search

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 September #339

Closed pyup-bot closed 3 years ago

pyup-bot commented 4 years ago

Update cython from 0.29.20 to 0.29.21.

Changelog ### 0.29.21 ``` ==================== Bugs fixed ---------- * Fix a regression in 0.29.20 where ``__div__`` failed to be found in extension types. (Github issue 3688) * Fix a regression in 0.29.20 where a call inside of a finally clause could fail to compile. Patch by David Woods. (Github issue 3712) * Zero-sized buffers could fail to validate as C/Fortran-contiguous. Patch by Clemens Hofreither. (Github issue 2093) * ``exec()`` did not allow recent Python syntax features in Py3.8+ due to https://bugs.python.org/issue35975. (Github issue 3695) * Binding staticmethods of Cython functions were not behaving like Python methods in Py3. Patch by Jeroen Demeyer and Michał Górny. (Github issue 3106) * Pythran calls to NumPy methods no longer generate useless method lookup code. * The ``PyUnicode_GET_LENGTH()`` macro was missing from the ``cpython.*`` declarations. Patch by Thomas Caswell. (Github issue 3692) * The deprecated ``PyUnicode_*()`` C-API functions are no longer used, except for Unicode strings that contain lone surrogates. Unicode strings that contain non-BMP characters or surrogate pairs now generate different C code on 16-bit Python 2.x Unicode deployments (such as MS-Windows). Generating the C code on Python 3.x is recommended in this case. Original patches by Inada Naoki and Victor Stinner. (Github issues 3677, 3721, 3697) * Some template parameters were missing from the C++ ``std::unordered_map`` declaration. Patch by will. (Github issue 3685) * Several internal code generation issues regarding temporary variables were resolved. (Github issue 3708) ```
Links - PyPI: https://pypi.org/project/cython - Changelog: https://pyup.io/changelogs/cython/ - Homepage: http://cython.org/

Update numpy from 1.19.0 to 1.19.1.

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 2.19.0 to 2.25.0.

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

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

Update scipy from 1.5.0 to 1.5.2.

Changelog ### 1.5.1 ``` compared to `1.5.0`. In particular, an issue where DLL loading can fail for SciPy wheels on Windows with Python `3.6` has been fixed. Authors ======= * Peter Bell * Loïc Estève * Philipp Thölke + * Tyler Reddy * Paul van Mulbregt * Pauli Virtanen * Warren Weckesser A total of 7 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 3.2.2 to 3.3.1.

Changelog ### 3.3.1 ``` This is the first bugfix release of the 3.3.x series. This release contains several critical bug-fixes: * fix docstring import issues when running Python with optimization * fix `hist` with categorical data, such as with Pandas * fix install on BSD systems * fix nbagg compatibility with Chrome 84+ * fix ordering of scatter marker size in 3D plots * fix performance regression when plotting `Path`s * fix reading from URL in `imread` * fix several regressions with new date epoch handling * fix some bad constrained and tight layout interactions with colorbars * fix use of customized toolbars in TkAgg and WXAgg backends ``` ### 3.3.0 ``` Highlights of this release include: - Provisional API for composing semantic axes layouts from text or nested lists - New Axes.sharex, Axes.sharey methods - Turbo colormap - colors.BoundaryNorm supports extend keyword argument - Text color for legend labels - Pcolor and Pcolormesh now accept shading='nearest' and 'auto' - Allow tick formatters to be set with str or function inputs - New Axes.axline method - Dates use a modern epoch - Improved font weight detection - Axes3D no longer distorts the 3D plot to match the 2D aspect ratio - More consistent toolbar behavior across backends - Toolbar icons are now styled for dark themes - Cursor text now uses a number of significant digits matching pointing precision - Functions to compute a Path's size - savefig() gained a backend keyword argument - Saving SVG now supports adding metadata - Saving PDF metadata via PGF now consistent with PDF backend - NbAgg and WebAgg no longer use jQuery & jQuery UI For the full details please see the [What's New](https://matplotlib.org/3.3.0/users/whats_new.html) and [API changes](https://matplotlib.org/3.3.0/api/api_changes.html) in the documentation. ```
Links - PyPI: https://pypi.org/project/matplotlib - Changelog: https://pyup.io/changelogs/matplotlib/ - Homepage: https://matplotlib.org

Update pandas from 1.0.5 to 1.1.1.

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

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

Update scikit-learn from 0.23.1 to 0.23.2.

Changelog ### 0.23.2 ``` We're happy to announce the 0.23.2 release with several bugfixes: You can see the changelog here: https://scikit-learn.org/stable/whats_new/v0.23.htmlversion-0-23-2 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 ```
Links - PyPI: https://pypi.org/project/scikit-learn - Changelog: https://pyup.io/changelogs/scikit-learn/ - Homepage: http://scikit-learn.org
pyup-bot commented 3 years ago

Closing this in favor of #342