In higher level APIs we need to follow up with automatic handling.
Changes:
Commit and fragment_metadata consolidation and vacuuming can improve the opening and query performance of SOMA experiments. Vacuuming requires slight coordination though and should not happen by default. Instead a platform config allows the user to control these operations based. This will be expanded to defaults for top-level
iopackages where its more likely a user is doing a one-shot ingestion and will want automatic handling.A new platform config,
consolidate_and_vacuumhas been added which is a boolean to handle this behavior.Notes for Reviewer: