Pandas error in sample Harmony code

ckbehemoth commented 5 years ago

Hello all,

We're trying out the Harmony code in the sample notebook and it runs fine until it hits the line: hvg_genes = harmony.utils.hvg_genes(norm_df) where it throws the following error:

    Traceback (most recent call last):
        ...
        [snip]
        ...  
        File "/home/.../.local/lib/python3.6/site-packages/pandas/core/indexes/category.py", line 503, in reindex
        raise ValueError("cannot reindex with a non-unique indexer")
    ValueError: cannot reindex with a non-unique indexer

Has anyone seen this before? Alternately, are there specific library versions we should be running against? Here are the versions ot the underlying libs that we're using:

Library	Version
Harmony	0.1
Palantir	0.2.1
Pandas	0.24.2
NumPy	1.16.3

We'd really love to use the software - so any ideas or advice is welcome.

Cheers, Bill

ManuSetty commented 5 years ago

Hello

Apologies for the delayed response. This issue has been fixed in the latest commit (e1f60a6a0117bfc429641660a4f1db72cb9069dd). Please pull the latest version of master and let us know if the issue still persists.

ckbehemoth commented 5 years ago

No worries - thanks for looking into it! We'll be trying it out ASAP.

Cheers,

B

dpeerlab / Harmony

Pandas error in sample Harmony code #5