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[BWARE] Add removeEmpty support to compressed column groups - #2504
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Implement removeEmptyRows and removeEmptyCols for compressed matrices without full decompression. Add CLALibRemoveEmpty driver and LibMatrixReorg helpers (rmemptyEarlyAbort/rmemptyUnsafe), per-column-group removeEmptyRows/removeEmptyColsSubset, dictionary sliceColumns, and offset/mapping support for index-only row removal.
Baunsgaard
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…ide effect - Add Apache license header to CLALibRemoveEmpty (fixes RAT license check) - Remove dead partition/swap helpers and unused imports in Dictionary/QDictionary (fixes checkstyle unused-import errors) - Make MatrixBlockDictionary.sliceColumns read-through instead of calling sparseToDense() in place, so it no longer mutates the shared dictionary block - Validate selected-row count up front in AMapToData.removeEmpty instead of catching ArrayIndexOutOfBoundsException for control flow - Lower the decompress-fallback log in CLALibRemoveEmpty to guarded debug - Document the null-return contract on removeEmptyCols and rmemptyEarlyAbort - Remove leftover commented-out debug code in AOffset and ColGroupSDCSingleZeros - Use Assume.assumeTrue for size-gated removeEmpty tests instead of silent skips - Revert unrelated CompressForce and EncodeSample test changes out of scope
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #2504 +/- ##
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+ Coverage 71.45% 71.54% +0.09%
- Complexity 48864 49043 +179
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Files 1573 1574 +1
Lines 189239 189565 +326
Branches 37128 37188 +60
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+ Hits 135215 135632 +417
+ Misses 43576 43457 -119
- Partials 10448 10476 +28 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Route CompressedMatrixBlock.removeEmptyOperations through CLALibRemoveEmpty.rmempty instead of always decompressing and delegating. This makes the compressed removeEmpty implementation (per-column-group removeEmptyRows/removeEmptyColsSubset, dictionary sliceColumns, and offset/mapping handling) actually reachable; it was previously dead code with 0% test coverage. The existing removeEmptyOperations tests in CompressedMatrixTest now exercise the compressed path, while the null-select case still falls back to full decompression.
Extend CompressedMatrixTest with additional removeEmptyOperations cases that exercise branches the existing tests missed: emptyReturn=true with a selection vector, a denser row selection, select-all (nothing removed), and the all-rows/all-cols-removed paths (rOut==0 / cOut==0). Each case compares the compressed result against the uncompressed reference across the full compression-config matrix.
CompressedMatrixBlock.removeEmptyOperations was wired to CLALibRemoveEmpty, but the select-based fast path iterated column groups and called removeEmptyRows/removeEmptyColsSubset with no fallback. OLE, RLE, LinearFunctional, and UncompressedArray groups throw NotImplementedException for these operations, so a compressed matrix containing one of them would hard-fail where the previous always-decompress implementation succeeded. Wrap the per-group loops in rmEmptyRows/rmEmptyCols and route to the existing decompression fallback on NotImplementedException, restoring the prior "works for any encoding" contract. Add CompressedRemoveEmptyForcedTest, which forces OLE/RLE encodings and asserts removeEmptyOperations matches the uncompressed reference instead of throwing.
Cover the per-encoding removeEmptyColsSubset dictionary-slicing paths that were previously untested by selecting a strict subset of a multi-column column group: - SDC, SDC-single, and SDCFOR (via sparsifyFOR) reference/default-tuple slicing branches. - DDC subset removal. - RLE/OLE fallback to decompression when index-only column removal is unsupported (NotImplementedException path). - Selection vectors with unknown (-1) non-zero counts, exercising the recompute branches in CLALibRemoveEmpty for both rows and columns. Identical columns are used so co-coding merges them into one multi-column group, guaranteeing the subset path is reached instead of the all-selected copyAndSet shortcut.
Bruno-Ignaz
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Sep 1, 2026
) Implement removeEmptyRows and removeEmptyCols for compressed matrices without full decompression. Add CLALibRemoveEmpty driver and LibMatrixReorg helpers (rmemptyEarlyAbort/rmemptyUnsafe), per-column-group removeEmptyRows/removeEmptyColsSubset, dictionary sliceColumns, and offset/mapping support for index-only row removal.
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Implement removeEmptyRows and removeEmptyCols for compressed matrices without full decompression. Add CLALibRemoveEmpty driver and LibMatrixReorg helpers (rmemptyEarlyAbort/rmemptyUnsafe), per-column-group removeEmptyRows/removeEmptyColsSubset, dictionary sliceColumns, and offset/mapping support for index-only row removal.