Biom-format

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Maintenance, bug fix, performance and feature release, May 9th 2024.

New features:

* Add Windows support. PR[951](https://github.com/biocore/biom-format/pull/951) revises codebase to be Windows compatible and adds this support to the CI testing matrix.
* Add NumPy 2.0 support. PR [950](https://github.com/biocore/biom-format/pull/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](https://github.com/biocore/biom-format/issues/937)
* NumPy 2.0 support, see issue [956](https://github.com/biocore/biom-format/issues/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](https://github.com/biocore/biom-format/issues/958)

Bug Fixes:

* Fixed an edge case on in `align_tree` when a feature was empty, see issue [948](https://github.com/biocore/biom-format/issues/948)
* In `subsample(..., with_replacement=True)`, it was possible to trigger a numerical stability on sum, see issue [952](https://github.com/biocore/biom-format/issues/952)
* `update_ids(..., strict=False)` could yield truncated IDs, see issue [957](https://github.com/biocore/biom-format/issues/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](https://github.com/biocore/biom-format/pull/933).
* Drastically reduce the memory needs of subsampling when sums are large. Also adds 64-bit support. See PR [935](https://github.com/biocore/biom-format/pull/935).
* Improve handling of not-perfectly-integer inputs. See PR [938](https://github.com/biocore/biom-format/pull/938).

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Maintenance and bug fix release, May 4th 2023.

Bug fixes:

* Allow `Table.to_json` to properly handle numpy types in metadata, see issue [886](https://github.com/biocore/biom-format/issues/886)
* Do not modify IDs in place in the presence of duplicate relabels, see issue [892](https://github.com/biocore/biom-format/issues/892)
* Catch an edge case where a failured ID update in place would actually change IDs, see issue [892](https://github.com/biocore/biom-format/issues/892)

New features:

* `biom.parse.save_table` makes saving less tedious, see issue [897](https://github.com/biocore/biom-format/issues/897)
* `biom.util.biom_open` now supports pathlib.Path, see issue [894](https://github.com/biocore/biom-format/issues/894)
* You can now set a random seed at the call to `Table.subsample`, see issue [914](https://github.com/biocore/biom-format/issues/914).

General maintenance:

* Allow specifying a creation time on write, see issue [895](https://github.com/biocore/biom-format/issues/895)
* h5py optional code blocks have been removed, see issue [896](https://github.com/biocore/biom-format/issues/896)
* Many warnings from the test suite have been resolved, see issue [912](https://github.com/biocore/biom-format/issues/912)
* Politely error when validating non biom-format files, see issue [901](https://github.com/biocore/biom-format/issues/901)
* Disallow `head` with `-n <= 0` and `-m <= 0`, see issue [899](https://github.com/biocore/biom-format/issues/899)

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Bug fix, released on 3 January 2023.

Bug:

* `Table.collapse(..., one_to_many=True)` had a lingering dense conversion being performed. Avoiding this conversion yields nearly a 100x performance gain [PR 888](https://github.com/biocore/biom-format/pull/888).

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Substantial performance improvement and bug fix, released on 9 December 2022.

Important:

* Python 3.6 testing support has been removed.

New features:

* `Table.collapse(..., one_to_many=True)` now uses a sparse matrix on construction, substantially reducing memory overhead [PR 884](https://github.com/biocore/biom-format/pull/884).

Bug fixes:

* `Table.metadata_to_dataframe()` now considers all rows for column names, see [PR 881](https://github.com/biocore/biom-format/pull/881)

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General maintenance and feature expansion, released on 25 March 2022.

Bug fixes:

* `Table.from_json` now respects the creation date [issue 770](https://github.com/biocore/biom-format/issues/770) in Python 3.7 and higher

New Features

* Python 3.10 support, see [PR 865](https://github.com/biocore/biom-format/pull/865)
* 10x improvement on `Table.collapse` when operating over many partitions, see [PR 866](https://github.com/biocore/biom-format/pull/866)
* Minor performance improvement, see [PR 871](https://github.com/biocore/biom-format/pull/871)
* Coerce consistent, and fixed width, types for IDs, see [PR 872](https://github.com/biocore/biom-format/pull/872)
* Table / metadata alignment support, see [PR 859](https://github.com/biocore/biom-format/pull/859)

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Bug fix, released on 16 November 2020.

Bug fixes:

* During deployment testing for QIIME 2 2020.11, it was observed that certain combinations of hdf5 or h5py dependencies can result in metadata strings parsing as ASCII rather than UTF-8. Parse of BIOM-Format 2.1.0 files now normalize metadata strings as UTF-8, see [PR 853](https://github.com/biocore/biom-format/pull/853).

New Features

* Added support for aligning dataframes and trees against biom tables with `Table.align_to_dataframe` and `Table.align_tree`. see [PR 859](https://github.com/biocore/biom-format/pull/859)