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Remove all-gap alignment columns without repeated list deletion - #1

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DylanCosto wants to merge 12 commits into

mainfrom

perf-linear-gap-column-removal

Closed

Remove all-gap alignment columns without repeated list deletion#1
DylanCosto wants to merge 12 commits into
mainfrom
perf-linear-gap-column-removal

Commits on Oct 11, 2026
- Remove all-gap alignment columns without repeated list deletion
  DylanCosto
  committed
  6549f1f
- Compact shared alignment components only once
  DylanCosto
  committed
  5637291
Commits on Oct 15, 2026
- Fix `revcomp` handling in `SeqFile`
  
  nsoranzo
  and
  claude
  committed
  91b676f
- Fix `species_to_lengths` passed to wrong parameter by `get_reader()` and `get_indexed()`
  
  nsoranzo
  and
  claude
  committed
  ba66f81
- Fix `remove_all_gap_columns()` for alignments with empty components
  
  nsoranzo
  and
  claude
  committed
  3ba2cc9
- Close the lengths file in `read_lengths_file()` on errors
  
  nsoranzo
  and
  claude
  committed
  47756bc
- Pass `memo` to the `deepcopy()` calls in `Alignment.__deepcopy__()`
  
  nsoranzo
  and
  claude
  committed
  60caafb
- Add type annotations to `bx.align.core`
  
  nsoranzo
  and
  claude
  committed
  7a02fcd
- Drop support for Python 3.10
  nsoranzo
  committed
  63502aa
- Temporarily drop support for PyPy3.12
  nsoranzo
  committed
  8cfd4f2
- Merge upstream/main into perf-linear-gap-column-removal
  
  nsoranzo
  and
  claude
  committed
  0499c89
Commits on Oct 20, 2026
- Also test `text_size`
  nsoranzo
  authored
  251e1e7