scipy upgrade (v1.13.0) break sonicparanoid
The lastest version of scipy package (v1.13.0) break sonicparanid.
For now the simplest solution is to downgrade to v1.12.0 using the following command:
pip install scipy==1.12.0
You would get the following error:
Traceback (most recent call last):
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/bin/sonicparanoid", line 33, in <module>
sys.exit(load_entry_point('sonicparanoid==2.0.4', 'console_scripts', 'sonicparanoid')())
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/bin/sonicparanoid", line 25, in importlib_load_entry_point
return next(matches).load()
File "/usr/lib/python3.9/importlib/metadata.py", line 86, in load
module = import_module(match.group('module'))
File "/usr/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/sonicparanoid-2.0.4-py3.9-linux-x86_64.egg/sonicparanoid/sonic_paranoid.py", line 28, in <module>
from sonicparanoid import archortho
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/sonicparanoid-2.0.4-py3.9-linux-x86_64.egg/sonicparanoid/archortho.py", line 17, in <module>
from sonicparanoid.d2v import compute_archs_and_embeddings
File "sonicparanoid/d2v.pyx", line 21, in init sonicparanoid.d2v
import gensim
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/gensim/__init__.py", line 11, in <module>
from gensim import parsing, corpora, matutils, interfaces, models, similarities, utils # noqa:F401
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/gensim/corpora/__init__.py", line 6, in <module>
from .indexedcorpus import IndexedCorpus # noqa:F401 must appear before the other classes
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/gensim/corpora/indexedcorpus.py", line 14, in <module>
from gensim import interfaces, utils
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/gensim/interfaces.py", line 19, in <module>
from gensim import utils, matutils
File "/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/gensim/matutils.py", line 20, in <module>
from scipy.linalg import get_blas_funcs, triu
ImportError: cannot import name 'triu' from 'scipy.linalg' (/home/salvocos/.virtualenvs/sp2-204-review-choose-by-biggest-proteome/lib/python3.9/site-packages/scipy/linalg/__init__.py)