bxlab/bx-python issues and pull requests

#102 - PyObject_AsWriteBuffer removed in Python3.13

Issue - State: closed - Opened by stefanor 3 months ago - 1 comment

#101 - Tests do not run in PEP517 out-of-source build (gentoo)

Issue - State: open - Opened by mschubert 5 months ago - 5 comments

#100 - Extend linting with ruff

Issue - State: open - Opened by nsoranzo 5 months ago

#99 - 0.12.0: Fails to build: error: incompatible integer to pointer conversion assigning to 'void **' from 'int'

Issue - State: open - Opened by yurivict 5 months ago - 1 comment

#98 - Build errors on osx-arm64 (bioconda)

Issue - State: closed - Opened by corneliusroemer 5 months ago - 2 comments

#97 - Fix typos

Pull Request - State: open - Opened by mr-c 5 months ago

#96 - remove psyco, it is only available for Python <= 2.6

Pull Request - State: closed - Opened by mr-c 5 months ago

#95 - Fix import statement s/cookbook/bx.cookbook/

Pull Request - State: closed - Opened by mr-c 5 months ago

#94 - Fix include for `strlen()`

Pull Request - State: closed - Opened by mr-c 9 months ago - 3 comments

#93 - post install testing

Pull Request - State: closed - Opened by mr-c 9 months ago - 2 comments

#92 - Add pytest 8.x compatibility

Pull Request - State: closed - Opened by mr-c 9 months ago - 1 comment

#91 - Fix compilation with cython 3

Pull Request - State: closed - Opened by mvdbeek over 1 year ago - 7 comments

#90 - From NumPy 1.24.0 ``np.float`` is deprecated

Pull Request - State: closed - Opened by lldelisle almost 2 years ago - 8 comments

#89 - fix exception message

Pull Request - State: closed - Opened by lldelisle almost 2 years ago

#88 - ERROR Missing dependencies: oldest-supported-numpy

Issue - State: closed - Opened by brobr almost 2 years ago - 2 comments

#87 - Format Python code with `black` and `isort`

Pull Request - State: closed - Opened by nsoranzo over 2 years ago

#86 - Skip building also other musllinux wheels

Pull Request - State: closed - Opened by nsoranzo over 2 years ago

#85 - Index TwoBitFile sequences by str not bytes

Pull Request - State: closed - Opened by nsoranzo over 2 years ago

#84 - Fix new E275 linting error

Pull Request - State: closed - Opened by nsoranzo over 2 years ago

#83 - Upgrade GitHub Actions

Pull Request - State: closed - Opened by cclauss over 2 years ago - 4 comments

#82 - upgrading bx-python to newer versions of python

Issue - State: closed - Opened by adeslatt over 2 years ago - 1 comment

#81 - multiple sequence alignment

Issue - State: open - Opened by huangnengCSU almost 3 years ago

#80 - add 32bit test

Pull Request - State: open - Opened by mr-c about 3 years ago

#79 - Add Linux AArch64 wheel build support

Pull Request - State: closed - Opened by odidev about 3 years ago - 2 comments

#78 - Add support to release linux aarch64 wheels

Issue - State: closed - Opened by odidev about 3 years ago - 1 comment

#77 - Improve maf handling

Pull Request - State: closed - Opened by lldelisle over 3 years ago - 8 comments

#76 - documentation?

Issue - State: open - Opened by mufernando over 3 years ago - 3 comments

#75 - 0.8.11 Doesn't install some built shared libraries

Issue - State: closed - Opened by yurivict over 3 years ago - 8 comments

#74 - Added ref to Debian package to README

Pull Request - State: closed - Opened by smoe almost 4 years ago

#73 - undefined symbol: PyUnicodeUCS2_FromStringAndSize

Issue - State: closed - Opened by jingydz almost 4 years ago - 2 comments

#72 - AddingPowerSupport_CI/Testing

Pull Request - State: closed - Opened by santosh653 almost 4 years ago - 3 comments

#71 - Failed to load seekbzip2 module when dealing with bz2 files

Issue - State: closed - Opened by songtaogui about 4 years ago - 1 comment

#70 - Fix ``lzop_build_offset_table.py`` and ``maf_build_index.py`` scripts under Python 3

Pull Request - State: closed - Opened by nsoranzo about 4 years ago

#69 - How to dealing with maf files compressed with bzip2 or lzop ?

Issue - State: closed - Opened by songtaogui about 4 years ago - 4 comments

#68 - Got wrong positions on chomped query maf subset

Issue - State: closed - Opened by songtaogui about 4 years ago - 2 comments

#67 - binned_bitsets_from_list errors when chromosome size is larger than set MAX (512M)

Issue - State: open - Opened by zxl124 over 4 years ago - 1 comment

#66 - ImportError: undefined symbol: PyUnicodeUCS2_FromStringAndSize

Issue - State: closed - Opened by prullens over 4 years ago - 1 comment

#65 - Misc fixes

Pull Request - State: closed - Opened by nsoranzo over 4 years ago

#64 - Use chain.from_iterable in bed_coverage.py

Pull Request - State: closed - Opened by cool-RR over 4 years ago - 1 comment

#63 - time.clock has been removed in Python 3.8

Issue - State: closed - Opened by tirkarthi over 4 years ago

#62 - Importing ABC directly from collections was deprecated and will be removed in Python 3.10. Use collections.abc

Issue - State: closed - Opened by tirkarthi over 4 years ago

#61 - get on bx.align.maf.MAFIndexedAccess results in wrong alignment blocks

Issue - State: closed - Opened by dandaman over 4 years ago - 4 comments

#60 - error can't found bx.intervals module

Issue - State: closed - Opened by shiyi-pan over 4 years ago

#59 - No source tarballs for the release 0.8.8 on the PyPI website

Issue - State: closed - Opened by yurivict almost 5 years ago - 1 comment

#58 - Restore NiceReaderWrapper.current_line

Pull Request - State: closed - Opened by mvdbeek almost 5 years ago - 4 comments

#57 - StopIteration fix

Pull Request - State: closed - Opened by mvdbeek almost 5 years ago - 4 comments

#56 - StopIteration transformed to RuntimeError on python >= 3.7

Issue - State: closed - Opened by mvdbeek almost 5 years ago

#55 - add 32bit test

Pull Request - State: closed - Opened by mr-c almost 5 years ago - 1 comment

#54 - fix error for 32bit systems

Pull Request - State: open - Opened by mr-c almost 5 years ago - 8 comments

#53 - Fix all flake8 and many other errors

Pull Request - State: closed - Opened by nsoranzo about 5 years ago

#52 - Fix #47

Pull Request - State: closed - Opened by nsoranzo about 5 years ago

#51 - Wheel for Python 3.8

Issue - State: closed - Opened by sebastiencdj about 5 years ago - 2 comments

#50 - Fix binary string padding on Python 3

Pull Request - State: closed - Opened by nsoranzo about 5 years ago
Labels: bug

#49 - Incompatible types str and byte under python3

Issue - State: closed - Opened by adthrasher about 5 years ago - 1 comment

#48 - Exception: 2147483648 is larger than the maximum possible size (2147483647)

Issue - State: open - Opened by mr-c about 5 years ago - 5 comments

#47 - TypeError: write() argument must be str, not bytes when running maf_build_index.py with python3.6

Issue - State: closed - Opened by mt1022 over 5 years ago - 2 comments

#46 - Bigwig headers extraction

Pull Request - State: closed - Opened by radmilak over 5 years ago - 1 comment

#45 - Support for using alternate index name for maf_extract_ranges_indexed.py

Issue - State: open - Opened by sorrywm over 5 years ago - 1 comment

#44 - Add missing ``build_ext`` step before creating sdist

Pull Request - State: closed - Opened by nsoranzo over 5 years ago

#43 - Build and upload wheels to PyPI

Pull Request - State: closed - Opened by nsoranzo over 5 years ago

#42 - Publish Wheels

Issue - State: closed - Opened by jmchilton over 5 years ago - 2 comments

#41 - Fix typo in the documentation index page

Pull Request - State: closed - Opened by juliangehring over 5 years ago - 1 comment

#40 - Fix deprecated ``assertEquals()``

Pull Request - State: closed - Opened by nsoranzo over 5 years ago

#39 - Fix loop counter in bpt_file.pyx

Pull Request - State: closed - Opened by ronin-gw almost 6 years ago

#38 - Remove deprecated ``sudo: false`` from .travis.yml

Pull Request - State: closed - Opened by nsoranzo almost 6 years ago

#37 - No module named 'UserDict' when import bx.intervals.io

Issue - State: closed - Opened by mikpom about 6 years ago - 2 comments

#36 - Readme install needs liblzo2-dev

Issue - State: closed - Opened by stevendavis over 6 years ago - 1 comment

#35 - Fix recursion bug seen in https://github.com/galaxyproject/galaxy/issues/6598

Pull Request - State: closed - Opened by mvdbeek over 6 years ago - 1 comment

#34 - Add link to ReadTheDocs in Github README

Issue - State: closed - Opened by scottgigante over 6 years ago - 1 comment

#33 - install problems without bitset.c file

Issue - State: closed - Opened by LujingF over 6 years ago - 4 comments

#32 - Added optional liftOver-like behavior for split alignments: longest s…

Pull Request - State: closed - Opened by adadiehl over 6 years ago

#31 - python3.5 - TwoBitFile chromosome name is byte string

Issue - State: closed - Opened by ma-tongji over 6 years ago

#30 - Delete intervals in interval tree

Issue - State: open - Opened by juancresc almost 7 years ago

#29 - Please fix clang warnings

Issue - State: open - Opened by yurivict almost 7 years ago

#28 - Make python-lzo optional again

Pull Request - State: closed - Opened by nsoranzo almost 7 years ago - 1 comment

#27 - Update project URL

Pull Request - State: closed - Opened by nsoranzo almost 7 years ago - 2 comments

#26 - asking for support of arbitary length integer

Issue - State: open - Opened by jinstrong almost 7 years ago

#25 - Python 3 compatibility

Pull Request - State: closed - Opened by mbargull about 7 years ago - 12 comments

#24 - Could you please add 0.8.0 to pypi and the releases page?

Issue - State: closed - Opened by endrebak about 7 years ago - 4 comments

#23 - ZeroDivisionError thrown by bx.intervals.intersection.IntervalNode.cinit

Issue - State: open - Opened by borissim about 7 years ago - 2 comments

#22 - about bx.intervals.operations.join module

Issue - State: open - Opened by pathkim about 7 years ago

#21 - OverflowError: value too large to convert to int

Issue - State: open - Opened by peterch405 over 7 years ago - 1 comment

#20 - pip install

Issue - State: closed - Opened by hmontenegro over 7 years ago - 2 comments

#19 - typo

Issue - State: closed - Opened by smoretti over 7 years ago

#18 - Error building bx-python for python-2.7.13

Issue - State: closed - Opened by wesbarris over 7 years ago - 2 comments

#17 - StringIO & Python 3.5

Issue - State: closed - Opened by MikeDMorgan over 7 years ago - 1 comment

#16 - Is there documentation for bx-python outside the codebase?

Issue - State: closed - Opened by alexlenail almost 8 years ago - 9 comments

#15 - Additional python3 support

Pull Request - State: closed - Opened by adamlabadorf almost 8 years ago - 1 comment

GitHub / bxlab/bx-python issues and pull requests