[r] Port re-indexer to the R API #2637
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Add `nomatch` parameter to `$get_indexer()` Update tests
Bump develop version [ci skip]
|
Better still after follow-up off-GH discussion. Should be read AFAICT. |
mojaveazure
deleted the
paulhoffman/sc-40890/r-c-add-r-support-for-c-reindexer
branch
|
The backport to To backport manually, run these commands in your terminal: # Fetch latest updates from GitHub
git fetch
# Create a new working tree
git worktree add .worktrees/backport-release-1.11 release-1.11
# Navigate to the new working tree
cd .worktrees/backport-release-1.11
# Create a new branch
git switch --create backport-2637-to-release-1.11
# Cherry-pick the merged commit of this pull request and resolve the conflicts
git cherry-pick --mainline 1 d97915ff69a0f4225c5b5218f799b91a725e0da8
# Push it to GitHub
git push --set-upstream origin backport-2637-to-release-1.11
# Go back to the original working tree
cd ../..
# Delete the working tree
git worktree remove .worktrees/backport-release-1.11Then, create a pull request where the |
mojaveazure
added a commit
that referenced
this pull request
Jun 14, 2024
Connect the re-indexer to the blockwise iterator, allowing reads to be re-indexed on-the-fly. This PR parallels #1792 and completes #2152 and #2637; in addition, provides new shorthand for `reindex_disable_on_axis`: - `TRUE`: disable re-indexing on all axes - `FALSE: re-index on all axes - `NA`: re-index only on major axis, disable re-indexing on all axes (default) `BlockwiseTableReadIter$concat()` and `BlockwiseSparseReadIter$concat()` are disabled when re-indexing is requested (paralleling Python) `BlockwiseSparseReadIter` now accepts `repr = "R"` or `repr = "C"` under certain circumstances: - axis 0 (`soma_dim_0`) must be re-indexed to allow `repr = "R"` - axis 1 (`soma_dim_1`) must be re-indexed to allow `repr = "C"` `repr` of `"T"` is allowed in all circumstances and continues to be the default Two new fields are available to blockwise iterators: - `$axes_to_reindex`: a vector of minor axes slated to be re-indexed - `$reindexable`: status indicator stating if _any_ axis (major or minor) is slated to be re-indexed resolves #2671
johnkerl
pushed a commit
that referenced
this pull request
Jun 17, 2024
Connect the re-indexer to the blockwise iterator, allowing reads to be re-indexed on-the-fly. This PR parallels #1792 and completes #2152 and #2637; in addition, provides new shorthand for `reindex_disable_on_axis`: - `TRUE`: disable re-indexing on all axes - `FALSE: re-index on all axes - `NA`: re-index only on major axis, disable re-indexing on all axes (default) `BlockwiseTableReadIter$concat()` and `BlockwiseSparseReadIter$concat()` are disabled when re-indexing is requested (paralleling Python) `BlockwiseSparseReadIter` now accepts `repr = "R"` or `repr = "C"` under certain circumstances: - axis 0 (`soma_dim_0`) must be re-indexed to allow `repr = "R"` - axis 1 (`soma_dim_1`) must be re-indexed to allow `repr = "C"` `repr` of `"T"` is allowed in all circumstances and continues to be the default Two new fields are available to blockwise iterators: - `$axes_to_reindex`: a vector of minor axes slated to be re-indexed - `$reindexable`: status indicator stating if _any_ axis (major or minor) is slated to be re-indexed resolves #2671
github-actions bot
pushed a commit
that referenced
this pull request
Jun 17, 2024
Connect the re-indexer to the blockwise iterator, allowing reads to be re-indexed on-the-fly. This PR parallels #1792 and completes #2152 and #2637; in addition, provides new shorthand for `reindex_disable_on_axis`: - `TRUE`: disable re-indexing on all axes - `FALSE: re-index on all axes - `NA`: re-index only on major axis, disable re-indexing on all axes (default) `BlockwiseTableReadIter$concat()` and `BlockwiseSparseReadIter$concat()` are disabled when re-indexing is requested (paralleling Python) `BlockwiseSparseReadIter` now accepts `repr = "R"` or `repr = "C"` under certain circumstances: - axis 0 (`soma_dim_0`) must be re-indexed to allow `repr = "R"` - axis 1 (`soma_dim_1`) must be re-indexed to allow `repr = "C"` `repr` of `"T"` is allowed in all circumstances and continues to be the default Two new fields are available to blockwise iterators: - `$axes_to_reindex`: a vector of minor axes slated to be re-indexed - `$reindexable`: status indicator stating if _any_ axis (major or minor) is slated to be re-indexed resolves #2671
johnkerl
pushed a commit
that referenced
this pull request
Jun 17, 2024
Connect the re-indexer to the blockwise iterator, allowing reads to be re-indexed on-the-fly. This PR parallels #1792 and completes #2152 and #2637; in addition, provides new shorthand for `reindex_disable_on_axis`: - `TRUE`: disable re-indexing on all axes - `FALSE: re-index on all axes - `NA`: re-index only on major axis, disable re-indexing on all axes (default) `BlockwiseTableReadIter$concat()` and `BlockwiseSparseReadIter$concat()` are disabled when re-indexing is requested (paralleling Python) `BlockwiseSparseReadIter` now accepts `repr = "R"` or `repr = "C"` under certain circumstances: - axis 0 (`soma_dim_0`) must be re-indexed to allow `repr = "R"` - axis 1 (`soma_dim_1`) must be re-indexed to allow `repr = "C"` `repr` of `"T"` is allowed in all circumstances and continues to be the default Two new fields are available to blockwise iterators: - `$axes_to_reindex`: a vector of minor axes slated to be re-indexed - `$reindexable`: status indicator stating if _any_ axis (major or minor) is slated to be re-indexed resolves #2671 Co-authored-by: Paul Hoffman <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Expose the re-indexer to the R API through a new
IntIndexerclass, this class takes a vector of integerish values to create the re-indexer, and has one method$get_indexer()that takes a vector of lookups to re-indexNew SOMA classes:
IntIndexer: an R6 wrapper around the C++ re-indexer$initialize(): takes an integerish vector to intitialize the C++ re-indexer$get_indexer(): takes an integerish vector or Arrow Array to perform a lookupbit64::integer64nomatch_nato adjust the nomatch value tobit64::NA_integer64_resolves #1610