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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.
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Scheduled monthly dependency update for May #137

Closed pyup-bot closed 2 years ago

pyup-bot commented 2 years ago

Update Cython from 0.29.23 to 0.29.28.

Changelog ### 0.29.28 ``` ==================== Bugs fixed ---------- * Due to backwards incompatible changes in CPython 3.11a4, the feature flags ``CYTHON_FAST_THREAD_STATE`` and ``CYTHON_USE_EXC_INFO_STACK`` are now disabled in Python 3.11 and later. They are enabled again in Cython 3.0. Patch by David Woods. (Github issue 4610) * A C compiler warning in older PyPy versions was resolved. Patch by Matti Picus. (Github issue 4236) ``` ### 0.29.27 ``` ==================== Features added -------------- * The ``cythonize`` command has a new option ``-M`` to generate ``.dep`` dependency files for the compilation unit. This can be used by external build tools to track these dependencies. Patch by Evgeni Burovski. (Github issue :issue:`1214`) Bugs fixed ---------- * Compilation failures on PyPy were resolved. Patches by Matti Picus. (Github issues :issue:`4509`, :issue:`4517`) * Calls to ``range()`` with more than three arguments did not fail. Original patch by Max Bachmann. (Github issue :issue:`4550`) * Some C compiler warnings about missing type struct initialisers in Py3.10 were resolved. * Cython no longer warns about using OpenMP 3.0 features since they are now considered generally available. ``` ### 0.29.26 ``` ==================== Bugs fixed ---------- * An incompatibility with CPython 3.11.0a3 was resolved. (Github issue :issue:`4499`) * The ``in`` operator failed on literal lists with starred expressions. Patch by Arvind Natarajan. (Github issue :issue:`3938`) * A C compiler warning in PyPy about a missing struct field initialisation was resolved. ``` ### 0.29.25 ``` ==================== Bugs fixed ---------- * Several incompatibilities with CPython 3.11 were resolved. Patches by David Woods, Victor Stinner, Thomas Caswell. (Github issues :issue:`4411`, :issue:`4414`, :issue:`4415`, :issue:`4416`, :issue:`4420`, :issue:`4428`, :issue:`4473`, :issue:`4479`, :issue:`4480`) * Some C compiler warnings were resolved. Patches by Lisandro Dalcin and others. (Github issue :issue:`4439`) * C++ ``std::move()`` should only be used automatically in MSVC versions that support it. Patch by Max Bachmann. (Github issue :issue:`4191`) * The ``Py_hash_t`` type failed to accept arbitrary "index" values. (Github issue :issue:`2752`) * Avoid copying unaligned 16-bit values since some platforms require them to be aligned. Use memcpy() instead to let the C compiler decide how to do it. (Github issue :issue:`4343`) * Cython crashed on invalid truthiness tests on C++ types without ``operator bool``. Patch by David Woods. (Github issue :issue:`4348`) * The declaration of ``PyUnicode_CompareWithASCIIString()`` in ``cpython.unicode`` was incorrect. Patch by Max Bachmann. (Github issue :issue:`4344`) ``` ### 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 1.22.3.

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 0.19.0.

Changelog ### 0.19.0 ``` ============== This release wraps htslib/samtools/bcftools version 1.15. * [1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands * [1078] Support BAM_CPAD in get_aligned_pairs * [1063] Run flake8 and fix some linting issues * [1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties * Write an absent AlignedSegment.qual as all-bytes-0xff * Fix BGZFile.read() behaviour near or at EOF * First API for the htslib modified bases interface ``` ### 0.18.0 ``` ============== This release wraps htslib/samtools/bcftools version 1.14. * [1048] and [1060], clarify documentation of index statistics with CRAM files * Prevent "retval may be used uninitialised" warning. * Add new "samples" subcommand to pysam/samtools.py * Introduce TupleProxyIterator iterator object class ``` ### 0.17.0 ``` ============== This release wraps htslib/samtools/bcftools version 1.13. Corresponding to new samtools commands, `pysam.samtools` now has additional functions `ampliconclip`, `ampliconstats`, `fqimport`, and `version`. Bugs fixed: * [447] The maximum QNAME length is fully restored to 254 * [506, 958, 1000] Don't crash the Python interpreter on ``pysam.bcftools.*()`` errors * [603] count_coverage: ignore reads that have no SEQ field * [928] Fix ``pysam.bcftools.mpileup()`` segmentation fault * [983] Add win32/\*.[ch] to MANIFEST.in * [994] Raise exception in ``get_tid()`` if header could not be parsed * [995] Choose TBI/CSI in ``tabix_index()`` via both min_shift and csi * [996] ``AlignmentFile.fetch()`` now works with large chromosomes longer than 2\ :sup:`29` bases * [1019] Fix Sphinx documentation generation by avoiding Python 2 ``ur'string'`` syntax * [1035] Improved handling of file iteration errors * [1038] ``tabix_index()`` no longer leaks file descriptors * [1040] ``print(aligned_segment)`` now prints the correct TLEN value (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based) * *setup.py* longer uses ``setup(use_2to3)`` for compatibility with setuptools >= v58.0.0 New facilities: * [PR 963] Additional VCF classes are exposed to pysam programmers * [998, PR 1001] Add ``get/set_encoding_error_handler()`` to control UTF-8 conversion * [PR 1012] Running ``python setup.py sdist`` now automatically runs cythonize * Running tests with ``pytest`` now automatically runs ``make`` to generate test data Documentation improvements: * [726] Clarify get_forward_sequence/get_forward_qualities documentation * [865] Improved example * [968] ``get_index_statstics`` parameters * [986] Clarify ``VariantFile.fetch`` start/stop region parameters are 0-based and half-open. * [990] Corrected ``PileupColumn.get_query_sequences`` documentation * [999] Fix documentation for ``AlignmentFile.get_reference_length()`` * [1002] Document the default min_base_quality for ``pileup()`` ```
Links - PyPI: https://pypi.org/project/pysam - Changelog: https://pyup.io/changelogs/pysam/ - Repo: https://github.com/pysam-developers/pysam

Update tables from 3.6.1 to 3.7.0.

Changelog ### 3.7.0 ``` 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). Bugfixes -------- - Fix `pkg-config` (`setup.py`) for Python 3.9 on Debian. Thanks to Marco Sulla PR 792. - Fix ROFileNode fails to return the `fileno()` (633). - Do not flush read only files (915 thanks to lrepiton). Other changes ------------- - Drop the deprecated `hdf5Version` and `File.open_count`. - the :func:`get_tables_version` and :func:`get_hdf5_version` functions are now deprecated please use the coresponding :data:`tables.__version__` and :data:`tables.hdf5_version` instead. ```
Links - PyPI: https://pypi.org/project/tables - Changelog: https://pyup.io/changelogs/tables/ - Homepage: https://www.pytables.org
pyup-bot commented 2 years ago

Closing this in favor of #139