qiime2 / q2-diversity / 588

100%

push

travis-ci

Pandas 1 fixes (#268)

* Use MultiIndex.codes instead of labels (no longer support)

Please see these links for the rational if interested:

https://github.com/pandas-dev/pandas/issues/13443

https://github.com/pandas-dev/pandas/pull/23752

* Unpack and name values returned by _reindex_with_metadata

This makes it easier to see what's going on below with the values
returned by this function.

* Initial patch to handle new pandas error

This prevents attempting to drop columns that don't exist in merged.columns
after setting the index, while still dropping columns that are present in
merged.columns.  Attempting to do so raises an exception in pandas >= 1.

Please see https://github.com/pandas-dev/pandas/issues/8594
for details.

* Avoid mutating `merged` in place by assigning to new variable

This avoids attempting to drop columns that had already been dropped in previous
calls to _reindex_with_metadata in the for loop in `alpha_rarefaction`.

Co-authored-by: Matthew Dillon <matthewrdillon@gmail.com>

Co-authored-by: Matthew Dillon <matthewrdillon@gmail.com>

214 of 216 branches covered (99.07%)

730 of 733 relevant lines covered (99.59%)

1.0 hits per line