Fix sorted-nearest version 0.0.33
Closed this issue · 2 comments
Dear Lapa,
FIX: this is a fix for all the blah below:
mamba install -c bioconda pyranges (it seems the pip version of pyranges does not have all that is required).
I have installed lap via pip install lapa (but I have to also do pip install cython). I have this in a conda environment running python 3.8.
If I run:
$ lapa
Traceback (most recent call last):
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/bin/lapa", line 5, in
from lapa.main import cli
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/lapa/init.py", line 1, in
from lapa.main import lapa
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/lapa/main.py", line 2, in
from lapa.lapa import lapa
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/lapa/lapa.py", line 3, in
import pyranges as pr
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/pyranges/init.py", line 137, in
import pyranges.genomicfeatures as gf
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/pyranges/genomicfeatures.py", line 7, in
from sorted_nearest.src.introns import find_introns
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/sorted_nearest/init.py", line 7, in
from sorted_nearest.src.k_nearest_ties import get_all_ties, get_different_ties
ImportError: cannot import name 'get_all_ties' from 'sorted_nearest.src.k_nearest_ties' (/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/sorted_nearest/src/k_nearest_ties.cpython-38-x86_64-linux-gnu.so)
Then if I force it to use python3.8 with a lapa.py version from github: I get the same error.
$ python3.8 "/mnt/shared/scratch/pthorpe/private/mustafa/lapa/lapa/lapa/lapa.py"
Traceback (most recent call last):
File "/mnt/shared/scratch/pthorpe/private/mustafa/lapa/lapa/lapa/lapa.py", line 3, in
import pyranges as pr
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/pyranges/init.py", line 137, in
import pyranges.genomicfeatures as gf
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/pyranges/genomicfeatures.py", line 7, in
from sorted_nearest.src.introns import find_introns
File "/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/sorted_nearest/init.py", line 7, in
from sorted_nearest.src.k_nearest_ties import get_all_ties, get_different_ties
ImportError: cannot import name 'get_all_ties' from 'sorted_nearest.src.k_nearest_ties' (/mnt/shared/scratch/pthorpe/apps/conda/envs/python38/lib/python3.8/site-packages/sorted_nearest/src/k_nearest_ties.cpython-38-x86_64-linux-gnu.so)
If I then run pip install pyranges. It says it is already satisfied ..
Thanks for reporting the issue. One of the dependencies of dependency on our package is broken. I will fix the version of the dependency and release a new version.
pip install sorted-nearest=0.0.33 resolves the issue see: pyranges/sorted_nearest#5