Closed AUldry closed 2 months ago
straussmaximilian
commented
2 months ago Hi, this looks like an issue coming from PIL. Can you try the following?
conda create --name alphapept python=3.8 -y
conda activate alphapept
conda install pillow
pip install "alphapept[stable,gui-stable]"
alphapept gui
AUldry
commented
2 months ago Dear Maximilian,
Many many thanks for your reply! You were right that this had to do with pillow. The solution to re-install it via conda did not work for me (got a different error message, a complain that a DLL could not be found), but with these 2 clues, I found randomly on the web that pillow==9.0.0 worked for somebody... and it worked for me too (with python 3.8.19). So all good now, thanks again!
Dear all,
I have been asked to install alphapept on a Windows 11 Education machine. I can install the program with the windows installer, which gives me the 0.5.0 version; this seems to work. Now I would like to install the 0.5.3, since it's available. I installed conda (miniconda) and created an alphapept environment, as described on your page. While everything installs without complaining, upon issuing alphapept gui, I get the following error:
AttributeError: module 'numpy.typing' has no attribute 'NDArray'
Screen shot, exact error message and descriptions of my python environment are below. Should perhaps a package be forced to a particular version? Thank you in advance for your help!
Anne-Christine
Describe the bug alphapept gui does not start properly and spits out a "AttributeError: module 'numpy.typing' has no attribute 'NDArray'" error.
To Reproduce Steps to reproduce the behavior: Installed miniconda on Windows 11 Education conda create --name alphapept python=3.8 conda activate alphapept pip install "alphapept[stable,gui-stable]" alphapept gui
Results:
/ /| | / / \/ \/ \/ // / \/ \/ / / _ |/ / // / / / / // / __/ _/ // / / // |/_/ .// //_,// _/ ./\/ // /_/ .................................................... . https://github.com/MannLabs/alphapept . . Mann Labs . . 0.5.3 . ....................................................
Starting AlphaPept Background Process 2024-07-01 13:50:33.354 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager Starting AlphaPept Server
You can now view your Streamlit app in your browser.
Local URL: http://localhost:8505 Network URL: http://130.92.40.214:8505
2024-07-01 13:50:34.176 Uncaught app exception Traceback (most recent call last): File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\streamlit\runtime\scriptrunner\script_runner.py", line 589, in _run_script exec(code, module.dict) File "C:\Users\pmscf\miniconda3\envs\alphapept\Lib\site-packages\alphapept\webui.py", line 2, in
from alphapept.gui import history, results, filewatcher, status, experiment, fasta, start, constants
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\alphapept\gui\history.py", line 4, in
import plotly.express as px
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\plotly\express__init__.py", line 14, in
from ._imshow import imshow
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\plotly\express_imshow.py", line 8, in
from plotly.utils import image_array_to_data_uri
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\plotly\utils.py", line 5, in
from _plotly_utils.data_utils import *
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages_plotly_utils\data_utils.py", line 6, in
from PIL import Image
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\PIL\Image.py", line 68, in
from ._typing import StrOrBytesPath, TypeGuard
File "C:\Users\pmscf\miniconda3\envs\alphapept\lib\site-packages\PIL_typing.py", line 10, in
NumpyArray = npt.NDArray[Any]
AttributeError: module 'numpy.typing' has no attribute 'NDArray'
2024-07-01 13:50:37.064 WARNING streamlit.runtime.caching.cache_data_api: No runtime found, using MemoryCacheStorageManager
2024-07-01 13:50:37.314385 Started queue_watcher
See screenshot of http://localhost:8505/
Expected behavior GUI
Screenshots
Version (please complete the following information):
Additional context Python version: Python 3.8.19 (default, Mar 20 2024, 19:55:45) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
pip list:
Package Version
alphabase 1.2.1 alphapept 0.5.3 alpharaw 0.1.0 alphatims 1.0.7 altair 5.3.0 attrs 23.2.0 biopython 1.79 blinker 1.8.2 cachetools 5.3.3 certifi 2024.6.2 cffi 1.16.0 charset-normalizer 3.3.2 click 8.1.7 cloudpickle 3.0.0 clr-loader 0.2.6 colorama 0.4.6 contextlib2 21.6.0 contourpy 1.1.1 cycler 0.12.1 dask 2023.5.0 fastcore 1.5.26 fonttools 4.53.0 fsspec 2024.6.1 gitdb 4.0.11 GitPython 3.1.43 greenlet 3.0.3 h5py 3.7.0 idna 3.7 importlib_metadata 8.0.0 importlib_resources 6.4.0 Jinja2 3.1.4 joblib 1.4.2 jsonschema 4.22.0 jsonschema-specifications 2023.12.1 kiwisolver 1.4.5 llvmlite 0.38.1 locket 1.0.0 markdown-it-py 3.0.0 MarkupSafe 2.1.5 matplotlib 3.6.1 mdurl 0.1.2 networkx 2.8.6 numba 0.55.2 numexpr 2.8.6 numpy 1.20.3 packaging 24.1 pandas 2.0.1 partd 1.4.1 patsy 0.5.6 pillow 10.4.0 pip 24.0 pkgutil_resolve_name 1.3.10 plotly 5.22.0 plotly-express 0.4.1 protobuf 5.27.2 psutil 5.9.1 pyahocorasick 2.1.0 pyarrow 16.1.0 pycparser 2.22 pydeck 0.9.1 Pygments 2.18.0 pyparsing 3.1.2 pyteomics 4.5.5 python-dateutil 2.9.0.post0 pythonnet 3.0.3 pytz 2024.1 pywin32 306 PyYAML 6.0 pyzstd 0.16.0 referencing 0.35.1 regex 2024.5.15 requests 2.32.3 rich 13.7.1 rpds-py 0.18.1 scikit-learn 1.1.2 scipy 1.8.1 setuptools 69.5.1 six 1.16.0 smmap 5.0.1 SQLAlchemy 1.4.39 statsmodels 0.14.1 streamlit 1.36.0 tables 3.6.1 tenacity 8.4.2 threadpoolctl 3.5.0 toml 0.10.2 toolz 0.12.1 tornado 6.4.1 tqdm 4.64.0 typing_extensions 4.12.2 tzdata 2024.1 urllib3 2.2.2 watchdog 2.1.9 wget 3.2 wheel 0.43.0 xxhash 3.4.1 zipp 3.19.2