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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
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Update the tutorial from `NSForest_v3dot9_1` to `nsforest` for the import #14

Closed jolespin closed 1 year ago

jolespin commented 1 year ago

Just installed via pip successfully: 

(base) jespinozlt2-osx:~ jespinoz$ conda activate soothsayer_py3.9_env
pip install (soothsayer_py3.9_env) jespinozlt2-osx:~ jespinoz$ pip install nsforest
Collecting nsforest
  Downloading nsforest-3.9.2.5-py3-none-any.whl (7.0 kB)
Requirement already satisfied: scanpy>=1.9.3 in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from nsforest) (1.9.3)
Requirement already satisfied: scikit-learn>=0.22 in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from scanpy>=1.9.3->nsforest) (1.0.2)
Requirement already satisfied: anndata>=0.7.4 in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from scanpy>=1.9.3->nsforest) (0.8.0)
Requirement already satisfied: patsy in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from scanpy>=1.9.3->nsforest) (0.5.2)
Requirement already satisfied: umap-learn>=0.3.10 in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from scanpy>=1.9.3->nsforest) (0.5.2)
Requirement already satisfied: seaborn in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from scanpy>=1.9.3->nsforest) (0.11.2)
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Requirement already satisfied: packaging in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from scanpy>=1.9.3->nsforest) (21.3)
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Requirement already satisfied: pillow>=6.2.0 in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from matplotlib>=3.4->scanpy>=1.9.3->nsforest) (9.0.1)
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Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from matplotlib>=3.4->scanpy>=1.9.3->nsforest) (0.11.0)
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Requirement already satisfied: stdlib-list in ./anaconda3/envs/soothsayer_py3.9_env/lib/python3.9/site-packages (from session-info->scanpy>=1.9.3->nsforest) (0.8.0)
Installing collected packages: nsforest
Successfully installed nsforest-3.9.2.5

Following this tutorial: https://jcventerinstitute.github.io/celligrate/tutorials/NS-Forest_tutorial.html

(soothsayer_py3.9_env) jespinozlt2-osx:~ jespinoz$ python
Python 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:55:37)
[Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import NSForest_v3dot9_1 as nsf
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'NSForest_v3dot9_1'
>>> import nsforest as nsf
>>> nsf.__version__
'3.9.2'

Looks like the import command needs to be changed to from nsforest import *

yunzhang813 commented 1 year ago

The tutorial is one version behind. Use the following to start.

import nsforest as ns
ns.NSForest()