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cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
287 stars 49 forks source link

Scheduled monthly dependency update for June #319

Closed pyup-bot closed 4 years ago

pyup-bot commented 4 years ago

Update cython from 0.29.17 to 0.29.19.

Changelog ### 0.29.19 ``` ==================== Bugs fixed ---------- * A typo in Windows specific code in 0.29.18 was fixed that broke "libc.math". (Github issue 3622) * A platform specific test failure in 0.29.18 was fixed. Patch by smutch. (Github issue 3620) ``` ### 0.29.18 ``` ==================== Bugs fixed ---------- * Exception position reporting could run into race conditions on threaded code. It now uses function-local variables again. * Error handling early in the module init code could lead to a crash. * Error handling in ``cython.array`` creation was improved to avoid calling C-API functions with an error held. * A memory corruption was fixed when garbage collection was triggered during calls to ``PyType_Ready()`` of extension type subclasses. (Github issue 3603) * Memory view slicing generated unused error handling code which could negatively impact the C compiler optimisations for parallel OpenMP code etc. Also, it is now helped by static branch hints. (Github issue 2987) * Cython's built-in OpenMP functions were not translated inside of call arguments. Original patch by Celelibi and David Woods. (Github issue 3594) * Complex buffer item types of structs of arrays could fail to validate. Patch by Leo and smutch. (Github issue 1407) * Decorators were not allowed on nested `async def` functions. (Github issue 1462) * C-tuples could use invalid C struct casting. Patch by MegaIng. (Github issue 3038) * Optimised ``%d`` string formatting into f-strings failed on float values. (Github issue 3092) * Optimised aligned string formatting (``%05s``, ``%-5s``) failed. (Github issue 3476) * When importing the old Cython ``build_ext`` integration with distutils, the additional command line arguments leaked into the regular command. Patch by Kamekameha. (Github issue 2209) * When using the ``CYTHON_NO_PYINIT_EXPORT`` option in C++, the module init function was not declared as ``extern "C"``. (Github issue 3414) * Three missing timedelta access macros were added in ``cpython.datetime``. * The signature of the NumPy C-API function ``PyArray_SearchSorted()`` was fixed. Patch by Brock Mendel. (Github issue 3606) ```
Links - PyPI: https://pypi.org/project/cython - Changelog: https://pyup.io/changelogs/cython/ - Homepage: http://cython.org/

Update numpy from 1.18.3 to 1.18.4.

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 2.15.0 to 2.17.2.

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

Update pandas from 1.0.3 to 1.0.4.

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

Update scikit-learn from 0.22.2.post1 to 0.23.1.

Changelog ### 0.23.0 ``` We're happy to announce the 0.23 release. You can read the release highlights under https://scikit-learn.org/stable/auto_examples/release_highlights/plot_release_highlights_0_23_0.html and the long version of the change log under https://scikit-learn.org/stable/whats_new/v0.23.htmlversion-0-23-0 This version supports Python versions 3.6 to 3.8. ```
Links - PyPI: https://pypi.org/project/scikit-learn - Changelog: https://pyup.io/changelogs/scikit-learn/ - Homepage: http://scikit-learn.org
alimanfoo commented 4 years ago

Cherry picked from #294 to fix flake8 error.