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draeger-lab / pymCADRE

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.
GNU General Public License v3.0
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Unable to download pymCADRE with 'pip install pymcadre' #2

Closed Alvis-Jiang closed 1 year ago

Alvis-Jiang commented 1 year ago

Dear Dräger Lab members,

Recently, I am planning to use pymCADRE to construct some tissue-specific GEM, But when I tried to install pymCADRE, it failed. PYMCADRE

Could you help me to solve this issue? pymCADRE is a very good tool, I really hope that I can use it in my research.

Thanks so much

NantiaL commented 1 year ago

Hey!

Could you please try again now? I adjusted some things in the setup file. Also which operating systems are you using? Did you try pip install via your command line?

Alvis-Jiang commented 1 year ago

Hi Nantia,

Thanks for your reply! I have just tried again, and this time, it reports

" Using cached pymCADRE-2.0.0-py3-none-any.whl (15 kB) Discarding https://files.pythonhosted.org/packages/16/08/3cce92661b4578d04932b2d0f25598067df3cc611506d3fdf11d32c9fbe7/pymCADRE-2.0.0-py3-none-any.whl (from https://pypi.org/simple/pymcadre/): Requested pymcadre from https://files.pythonhosted.org/packages/16/08/3cce92661b4578d04932b2d0f25598067df3cc611506d3fdf11d32c9fbe7/pymCADRE-2.0.0-py3-none-any.whl has inconsistent version: expected '2.0.0', but metadata has '1.0.0' Using cached pymCADRE-1.2.0-py3-none-any.whl (14 kB) Installing collected packages: pymcadre Successfully installed pymcadre-1.2.0".

But when I run 'from rank.rank_reactions import or from prune.prune_model import ', it still reports there is no module named rank or prune. I have checked the directory where pymcadre is installed, and only found the folder of 'pymCADRE-1.2.0.dist-info'.

I also tried pip install via the command line and got the same report. I am using the Linux version 3.10.0-1062.9.1.el7.x86_64

Thanks so much for your help!

NantiaL commented 1 year ago

Thank you very much for reporting this! I will take a deeper look at it! In the meantime, you can either clone the repository or download it as .zip file to be able to use it.

NantiaL commented 1 year ago

Dear Alvis, I have re-creacted the source distribution and ensured that all files are included in there. You may now uninstall and install again pymCADRE via pip to get the corrected version. You can import the whole package in your jupyter notebook using import pymCADRE or sub-modules using from pymCADRE.rank import *.

Please let me know if further issues occur.

Alvis-Jiang commented 1 year ago

Hi Nantia,

Thanks a lot for your help! This time I have successfully installed pymCADRE. But when I ran the test data, there is still something wrong. I think it might be because of the file "rank_reactions.py", could you help to check it?

Thanks again. rank_reaction rank

NantiaL commented 1 year ago

Hey Alvis, whenever a module is called within a script, you have always to call first the pymcadre package. That means instead of from rank.parse_gprs import * it should be from pymcadre.rank.parse_gprs import *. This is only the case when you install the package via pip. If you just download locally the code, the scripts should run as they are. I hope this helps you further!

Alvis-Jiang commented 1 year ago

Hi Nantial,

I have successfully ran pymCADRE on my computer after manually modifying all "from rank/prune/chekc.xxx import " into "from pymCADRE .rank/prune/check.xxx import " in codes. Thanks so much for your help!