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REL: denote 2.1.16 #968

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REL: denote 2.1.16 #968

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REL: denote 2.1.16
wasade May 9, 2024
8cf3c12
Minor reorg on changelog
wasade May 9, 2024
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10 changes: 6 additions & 4 deletions ChangeLog.md
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@@ -1,11 +1,15 @@
BIOM-Format ChangeLog
=====================

biom 2.1.15-dev
---------------
biom 2.1.16
-----------

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)
Expand All @@ -18,8 +22,6 @@ Bug Fixes:

Performance improvements:

* 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.
* 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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2 changes: 1 addition & 1 deletion biom/util.py
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__maintainer__ = "Daniel McDonald"
__email__ = "[email protected]"
__format_version__ = (2, 1)
__version__ = "2.1.15-dev"
__version__ = "2.1.16"


def generate_subsamples(table, n, axis='sample', by_id=False):
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6 changes: 3 additions & 3 deletions doc/conf.py
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Expand Up @@ -57,15 +57,15 @@

# General information about the project.
project = 'biom-format'
copyright = '2011-2022 The BIOM Format Development Team'
copyright = '2011-2024 The BIOM Format Development Team'

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The full version, including alpha/beta/rc tags.
version = "2.1.15-dev"
release = "2.1.15-dev"
version = "2.1.16"
release = "2.1.16"

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -32,7 +32,7 @@
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Jose Clemente",
"Jai Ram Rideout", "Jorge Cañardo Alastuey", "Michael Hall"]
__license__ = "BSD"
__version__ = "2.1.15-dev"
__version__ = "2.1.16"
__maintainer__ = "Daniel McDonald"
__email__ = "[email protected]"

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