Installation unclear - Githubissues

rrydbirk commented 11 months ago

In the README, it's stated that the package can be directly downloaded for usage. However, it's not possible to install via pip, nor via ZIP/git. Please advise.

/work/01_notebooks via 🐍 v3.8.12 via 🅒 tfvelo took 5s 
[ 13:06:01 ] ✗  pip install https://github.com/xiaoyeye/TFvelo/archive/refs/heads/main.zip
Collecting https://github.com/xiaoyeye/TFvelo/archive/refs/heads/main.zip
  Downloading https://github.com/xiaoyeye/TFvelo/archive/refs/heads/main.zip
     | 16.8 MB 27.2 MB/s 0:00:01
ERROR: https://github.com/xiaoyeye/TFvelo/archive/refs/heads/main.zip does not appear to be a Python project: neither 'setup.py' nor 'pyproject.toml' found.

AlePur commented 10 months ago

I think you can't install this as package it doesn't provide a setup.py. You can clone the git repo and import TFv when you set the working directory to be TFVelo

rrydbirk commented 9 months ago

Hi @AlePur Indeed, it's not possible to install the package, therefore I don't think the instructions are straight forward. As you suggest, it's possible to import the package by setting WD to TFVelo or by using 'sys.path.insert(0, "/path/to/package/TFvelo/")'

vasikara17 commented 7 months ago

Hello, thanks for the interesting package. Could you give some more information about the installation and run? Do we need to download only the two .py scripts to run it?

Best, Vasiliki

noamiz5060 commented 5 months ago

did you manage to solve it?

vasikara17 commented 5 months ago

Hello, not yet, it would be really nice to install and test with our data.

rrydbirk commented 5 months ago

@vasikara17 I created a Conda venv named tfvelo in .../miniconda3/envs/tfvelo, and installed TFvelo in .../miniconda3/envs/tfvelo/TFvelo. From there, I'm able to run python TFvelo_run_demo.py ... In Python, this works for me:

import sys
sys.path.insert(0, "/work/miniconda3/envs/tfvelo/TFvelo/")
import TFvelo

I was able to run TFvelo_run_demo.py but not TFvelo_analysis_demo.py. I did the plotting in a Jupyter Notebook instead.

noamiz5060 commented 5 months ago

@vasikara17 I created a Conda venv named tfvelo in .../miniconda3/envs/tfvelo, and installed TFvelo in .../miniconda3/envs/tfvelo/TFvelo. From there, I'm able to run python TFvelo_run_demo.py ... In Python, this works for me:
import sys
sys.path.insert(0, "/work/miniconda3/envs/tfvelo/TFvelo/")
import TFvelo
I was able to run TFvelo_run_demo.py but not TFvelo_analysis_demo.py. I did the plotting in a Jupyter Notebook instead.

how did you 'install' TFvelo in the tfvelo env?

rrydbirk commented 5 months ago

Sorry, kind off missed the whole point of the problem stating that I "installed" the app. I used git clone.

noamiz5060 commented 5 months ago

Sorry, kind off missed the whole point of the problem stating that I "installed" the app. I used git clone.

God bless you my brother

AAA-3 commented 3 weeks ago

Not the developer her ebut the instructions in the README say that we can just run the two .py scripts as is from CLI, but I agree it would be nice for us to know how to reproduce their notebooks. When I try to run the TFvelo_demo.ipynb, I get errors

xiaoyeye / TFvelo

Installation unclear #2