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 1.7.3 to 1.8.0 #111

Closed dependabot[bot] closed 2 years ago

dependabot[bot] commented 2 years ago

Bumps scipy from 1.7.3 to 1.8.0.

Release notes

Sourced from scipy's releases.

SciPy 1.8.0 Release Notes

SciPy 1.8.0 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 1.8.x branch, and on adding new features on the master branch.

This release requires Python 3.8+ and NumPy 1.17.3 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

  • A sparse array API has been added for early testing and feedback; this work is ongoing, and users should expect minor API refinements over the next few releases.
  • The sparse SVD library PROPACK is now vendored with SciPy, and an interface is exposed via scipy.sparse.svds with solver='PROPACK'. It is currently default-off due to potential issues on Windows that we aim to resolve in the next release, but can be optionally enabled at runtime for friendly testing with an environment variable setting of USE_PROPACK=1.
  • A new scipy.stats.sampling submodule that leverages the UNU.RAN C library to sample from arbitrary univariate non-uniform continuous and discrete distributions
  • All namespaces that were private but happened to miss underscores in their names have been deprecated.

New features

scipy.fft improvements

Added an orthogonalize=None parameter to the real transforms in scipy.fft which controls whether the modified definition of DCT/DST is used without changing the overall scaling.

scipy.fft backend registration is now smoother, operating with a single

... (truncated)

Commits
  • b5d8bab REL: 1.8.0 release commit.
  • d84f731 Merge pull request #15521 from tylerjereddy/treddy_prep_180_final
  • 315dd53 DOC: update 1.8.0 relnotes.
  • b54b7ae MAINT: fix broken link and remove CI badges
  • 920e27b REL: 1.8.0 unreleased.
  • ea004bd REL: 1.8.0rc4 released.
  • 4f3969d Merge pull request #15479 from tylerjereddy/treddy_180rc4
  • 8ed6aa9 DOC: update 1.8.0 relnotes.
  • efe4ca5 MAINT: PR 15479 revisions
  • 1803913 MAINT: remove non-default settings (except shallow) in .gitmodules
  • Additional commits viewable in compare view


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