Release Maintenance, bug fix, performance and feature release · biocore/biom-format

New features:

Add Windows support. PR #951 revises codebase to be Windows compatible and adds this support to the CI testing matrix.
Add NumPy 2.0 support. PR #950 ensures code compatibility with NumPy 2.0. This support is yet to be added to the CI testing matrix.
Expand API for Table.partition to allow for passing dict mappings from ids to groups and vice versa, remove of empty vectors, and ignoring None partitions. See issue #937
NumPy 2.0 support, see issue #956
The optimized subsample without replacement method is now exposed as biom.subsample. Note that this method operates inplace on SciPy csr_matrix and csc_matrix objects. See issue #958

Bug Fixes:

Fixed an edge case on in align_tree when a feature was empty, see issue #948
In subsample(..., with_replacement=True), it was possible to trigger a numerical stability on sum, see issue #952
update_ids(..., strict=False) could yield truncated IDs, see issue #957

Performance improvements:

Revise Table._fast_merge to use COO directly. For very large tables, this reduces runtime by ~50x and memory by ~5x. See PR #913.
Drastically reduce the memory needs of subsampling when sums are large. Also adds 64-bit support. See PR #935.
Improve handling of not-perfectly-integer inputs. See PR #938.

New Contributors

Full Changelog: 2.1.15.2...2.1.16