cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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Scheduled monthly dependency update for January #373

Closed pyup-bot closed 2 years ago

pyup-bot commented 2 years ago

Update cython from 0.29.24 to 0.29.26.

Changelog ### 0.29.26 ``` ==================== Bugs fixed ---------- * An incompatibility with CPython 3.11.0a3 was resolved. (Github issue :issue:`4499`) * The ``in`` operator failed on literal lists with starred expressions. Patch by Arvind Natarajan. (Github issue :issue:`3938`) * A C compiler warning in PyPy about a missing struct field initialisation was resolved. ``` ### 0.29.25 ``` ==================== Bugs fixed ---------- * Several incompatibilities with CPython 3.11 were resolved. Patches by David Woods, Victor Stinner, Thomas Caswell. (Github issues :issue:`4411`, :issue:`4414`, :issue:`4415`, :issue:`4416`, :issue:`4420`, :issue:`4428`, :issue:`4473`, :issue:`4479`, :issue:`4480`) * Some C compiler warnings were resolved. Patches by Lisandro Dalcin and others. (Github issue :issue:`4439`) * C++ ``std::move()`` should only be used automatically in MSVC versions that support it. Patch by Max Bachmann. (Github issue :issue:`4191`) * The ``Py_hash_t`` type failed to accept arbitrary "index" values. (Github issue :issue:`2752`) * Avoid copying unaligned 16-bit values since some platforms require them to be aligned. Use memcpy() instead to let the C compiler decide how to do it. (Github issue :issue:`4343`) * Cython crashed on invalid truthiness tests on C++ types without ``operator bool``. Patch by David Woods. (Github issue :issue:`4348`) * The declaration of ``PyUnicode_CompareWithASCIIString()`` in ``cpython.unicode`` was incorrect. Patch by Max Bachmann. (Github issue :issue:`4344`) ```
Links - PyPI: https://pypi.org/project/cython - Changelog: https://pyup.io/changelogs/cython/ - Homepage: http://cython.org/

Update numpy from 1.21.2 to 1.22.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/numpy - Homepage: https://www.numpy.org

Update dask[array] from 2021.9.1 to 2021.12.0.

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Links - PyPI: https://pypi.org/project/dask - Repo: https://github.com/dask/dask/

Update scipy from 1.7.1 to 1.7.3.

Changelog ### 1.7.3 ``` for MacOS arm64 with Python `3.8`, `3.9`, and `3.10`. The MacOS arm64 wheels are only available for MacOS version `12.0` and greater, as explained in [Issue 14688](https://github.com/scipy/scipy/issues/14688). Authors ======= * Anirudh Dagar * Ralf Gommers * Tyler Reddy * Pamphile Roy * Olivier Grisel * Isuru Fernando A total of 6 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. ``` ### 1.7.2 ``` compared to `1.7.1`. Notably, the release includes wheels for Python `3.10`, and wheels are now built with a newer version of OpenBLAS, `0.3.17`. Python `3.10` wheels are provided for MacOS x86_64 (thin, not universal2 or arm64 at this time), and Windows/Linux 64-bit. Many wheels are now built with newer versions of manylinux, which may require newer versions of pip. Authors ======= * Peter Bell * da-woods + * Isuru Fernando * Ralf Gommers * Matt Haberland * Nicholas McKibben * Ilhan Polat * Judah Rand + * Tyler Reddy * Pamphile Roy * Charles Harris * Matti Picus * Hugo van Kemenade * Jacob Vanderplas A total of 14 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete. ```
Links - PyPI: https://pypi.org/project/scipy - Changelog: https://pyup.io/changelogs/scipy/ - Repo: https://github.com/scipy/scipy/releases - Homepage: https://www.scipy.org

Update matplotlib from 3.4.3 to 3.5.1.

Changelog ### 3.5.1 ``` This is the first bugfix release of the 3.5.x series. This release contains several critical bug-fixes: * fix installation issues when setting a default backend * fix `add_lines` on horizontal colorbars * fix `streamplot` with start points on right or top edge * fix colorbars with boundaries or `NoNorm` * fix colorbars with negative contours * fix colorbars with tight layout * fix setting Axis label alignment to center * fix subfigure tight bounding box * fix subplot parameter window on macosx backend * fix unit handling in `Collections.set_offsets` * fix unyt integration in `errorbar` * re-display date offset in `ConciseDataFormatter` after zoom * reduce `do_3d_projection` deprecation warnings in external artists ```
Links - PyPI: https://pypi.org/project/matplotlib - Changelog: https://pyup.io/changelogs/matplotlib/ - Homepage: https://matplotlib.org

Update pandas from 1.3.3 to 1.3.5.

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Links - PyPI: https://pypi.org/project/pandas - Homepage: https://pandas.pydata.org

Update scikit-learn from 1.0 to 1.0.2.

Changelog ### 1.0.2 ``` We're happy to announce the 1.0.2 release with several bugfixes: You can see the changelog here: https://scikit-learn.org/dev/whats_new/v1.0.html#version-1-0-2 You can upgrade with pip as usual: pip install -U scikit-learn The conda-forge builds will be available shortly, which you can then install using: conda install -c conda-forge scikit-learn ``` ### 1.0.1 ``` We're happy to announce the 1.0.1 release with several bugfixes: You can see the changelog here: https://scikit-learn.org/dev/whats_new/v1.0.html#version-1-0-1 You can upgrade with pip as usual: pip install -U scikit-learn The conda-forge builds will be available shortly, which you can then install using: conda install -c conda-forge scikit-learn ```
Links - PyPI: https://pypi.org/project/scikit-learn - Changelog: https://pyup.io/changelogs/scikit-learn/ - Homepage: http://scikit-learn.org

Update h5py from 3.4.0 to 3.6.0.

Changelog
Links - PyPI: https://pypi.org/project/h5py - Changelog: https://pyup.io/changelogs/h5py/ - Homepage: http://www.h5py.org

Update numexpr from 2.7.3 to 2.8.1.

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Links - PyPI: https://pypi.org/project/numexpr - Changelog: https://pyup.io/changelogs/numexpr/ - Repo: https://github.com/pydata/numexpr

Update zarr from 2.10.1 to 2.10.3.

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Links - PyPI: https://pypi.org/project/zarr - Repo: https://github.com/zarr-developers/zarr-python

Update pomegranate from 0.14.5 to 0.14.7.

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Links - PyPI: https://pypi.org/project/pomegranate - Homepage: http://pypi.python.org/pypi/pomegranate/

Update ipython from 7.28.0 to 7.30.1.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/ipython - Changelog: https://pyup.io/changelogs/ipython/ - Homepage: https://ipython.org
pyup-bot commented 2 years ago

Closing this in favor of #378