Re: Bug#954170: Help: Test suite failures (Was: ITP: anndata -- Annotated gene by sample numpy matrix)
On Thu, 2020-11-05 at 14:59 -0800, Diane Trout wrote:
> On Thu, 2020-11-05 at 21:08 +0100, Andreas Tille wrote:
> > Control: tags -1 help
> >
> > Hi Diane and Steffen,
> >
> > I fixed the Build-Depends in this package which leads to the
> > effect that
> >
> > a) the Build-time test is run
> > b) shows the same errors as the autopkgtest
>
> I went ahead and filed an upstream bug asking for any advice about
> the
> unexpected warning.
>
> https://github.com/theislab/anndata/issues/443
I discovered anndata is having trouble with the version of pandas we're
shipping. This patch fixes the test failure, though I thought I'd ask
upstream if they want to do this, or be more accepting of warnings.
(I'm not sure which versions of pandas they want to support).
Should we wait for upstream or just go ahead and add the patches to our
packaging?
Diane
--- anndata/_core/anndata.py 2020-11-05 12:23:54.976471806 -0800
+++ /run/schroot/mount/unstable-amd64-sbuild-6f63c09f-36e0-4302-9409-
6689c5b05354/build/python-anndata-exfcES/python-anndata-
0.7.4+ds/anndata/_core/anndata.py 2020-11-05 15:28:33.517496264
-0800
@@ -19,5 +19,5 @@
from numpy import ma
import pandas as pd
-from pandas.api.types import is_string_dtype, is_categorical
+from pandas.api.types import is_string_dtype, is_categorical_dtype
from scipy import sparse
from scipy.sparse import issparse
@@ -1089,8 +1089,8 @@
def _remove_unused_categories(self, df_full, df_sub, uns):
- from pandas.api.types import is_categorical
+ from pandas.api.types import is_categorical_dtype
for k in df_full:
- if not is_categorical(df_full[k]):
+ if not is_categorical_dtype(df_full[k]):
continue
all_categories = df_full[k].cat.categories
@@ -1190,5 +1190,5 @@
key
for key in df.columns
- if is_string_dtype(df[key]) and not
is_categorical(df[key])
+ if is_string_dtype(df[key]) and not
is_categorical_dtype(df[key])
]
for key in string_cols:
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