Can't install ipfx library - python 3.9.13 Jupyter Notebook

[gouwens]

@MPanday

I restarted the Kernel, and then closed and reopened everything. Sometimes I find that clears things up. I did get the same error message when trying to run ipfx. Again, it was after I tried running the import lines - with punctuation corrected.

You could try to simplify the situation to try to figure out what’s going on. I’d try running something minimal outside of Jupyter to see if that clarifies the issue. You can open a Python prompt from a terminal/console, and just try to import something from ipfx.

I created a new environment and installed just the packages that your error message suggests you have installed (h5py, numpy, pandas, pynwb, pyyaml), as well as installing ipfx (with the --no-deps) option. When I run just the from ipfx.dataset.create import create_ephys_data_set line, this is what I get:

Python 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:58:50) 
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from ipfx.dataset.create import create_ephys_data_set
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/local1/anaconda3/envs/test_ipfx_empty/lib/python3.9/site-packages/ipfx/dataset/create.py", line 8, in <module>
    import allensdk.core.json_utilities as ju
ModuleNotFoundError: No module named 'allensdk'
>>> 

So this would mean that I’d need to install allensdk (likely using the --no-deps option in order to not deal with downgrading issues), try it again, and then see if there are additional packages I need to install. But I’m not seeing anything from pip when I run it in this minimal way.

@MPanday

As I was following the model Jupyter notebook. I noticed there was a file “select_markers” that I can’t seem to find anywhere. Would you happen to know where I would be able to find that file. I’d like to try recreating the umap to explore the transcriptomic data. Thank you again for all the help!

Here is a thread about creating a select_markers file: Question on PatchSeq jupyter example

You could also take something like this file of marker genes and turn it into a text file with a single gene name on each line:

AllenInstitute/patchseqtools/blob/master/manuscript_data/class_markers.csv

That probably would get you fewer genes than you’d find by following the procedure in the linked thread, but it still would likely make a reasonable UMAP.