Dear @tschuelia,
I tried many times, still can not use it, Is there any easy way to install it?
pythia -h
Traceback (most recent call last):
File "/Users/liamxg/opt/miniconda3/envs/pythia/bin/pythia", line 6, in
from pypythia.prediction import main
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/pypythia/prediction.py", line 11, in
from pypythia.predictor import DifficultyPredictor
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/pypythia/predictor.py", line 4, in
from lightgbm import LGBMRegressor
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/lightgbm/init.py", line 11, in
from .basic import Booster, Dataset, Sequence, register_logger
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/lightgbm/basic.py", line 29, in
from .compat import (
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/lightgbm/compat.py", line 10, in
from sklearn import version as _sklearn_version
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/sklearn/init.py", line 82, in
from .base import clone
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/sklearn/base.py", line 17, in
from .utils import _IS_32BIT
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/sklearn/utils/init.py", line 19, in
from .murmurhash import murmurhash3_32
File "sklearn/utils/murmurhash.pyx", line 1, in init sklearn.utils.murmurhash
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
(pythia) liamxg@192 ~ % pythia -h
Traceback (most recent call last):
File "/Users/liamxg/opt/miniconda3/envs/pythia/bin/pythia", line 6, in
from pypythia.prediction import main
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/pypythia/prediction.py", line 11, in
from pypythia.predictor import DifficultyPredictor
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/pypythia/predictor.py", line 4, in
from lightgbm import LGBMRegressor
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/lightgbm/init.py", line 11, in
from .basic import Booster, Dataset, Sequence, register_logger
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/lightgbm/basic.py", line 29, in
from .compat import (
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/lightgbm/compat.py", line 10, in
from sklearn import version as _sklearn_version
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/sklearn/init.py", line 82, in
from .base import clone
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/sklearn/base.py", line 17, in
from .utils import _IS_32BIT
File "/Users/liamxg/opt/miniconda3/envs/pythia/lib/python3.11/site-packages/sklearn/utils/init.py", line 19, in
from .murmurhash import murmurhash3_32
File "sklearn/utils/murmurhash.pyx", line 1, in init sklearn.utils.murmurhash
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
(pythia) liamxg@192 ~ % conda install conda=25.1.1
Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the . and treating it as 1.7.1
done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=25.1.1
Collecting package metadata (repodata.json): failed
Hi Liam, I'm sorry for the very very late answer, but I have been working heavily on the release of the new version Pythia 2.0. I think it is the easiest if you try to use this new version. With the old versions there were continuously issues with dependencies (such as that you have encountered).
I'd recommend you to create a new conda environment and install the new version like this:
conda env create -n pythia
conda install "python=3.12"
conda install pythiaphylopredictor -c conda-forge
Note that the name of the package changed from PyPythia to pythiaphylopredictor . This was required to comply with the naming scheme of PyPi, but now Pythia is also available there so you can also try to install the latest version via pip:
pip install pythiaphylopredictor
I hope this helps and resolves your issues 🙂
Dear @tschuelia ,
Thank you for your reply, and no worries about the late response! I understand that you've been busy with the release of Pythia 2.0. I appreciate the update and the instructions. It’s working now!
BTW, I find the result using the old version: The predicted difficulty for MSA SC2.fas is: 0.56.
the result using the new version: The predicted difficulty for MSA SC2.fas is: 0.36, why they are so different?
Best,
Liam
Would it be possible to update the conda package name here https://tschuelia.github.io/PyPythia/install/?
Thanks!
The 2.0.0 version of the docs should show the correct package name: https://tschuelia.github.io/PyPythia/latest/install/
I see, then the link in the readme should be updated as it still redirects to https://tschuelia.github.io/PyPythia/
Done, good catch, thanks @fdecarpentier 😊
tschuelia
