Diane Trout

It's a minor issue but your setup.py probably should indicate your package requires biopython.

Crash when generating a genomebam (Could I have a better error instead)

2

Hi I was getting a segmentation fault when trying to generate a genomebam, the command was roughly: ``` kallisto quant -t 6 \ -i mm10-M21_minimal-male/mm10-M21_minimal-male-kallisto-0.46.2.idx \ -o 19906_A5 \ --single...

While running tests on the development branch with these software versions; attrs==21.4.0,iniconfig==1.1.1,numpy==1.22.3,packaging==21.3,pandas==1.4.2,pluggy==1.0.0,py==1.11.0,pybedtools==0.9.0,pyfaidx==0.6.4,pyparsing==3.0.8,pysam==0.15.4,pytest==7.1.1,python-dateutil==2.8.2,pytz==2022.1,six==1.16.0,talon @ file:///woldlab/loxcyc/home/diane/proj/talon/.tox/.tmp/package/1/talon-5.0.zip,tomli==2.0.1 I got this error: ```python test_longest_ends.py:22: _ _ _ _ _ _ _ _ _ _...

Avoid checking the returned sqlite dtype on all 32 bit platforms.

3

There's still some 32-bit linux targets in addition to win32. - [X] Closes? #8620 It's really more of a work around, the problem of sqlite's data types not being consistent...

various seg faults on Debian arm64 with numba 0.57.1

13

This may be related to #6657 but I'm not sure. ## Reporting a bug - [X] I have tried using the latest released version of Numba 0.57.1 (with a few...

pytest 8.1.1: import file mismatch

2

Hello, I was updating the Debian package for python-graphviz 0.20.2 and was having problems running with pytest 8.1.1. ``` ___ ERROR collecting .pybuild/cpython3_3.11_graphviz/build/tests/conftest.py ___ import file mismatch: imported module 'conftest'...

Hello, I've been using your project for a while, but have finally decided to try to move all my work to python3, and unfortunately gcat isn't currently python3 compatible. I...

command line arguments are easily visible to other processes on linux

1

```lisp (format "echo %s | \ keepassxc-cli %s %s %s 2>&1 | \ egrep -v '[Insert|Enter] password to unlock %s'" (shell-quote-argument keepass-mode-password) ``` It's pretty easy to read command line...

importmagic 0.1.7 uses distutils.sysconfig to find some library paths and unfortunately distutils was removed in Python 3.12. This was my stab at replacing it. After glancing at I'm not sure...

Hello, Rebecca Palmer noticed out that test_serialization in partd version 1.2.0's tests occasionally fail on ppc64el and s390x . ( https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1005045 ) ``` =================================== FAILURES =================================== ______________________________ test_serialization ______________________________ def...