rna-import requires old pandas version

[adamp83]

cnvkit.py raises an issue

AttributeError: 'Series' object has no attribute 'clip_upper'

when running rna-import. This occurs on a fresh install on MacOS, and also affects the docker container. It seems to be related to pandas, which removed the clip_upper method in their 1.0 release in Jan 2020 (https://pandas.pydata.org/docs/whatsnew/v1.0.0.html#removal-of-prior-version-deprecations-changes). Reverting to pandas 0.25 fixes it. Specifying the dependency version or updating the clip_upper method to clip(upper=threshold) here:

cnvkit/cnvlib/rna.py

Line 267 in fa86632

weights = [np.sqrt((gene_counts / gene_counts.quantile(.75)).clip_upper(1))]

(as described here: https://pandas.pydata.org/pandas-docs/version/0.24.2/reference/api/pandas.Series.clip_upper.html) should sort this.

Hope this helps.

[etal]

Thanks, looks like an easy fix.

[etal]

Fixed on git just now: 0860c97

[harbourlab]

I still have this issue. Works with down-grading Pandas.