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MannLabs / alphapept

A modular, python-based framework for mass spectrometry. Powered by nbdev.
https://mannlabs.github.io/alphapept/
Apache License 2.0
168 stars 31 forks source link

Bump tables from 3.6.1 to 3.8.0 #531

Open dependabot[bot] opened 1 year ago

dependabot[bot] commented 1 year ago

Bumps tables from 3.6.1 to 3.8.0.

Release notes

Sourced from tables's releases.

Release v3.8.0

Changes from 3.7.0 to 3.8.0

Improvements

  • Support for Python 3.11 has been added (PR #962).
  • Support for Python 3.6 and Python 3.7 has been dropped (PR #966).
  • Added a new (registered) HDF5 filter for Blosc2 compressor (PR #969).
  • Added optimized paths for Blosc2 reading and writing in tables. This bypasses the HDF5 filter pipeline by building the Blosc2 CFrames and sending them to the HDF5 direct chunking machinery (PR #969).
  • Internal C-Blosc sources updated to 1.21.2.
  • Thanks to Oscar Guiñon, Francesc Alted for implementing Blosc2 the support and NumFOCUS for providing a grant for that.

Other changes

  • Starting form this release, C source files generated by Cython are no longer included in the source distribution package.
  • Pre-built HTML documentation is no longer included in the source package.

Release v3.7.0

Improvements

  • Compatibility with Python 3.10, numpy 1.21 and HDF5 1.12.
  • Support for Python 3.5 has been dropped (#840 and #850).
  • Windows: Significantly faster import tables PR #781. Thanks to Christoph Gohlke.
  • Internal C-Blosc sources updated to 1.21.1 (#931). Note that, starting from C-Blosc 1.19 does not include the Snappy codec sources anymore, so Snappy will be not available if you compile from included sources; other packages (like conda or wheels), may (or may not) include it.
  • Stop using appveyor and deprecated ci-helpers (closes #827).
  • Switch to git submodule for the management of vendored c-blosc sources.
  • CI moved to GitHub Actions (GHA).
  • Drop Travis-CI.
  • Improved code formatting and notation consistency (#873, #868, #865 thanks to Miroslav Šedivý).
  • Improve the use of modern Python including :mod:pathlib, f-strings (#859, #855, #839 and #818 thanks to Miroslav Šedivý).
  • Several improvements to wheels generation in CI (thanks to Andreas Motl @​amotl and Matthias @​xmatthias).
  • Simplified management of version information.
  • Drop dependency on the deprecated distutils.
  • Modernize the setup script and add support for PEP517 (#907).

... (truncated)

Changelog

Sourced from tables's changelog.

Changes from 3.8.0 to 3.9.0

XXX version-specific blurb XXX

Changes from 3.7.0 to 3.8.0

Improvements

  • Support for Python 3.11 has been added (PR #962).
  • Support for Python 3.6 and Python 3.7 has been dropped (PR #966).
  • Added a new (registered) HDF5 filter for Blosc2 compressor (PR #969).
  • Added optimized paths for Blosc2 reading and writing in tables. This bypasses the HDF5 filter pipeline by building the Blosc2 CFrames and sending them to the HDF5 direct chunking machinery (PR #969).
  • Internal C-Blosc sources updated to 1.21.2.
  • Thanks to Oscar Guiñon, Francesc Alted for implementing Blosc2 the support and NumFOCUS for providing a grant for that.

Other changes

  • Starting form this release, C source files generated by Cython are no longer included in the source distribution package.
  • Pre-built HTML documentation is no longer included in the source package.
Commits
  • e34d1f7 Update copyright year
  • f1e9fc3 Add a performance comparison with pandas
  • ce2c32d Getting ready for release 3.8.0
  • 0f28388 Prevent PyPy builds on linux too
  • 53eaed0 Prevent building macos pypy wheels.
  • e241459 Merge pull request #979 from PyTables/tables-3.8.0
  • 0f14177 Continue silencing warnings for recent NumPy (1.24)
  • 5d02ad6 Merge branch 'master' into tables-3.8.0
  • a0fccf2 Silence more warnings for recent NumPy (1.24)
  • 8ea4b98 Silence a warning for recent NumPy
  • Additional commits viewable in compare view


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dependabot[bot] commented 1 year ago

The following labels could not be found: pip dependencies.