JCVenterInstitute / NSForest

A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing
MIT License
53 stars 20 forks source link

Conda Env YML Outdated and Suggestion for Version Control Addition #17

Open Charithwij opened 3 months ago

Charithwij commented 3 months ago

The current conda yml environment contains several python built-in packages (which should be removed from the yml file) or packages supported by conda (which do not require a pip installation). Of the dependencies on the current list:

Additionally, the yml file is missing ipython, which seen in the tutorial's import lines. One last suggestion would be to implement strict package version control in the conda env itself prevent conda installing higher version and to avoid future issues that may arise with updates to these packages.

adeslatt commented 3 months ago

I think the yml file is no longer needed for the tutorial if we go ahead with the jupyter lab notebook. In my forked version: https://github.com/adeslatt/NSForest/blob/master/ipynb/Tutorial.ipynb

you can see the identical to readthedocs. Once the pull request is accepted - we can add these packages in the markdown to say to install them when making a clean environment.