Installation issues for xengsort (2.0.3/2.0.4) via conda/with pip from the cloned git directory
Hi, I am trying to install xengsort (on a Linux system). If I use the conda installation and run xengsort index, I get the following error message:
Traceback (most recent call last):
File "/da/cbt/GX/python/envs/xenoprepare/bin/xengsort", line 10, in <module>
sys.exit(main())
File "/da/cbt/GX/python/envs/xenoprepare/lib/python3.10/site-packages/xengsort/xengsort/xengsort_main.py", line 219, in main
m = import_module("." + module, __package__)
File "/da/cbt/GX/python/envs/xenoprepare/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 883, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/da/cbt/GX/python/envs/xenoprepare/lib/python3.10/site-packages/xengsort/xengsort/xengsort_index.py", line 23, in <module>
from ..io.hashio import save_hash
File "/da/cbt/GX/python/envs/xenoprepare/lib/python3.10/site-packages/xengsort/io/hashio.py", line 53, in <module>
from ..lowlevel.libc import write_block, write_uint64
ImportError: cannot import name 'write_uint64' from 'xengsort.lowlevel.libc' (/da/cbt/GX/python/envs/xenoprepare/lib/python3.10/site-packages/xengsort/lowlevel/libc.py)
I checked the code and saw that 'write_uint64' was introduced in xengsort-2.0.4 and the conda xengsort version is 2.0.3 - too bad.
Then I cloned the git directory to my hard drive and tried to install xengsort from the cloned directory with
pip install -e xengsort
but this did not work (Python did not find "main" in the import "from xengsort.xengsort.xengsort_main import main" in the binary).
So what I did now is to install xengsort via conda and then replace the xengsort version 2.0.3 directory in lib/python3.10/site-packages with the xengsort version 2.0.4 directory from the cloned repository. This seems to work.
Best regards,
Sven