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cnapy-org / CNApy

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
https://cnapy-org.github.io/CNApy-guide/
Apache License 2.0
46 stars 7 forks source link

error running CNApy #470

Closed Laminsecin closed 1 year ago

Laminsecin commented 1 year ago

I installed CNApy as conda package. after the installation was done I activated cnapy-1.1.6 and when I wanted to run cnapy I encounter the following error: URLs with no authority component cannot have a path starting with '//'. can somebody help me? I also want to know if it is possible to install CNApy on pycharm and how.

axelvonkamp commented 1 year ago

The bug is an issue from cobrapy, you need to upgrade to version 0.26.3.

Laminsecin commented 1 year ago

The bug is an issue from cobrapy, you need to upgrade to version 0.26.3.

Thanks for your response, but unfortunately after upgrading cobrapy the error appears again and the CNApy 1.1.6 suddenly closes.

axelvonkamp commented 1 year ago

Can you copy & paste the complete stack trace here? This may help to figure out what is going on.

Laminsecin commented 1 year ago

Yes, sure. this is my version of cobra: (base) C:\Users\asus>conda list packages in environment at C:\Users\asus\miniconda3:

Name Version Build Channel cobra 0.26.3 pyhd8ed1ab_0 conda-forge

and this is the error I get running cnapy: (base) C:\Users\asus>conda activate cnapy-1.1.6

(cnapy-1.1.6) C:\Users\asus>cnapy Traceback (most recent call last): File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\Scripts\cnapy-script.py", line 6, in from cnapy.main import main_cnapy File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cnapy__main.py", line 31, in from cnapy.application import Application File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cnapy\application.py", line 25, in import cobra File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cobra__init.py", line 17, in from cobra import io File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cobra\io__init__.py", line 9, in from cobra.io.web import AbstractModelRepository, BiGGModels, BioModels, load_model File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cobra\io\web\init.py", line 7, in from .load import load_model File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cobra\io\web\load.py", line 31, in Cobrapy(), File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cobra\io\web\cobrapy_repository.py", line 36, in init super().init(url="file:////", **kwargs) File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\cobra\io\web\abstract_model_repository.py", line 55, in init__ self._url = httpx.URL(url=url) File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\httpx_urls.py", line 113, in init__ self._uri_reference = urlparse(url, **kwargs) File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\httpx_urlparse.py", line 252, in urlparse validate_path(path, has_scheme=has_scheme, has_authority=has_authority) File "C:\Users\asus\miniconda3\envs\cnapy-1.1.6\lib\site-packages\httpx_urlparse.py", line 367, in validate_path raise InvalidURL( httpx.InvalidURL: URLs with no authority component cannot have a path starting with '//'

axelvonkamp commented 1 year ago

The updated cobra package appears to be in the (base) environment, but is it also updated in the (cnapy-1.1.6) environment?