cggh / scikit-allel

A Python package for exploring and analysing genetic variation data
MIT License
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Scheduled monthly dependency update for April #358

Closed pyup-bot closed 3 years ago

pyup-bot commented 3 years ago

Update numpy from 1.20.1 to 1.20.2.

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 2021.2.0 to 2021.3.1.

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

Update scipy from 1.6.1 to 1.6.2.

Changelog ### 1.6.2 ``` compared to `1.6.1`. This is also the first SciPy release to place upper bounds on some dependencies to improve the long-term repeatability of source builds. Authors ======= * Pradipta Ghosh + * Tyler Reddy * Ralf Gommers * Martin K. Scherer + * Robert Uhl * Warren Weckesser 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. ```
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 3.3.4 to 3.4.1.

Changelog ### 3.4.1 ``` This is the first bugfix release of the 3.4.x series. This release contains several critical bug-fixes: * fix errorbar when specifying fillstyle * fix Inkscape cleanup at exit on Windows for tests * fix legends of colour-mapped scatter plots * fix positioning of annotation fancy arrows * fix size and color rendering for 3D scatter plots * fix suptitle manual positioning when using constrained layout * respect antialiasing settings in cairo backends as well ``` ### 3.4.0 ``` Highlights of this release include: - Figure and Axes creation / management - New subfigure functionality - Single-line string notation for `subplot_mosaic` - Changes to behavior of Axes creation methods (`gca`, `add_axes`, `add_subplot`) - `add_subplot`/`add_axes` gained an *axes_class* parameter - Subplot and subplot2grid can now work with constrained layout - Plotting methods - `axline` supports transform parameter - New automatic labeling for bar charts - A list of hatches can be specified to `bar` and `barh` - Setting `BarContainer` orientation - Contour plots now default to using `ScalarFormatter` - `Axes.errorbar` cycles non-color properties correctly - `errorbar` *errorevery* parameter matches *markevery* - `hexbin` supports data reference for *C* parameter - Support callable for formatting of Sankey labels - `Axes.spines` access shortcuts - New `stairs` method and `StepPatch` artist - Added *orientation* parameter for stem plots - Angles on Bracket arrow styles - `TickedStroke` patheffect - Colors and colormaps - Collection color specification and mapping - Transparency (alpha) can be set as an array in collections - pcolormesh has improved transparency handling by enabling snapping - IPython representations for Colormap objects - `Colormap.set_extremes` and `Colormap.with_extremes` - Get under/over/bad colors of Colormap objects - New `cm.unregister_cmap` function - New `CenteredNorm` for symmetrical data around a center - New `FuncNorm` for arbitrary normalizations - GridSpec-based colorbars can now be positioned above or to the left of the main axes - Titles, ticks, and labels - supxlabel and supylabel - Shared-axes `subplots` tick label visibility is now correct for top or left labels - An iterable object with labels can be passed to `Axes.plot` - Fonts and Text - Text transform can rotate text direction - `matplotlib.mathtext` now supports *overset* and *underset* LaTeX symbols - *math_fontfamily* parameter to change `Text` font family - `TextArea`/`AnchoredText` support *horizontalalignment* - PDF supports URLs on Text artists - rcParams improvements - New rcParams for dates: set converter and whether to use interval_multiples - Date formatters now respect *usetex* rcParam - Setting *image.cmap* to a Colormap - Tick and tick label colors can be set independently using rcParams - 3D Axes improvements - Errorbar method in 3D Axes - Stem plots in 3D Axes - 3D Collection properties are now modifiable - Panning in 3D Axes - Interactive tool improvements - New `RangeSlider` widget - Sliders can now snap to arbitrary values - Pausing and Resuming Animations - Sphinx extensions - `plot_directive` *caption* option - Backend-specific improvements - Consecutive rasterized draws now merged - Support raw/rgba frame format in `FFMpegFileWriter` - nbAgg/WebAgg support middle-click and double-click - nbAgg support binary communication - Indexed color for PNG images in PDF files when possible - Improved font subsettings in PDF/PS - Kerning added to strings in PDFs - Fully-fractional HiDPI in QtAgg - wxAgg supports fullscreen toggle ``` ### 3.4.0rc3 ``` This is the third release candidate for Matplotlib 3.4.0. ``` ### 3.4.0rc2 ``` This is the second release candidate for Matplotlib 3.4.0. ``` ### 3.4.0rc1 ``` This is the first release candidate for Matplotlib 3.4.0. ```
Links - PyPI: https://pypi.org/project/matplotlib - Changelog: https://pyup.io/changelogs/matplotlib/ - Homepage: https://matplotlib.org

Update pandas from 1.2.2 to 1.2.3.

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 h5py from 3.1.0 to 3.2.1.

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

Update numexpr from 2.7.2 to 2.7.3.

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

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

Update zarr from 2.6.1 to 2.7.0.

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

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

Update pomegranate from 0.14.2 to 0.14.4.

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

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

Update ipython from 7.21.0 to 7.22.0.

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 3 years ago

Closing this in favor of #360