compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
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Bump numpy from 1.18.4 to 1.19.0 #85

Closed dependabot-preview[bot] closed 4 years ago

dependabot-preview[bot] commented 4 years ago

Bumps numpy from 1.18.4 to 1.19.0.

Release notes

Sourced from numpy's releases.

v1.19.0

NumPy 1.19.0 Release Notes

This NumPy release is marked by the removal of much technical debt: support for Python 2 has been removed, many deprecations have been expired, and documentation has been improved. The polishing of the random module continues apace with bug fixes and better usability from Cython.

The Python versions supported for this release are 3.6-3.8. Downstream developers should use Cython >= 0.29.16 for Python 3.8 support and OpenBLAS >= 3.7 to avoid problems on the Skylake architecture.

Highlights

  • Code compatibility with Python versions < 3.6 (including Python 2) was dropped from both the python and C code. The shims in numpy.compat will remain to support third-party packages, but they may be deprecated in a future release. Note that 1.19.x will not compile with earlier versions of Python due to the use of f-strings.

    (gh-15233)

Expired deprecations

numpy.insert and numpy.delete can no longer be passed an axis on 0d arrays

This concludes a deprecation from 1.9, where when an axis argument was passed to a call to ~numpy.insert and ~numpy.delete on a 0d array, the axis and obj argument and indices would be completely ignored. In these cases, insert(arr, "nonsense", 42, axis=0) would actually overwrite the entire array, while delete(arr, "nonsense", axis=0) would be arr.copy()

Now passing axis on a 0d array raises ~numpy.AxisError.

(gh-15802)

numpy.delete no longer ignores out-of-bounds indices

This concludes deprecations from 1.8 and 1.9, where np.delete would ignore both negative and out-of-bounds items in a sequence of indices. This was at odds with its behavior when passed a single index.

Now out-of-bounds items throw IndexError, and negative items index from the end.

Changelog

Sourced from numpy's changelog.

This file gives an overview of what is necessary to build binary releases for NumPy.

Current build and release info

The current info on building and releasing NumPy and SciPy is scattered in several places. It should be summarized in one place, updated, and where necessary described in more detail. The sections below list all places where useful info can be found.

Source tree

  • INSTALL.rst.txt
  • release.sh
  • pavement.py

NumPy Docs

SciPy.org wiki

Release Scripts

Supported platforms and versions

:ref:NEP 29 <NEP29> outlines which Python versions are supported; For the first half of 2020, this will be Python >= 3.6. We test NumPy against all these versions every time we merge code to master. Binary installers may be available for a subset of these versions (see below).

OS X

OS X versions >= 10.9 are supported, for Python version support see :ref:NEP 29 <NEP29>. We build binary wheels for OSX that are compatible with Python.org Python, system Python, homebrew and macports - see this OSX wheel building summary <https://github.com/MacPython/wiki/wiki/Spinning-wheels>_ for details.

Windows

Commits
  • 92ebe1e REL: NumPy 1.14.5 release.
  • 8f364cd Merge pull request #16645 from charris/prepare-1.19.0-release
  • 7a06267 DOC: Update 1.19.0-changelog.rst for 1.19.0 release.
  • 516d70d Merge pull request #16602 from charris/test_ignore_nan_ulperror
  • 8ecbf34 MAINT: Move and improve test_ignore_nan_ulperror.
  • c17b6fa Merge pull request #16586 from charris/backport-16572
  • a1e166a Add test for sin/cos for strided large inputs
  • d90f20f BUG: fix sin/cos bug when input is strided
  • d167bb7 Merge pull request #16563 from charris/backport-16551
  • a9a7993 DOC: Add release note.
  • Additional commits viewable in compare view


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