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cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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Scheduled monthly dependency update for October #342

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 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 1.19.2.

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 2.28.0.

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 3.3.2.

Changelog ### 3.3.2 ``` This is the second bugfix release of the 3.3.x series. This release contains several critical bug-fixes: * fix `Axis` scale on twinned `Axes` * fix auto-close of `Figure`s in nbagg * fix automatic title placement if `Axes` is off the `Figure` * fix autoranging of log scales with barstacked histogram * fix extra redraws when using `Button` or `TextBox` widgets * fix imshow with `LogNorm` and large vmin/vmax ranges * fix plotting Pandas `DataFrame` with string `MultiIndex` * fix `scatter` with `marker=''` * fix `scatter3d` color/linewidth re-projection * fix state of mode buttons in TkAgg backends * include license files in built distribution * reduce Visual C++ runtime requirements on Windows ``` ### 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 seaborn from 0.10.1 to 0.11.0.

Changelog ### 0.11.0 ``` This is a major release with important new features, enhancements to existing functions, and changes to the library. Highlights include an overhaul and modernization of the distributions plotting functions, more flexible data specification, new colormaps, and better narrative documentation. Complete release notes are available on the [seaborn website](https://seaborn.pydata.org/whatsnew.html). ``` ### 0.11.0.rc0 ``` This is the first release candidate for v0.11.0, a major release with several important new features and changes to the library. Highlights of the new version include: - A modernization of the distributions module, with the introduction of [`displot`](https://github.com/mwaskom/seaborn/pull/2157), [`histplot`](https://github.com/mwaskom/seaborn/pull/2125), and [`ecdfplot`](https://github.com/mwaskom/seaborn/pull/2141), a complete rewrite of [`kdeplot`](https://github.com/mwaskom/seaborn/pull/2104), and substantial enhancements to [`jointplot`](https://github.com/mwaskom/seaborn/pull/2210) and [`pairplot`](https://github.com/mwaskom/seaborn/pull/2234) - Centralized [input data processing](https://github.com/mwaskom/seaborn/pull/2071) allowing for both standardization and increased flexibility of long- and wide-form variable specification - Substantial [internal refactoring](https://github.com/mwaskom/seaborn/pull/2090) to support the new distributions functions and planned improvements in other modules - Warning-based enforcement of [keyword-only parameters](https://github.com/mwaskom/seaborn/pull/2081) in most functions - New [perceptually uniform colormaps](https://github.com/mwaskom/seaborn/pull/2237) and better tools for creating custom numeric color palettes - Improvements to the narrative documentation, including user guide chapters on function types and data structures, along with better cross-linking within the seaborn docs and between the seaborn and matplotlib docs - Numerous other [targeted enhancements and bug fixes](https://github.com/mwaskom/seaborn/blob/v0.11.0.rc0/doc/releases/v0.11.0.txt) Please test the release by installing from here or with `python -m pip install --upgrade --pre seaborn` ```
Links - PyPI: https://pypi.org/project/seaborn - Changelog: https://pyup.io/changelogs/seaborn/ - Repo: https://github.com/mwaskom/seaborn/ - Homepage: https://seaborn.pydata.org

Update pandas from 1.0.5 to 1.1.2.

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

Update hmmlearn from 0.2.3 to 0.2.4.

Changelog ### 0.2.4 ``` ------------- Released on September 12th, 2020. - Bumped previously incorrect dependency bound on scipy to 0.19. - Bug fix for 'params' argument usage in GMMHMM. - Warn when an explicitly set attribute would be overridden by ``init_params_``. ```
Links - PyPI: https://pypi.org/project/hmmlearn - Changelog: https://pyup.io/changelogs/hmmlearn/ - Repo: https://github.com/hmmlearn/hmmlearn
pyup-bot commented 3 years ago

Closing this in favor of #344