smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
http://doi.org/djv4
GNU General Public License v3.0
28 stars 8 forks source link

Bump scipy from 1.5.4 to 1.6.0 #28

Closed dependabot[bot] closed 3 years ago

dependabot[bot] commented 3 years ago

Bumps scipy from 1.5.4 to 1.6.0.

Release notes

Sourced from scipy's releases.

SciPy 1.6.0 Release Notes

SciPy 1.6.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.6.x branch, and on adding new features on the master branch.

This release requires Python 3.7+ and NumPy 1.16.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

  • scipy.ndimage improvements: Fixes and ehancements to boundary extension modes for interpolation functions. Support for complex-valued inputs in many filtering and interpolation functions. New grid_mode option for scipy.ndimage.zoom to enable results consistent with scikit-image's rescale.
  • scipy.optimize.linprog has fast, new methods for large, sparse problems from the HiGHS library.
  • scipy.stats improvements including new distributions, a new test, and enhancements to existing distributions and tests

New features

scipy.special improvements

scipy.special now has improved support for 64-bit LAPACK backend

scipy.odr improvements

scipy.odr now has support for 64-bit integer BLAS

scipy.odr.ODR has gained an optional overwrite argument so that existing files may be overwritten.

scipy.integrate improvements

Some renames of functions with poor names were done, with the old names retained without being in the reference guide for backwards compatibility

... (truncated)

Commits
  • ab1c090 REL: set version to 1.6.0 released
  • 9fe5791 Merge pull request #13309 from tylerjereddy/treddy_160_final_prep
  • 74fcaa6 MAINT: prepare for 1.6.0 final
  • ff1fb19 MAINT: backport gh-13255
  • 86ba0d0 REL: set version to 1.6.0rc2
  • 939ecfc Merge pull request #13279 from tylerjereddy/treddy_160rc2_backports
  • 550f87e DOC: update 1.6.0 relnotes
  • 5e5ec9f CI: github actions: In the linux dbg tests, update apt before install packages.
  • caa3eb2 CI: a few other packages
  • 6558739 CI: reactivate CI selectivity
  • Additional commits viewable in compare view


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