Problem in the Installation of CellBender

[danielbarhanin]

Hey!
Following the instrucation for installing CellBender, I got this following error:
ERROR: CellBender is not a valid editable requirement. It should either be a path to a local project or a VCS URL (beginning with bzr+http, bzr+https, bzr+ssh, bzr+sftp, bzr+ftp, bzr+lp, bzr+file, git+http, git+https, git+ssh, git+git, git+file, hg+file, hg+http, hg+https, hg+ssh, hg+static-http, svn+ssh, svn+http, svn+https, svn+svn, svn+file).

This happens when i did the command:
pip install -e CellBender

So i tried to install the package like it's instructed above with this command:
pip install git+https://github.com/broadinstitute/CellBender.git

But when I tried to run cellbender remove-background I get the following error:
Traceback (most recent call last):
File "/usr/local/bin/cellbender", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.7/site-packages/cellbender/base_cli.py", line 90, in main
parser = get_populated_argparser()
File "/usr/local/lib/python3.7/site-packages/cellbender/base_cli.py", line 76, in get_populated_argparser
module_argparse = importlib.import_module('.'.join(module_argparse_str_list))
File "/usr/local/lib/python3.7/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 953, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 965, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'cellbender.remove_background'

Is there a solution for that? or new instructions for the installation?

Thanks in advance!

[sjfleming]

I think the problem is likely that pip install -e CellBender might not be pointing to your local cloned repository.

Can you try the following?

git clone https://github.com/broadinstitute/CellBender.git CellBender

then double-check that when you do

ls CellBender

you should be able to see the file setup.py in that directory. If you can see that file, then

pip install -e CellBender

should work.

Alternatively, you can navigate into the directory where CellBender's setup.py file is located, and then do

pip install -e .

[bbimber]

@sjfleming We're also interested in this. Is there any reason why we should need to clone the repo and do a local install, as opposed to:

pip install git+https://github.com/broadinstitute/CellBender.git

The latter would be much nicer since package could declare a dependency on the github URL, as opposed to manually cloning and installing. I would have guessed that the pip install command above basically does a clone/install anyway.

Do you know a reason the command above would not work?

[bbimber]

A couple other observations:

If I manually clone the repo, do 'pip install -e', and then delete the local git copy, the tool fails. I would have expected pip install to copy the relevant code into a python library folder - is this not the case?

[mxposed]

@sjfleming please merge this #118 this would fix the issue

[sjfleming]

Thanks @mxposed , I will get that merged in before too long.

@bbimber , I think @mxposed 's PR will fix your first comment. As for the other observation, I think that is actually expected behavior based on the -e flag I have included. -e installs in an editable mode. I like this because I like to make edits, but it's true that it doesn't always make sense. :)
If you install without the -e, then it should (?) continue to work after you delete the local git repo.

[sjfleming]

Closed by #238