search

labsyspharm / minerva_analysis

MIT License
25 stars 6 forks source link

python bug #128

Open pr4deepr opened 1 year ago

pr4deepr commented 1 year ago

Hi After following installation instructions for minerva_analysis using conda on a Windows 10 machine, I get the following bug:

Traceback (most recent call last):
  File "C:\Users\rajasekhar.p\minerva_analysis\run.py", line 5, in <module>
    from minerva_analysis import app
  File "C:\Users\rajasekhar.p\minerva_analysis\minerva_analysis\__init__.py", line 1, in <module>
    from flask import Flask
  File "C:\Users\rajasekhar.p\.conda\envs\minerva_analysis2\lib\site-packages\flask\__init__.py", line 14, in <module>
    from jinja2 import escape
ImportError: cannot import name 'escape' from 'jinja2' (C:\Users\rajasekhar.p\.conda\envs\minerva_analysis2\lib\site-packages\jinja2\__init__.py)

I get this for extensions: gating and lensing..

BTW, these are some really cool tools you've created!

looking forward to playing with them.

Cheers Pradeep

nchuynh commented 1 year ago

Hi Pradeep, thanks for checking out our tools!

Did you create your conda environment using the requirements.yml file from the Master branch? If yes, you'll just need to re-create your environment using the requirements from the specific branch you want to use (i.e. Visinity, Gater).

I believe this error is caused by an older version of Flask that's specified for the Master branch. Also the branches have deviated a bit from each other as we developed them and it's important to create specific environments for using each one. We're working on eventually harmonizing them.

pr4deepr commented 1 year ago

Thanks Yes, I used the yml file from the master branch. I tried your suggestion, which worked for the 'gating' extension, but not the 'lensing' branch. Got the same error as above.

nchuynh commented 1 year ago

Hi Pradeep, sorry for the delayed response. I chatted with the people that developed the lensing branch and they said that for the lensing tool, you should clone this repo: https://github.com/labsyspharm/scope2screen

The requirements yml file there should work for that tool.

pr4deepr commented 1 year ago

Thanks, is this in the README files? I couldn't find any info.

Cheers Pradeep

nchuynh commented 1 year ago

It isn't in the README file. Scope2screen (i.e. the lensing tool) was published in IEEE and the developers created a separate repo for it. Visinity was also published and the repo is here: https://github.com/labsyspharm/visinity