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catalystneuro / nwb-conversion-tools

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.
https://nwb-conversion-tools.readthedocs.io/en/main/
BSD 3-Clause "New" or "Revised" License
25 stars 12 forks source link

Bump numpy from 1.21.0 to 1.22.0 #554

Closed dependabot[bot] closed 2 years ago

dependabot[bot] commented 2 years ago

Bumps numpy from 1.21.0 to 1.22.0.

Release notes

Sourced from numpy's releases.

v1.22.0

NumPy 1.22.0 Release Notes

NumPy 1.22.0 is a big release featuring the work of 153 contributors spread over 609 pull requests. There have been many improvements, highlights are:

  • Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release.
  • A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across application such as CuPy and JAX.
  • NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data.
  • New methods for quantile, percentile, and related functions. The new methods provide a complete set of the methods commonly found in the literature.
  • A new configurable allocator for use by downstream projects.

These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation.

The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays.

Expired deprecations

Deprecated numeric style dtype strings have been removed

Using the strings "Bytes0", "Datetime64", "Str0", "Uint32", and "Uint64" as a dtype will now raise a TypeError.

(gh-19539)

Expired deprecations for loads, ndfromtxt, and mafromtxt in npyio

numpy.loads was deprecated in v1.15, with the recommendation that users use pickle.loads instead. ndfromtxt and mafromtxt were both deprecated in v1.17 - users should use numpy.genfromtxt instead with the appropriate value for the usemask parameter.

(gh-19615)

... (truncated)

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CodyCBakerPhD commented 2 years ago

Ah, right. Nothing we can do to resolve this conflict until PyNWB updates https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/setup.py#L24

See https://github.com/NeurodataWithoutBorders/pynwb/pull/1488

CodyCBakerPhD commented 2 years ago

Question asked on PyNWB: https://github.com/NeurodataWithoutBorders/pynwb/pull/1488

CodyCBakerPhD commented 2 years ago

Should now operate with PyNWB 2.1.0

CodyCBakerPhD commented 2 years ago

Hmmm yet numpy 1.22 is not available to pyVer 3.7... will have to think about how to handle this on our end