I want to install a package name scanpy on Jupyter notebook so I run:
! pip3 install scanpy, I got this:
WARNING: You are using pip version 21.1.1; however, version 22.2.2 is available. You should consider upgrading via the ‘/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9 -m pip install --upgrade pip’ command.
Then: import scanpy as sc doesn’t work even though I updated pip to 22.2.2. I used conda to install as an alternative way.
sc.pp.highly_variable_genes(adata, n_top_genes = 2000, subset = True, flavor = 'seurat_v3')
ModuleNotFoundError Traceback (most recent call last) ~/opt/anaconda3/lib/python3.8/site-packages/scanpy/preprocessing/_highly_variable_genes.py in _highly_variable_genes_seurat_v3(adata, layer, n_top_genes, batch_key, check_values, span, subset, in place)
52 try: --->
53 from skmisc.loess import loess
54 except ImportError: ModuleNotFoundError: No module named 'skmisc'
I run this code:
Do you know how to fix these errors? Thank you so much!
Thank you for your help. I don't see error any more but Jupiter notebook show * before each cell instead of a number.
So I try
conda create -n scvi-env python=3.9but I don't know how to choose yes.
conda createused this way is supposed to be used on command line. (in Jupyter you have the option of running
notebookfor such interactive commands, however, I totally recommend to use your system shell instead of the jupyter-browser interface). You can choose yes beforehand by providing
-yoption to the command. Note, that this will say yes to everything, even to mistyped env and package names, so use it with caution.
More over, I fail to see, how creating new environment with
condarelates to your missing
scikit-misc(as, prosumably, you already have some environment...).
Thank you so much for your help!
If I would like to add
-y, it will but at the end of the command, right? Jupyter notebook keeps a star sign, so I don't know if the code is correct.
It would be
conda create -n scvi-env python=3.9 -y. See https://docs.conda.io/projects/conda/en/latest/commands/create.html for more information.
*means that the cell is either running or waiting in queue to be executed.
If you are stuck with the install, you will probably need to interupt / restart the kernel.