alimanfoo / pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
189 stars 43 forks source link

Scheduled monthly dependency update for November #130

Closed pyup-bot closed 2 years ago

pyup-bot commented 2 years ago

Update Cython from 0.29.23 to 0.29.24.

Changelog ### 0.29.24 ``` ==================== Bugs fixed ---------- * Inline functions in pxd files that used memory views could lead to invalid C code if the module that imported from them does not use memory views. Patch by David Woods. (Github issue :issue:`1415`) * Several declarations in ``libcpp.string`` were added and corrected. Patch by Janek Bevendorff. (Github issue :issue:`4268`) * Pickling unbound Cython compiled methods failed. Patch by Pierre Glaser. (Github issue :issue:`2972`) * The tracing code was adapted to work with CPython 3.10. * The optimised ``in`` operator failed on unicode strings in Py3.9 and later that were constructed from an external ``wchar_t`` source. Also, related C compiler warnings about deprecated C-API usage were resolved. (Github issue :issue:`3925`) * Some compiler crashes were resolved. Patch by David Woods. (Github issues :issue:`4214`, :issue:`2811`) * An incorrect warning about 'unused' generator expressions was removed. (GIthub issue :issue:`1699`) * The attributes ``gen.gi_frame`` and ``coro.cr_frame`` of Cython compiled generators and coroutines now return an actual frame object for introspection, instead of ``None``. (Github issue :issue:`2306`) ```
Links - PyPI: https://pypi.org/project/cython - Changelog: https://pyup.io/changelogs/cython/ - Homepage: http://cython.org/

Update numpy from 1.21.0 to 1.21.3.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/numpy - Homepage: https://www.numpy.org

Update pysam from 0.16.0.1 to 0.17.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/pysam - Changelog: https://pyup.io/changelogs/pysam/ - Repo: https://github.com/pysam-developers/pysam
pyup-bot commented 2 years ago

Closing this in favor of #131