Example error

[heikostark]

The example (https://github.com/ACCLAB/DABEST-python) doesn't work.

python3 0
Traceback (most recent call last):
File "0", line 12, in
iris_dabest.mean_diff.plot();
File "/usr/local/lib/python3.7/site-packages/dabest/_classes.py", line 1258, in plot
out = EffectSizeDataFramePlotter(self, **all_kwargs)
File "/usr/local/lib/python3.7/site-packages/dabest/plotter.py", line 377, in EffectSizeDataFramePlotter
**group_summary_kwargs)
File "/usr/local/lib/python3.7/site-packages/dabest/plot_tools.py", line 162, in gapped_lines
quantiles = data.groupby(x)[y].quantile([0.25, 0.75])
File "/usr/local/lib64/python3.7/site-packages/pandas/core/groupby/groupby.py", line 1953, in quantile
return result.take(indices)
File "/usr/local/lib64/python3.7/site-packages/pandas/core/series.py", line 4432, in take
new_index = self.index.take(indices)
File "/usr/local/lib64/python3.7/site-packages/pandas/core/indexes/multi.py", line 2032, in take
na_value=-1,
File "/usr/local/lib64/python3.7/site-packages/pandas/core/indexes/multi.py", line 2060, in _assert_take_fillable
taken = [lab.take(indices) for lab in self.codes]
File "/usr/local/lib64/python3.7/site-packages/pandas/core/indexes/multi.py", line 2060, in
taken = [lab.take(indices) for lab in self.codes]
IndexError: index 6 is out of bounds for size 6

---

Requirement already satisfied, skipping upgrade: scipy>=0.14.0 in /usr/local/lib64/python3.7/site-packages (from seaborn) (1.3.1)
Requirement already satisfied, skipping upgrade: matplotlib>=1.4.3 in /usr/local/lib64/python3.7/site-packages (from seaborn) (3.1.1)
Requirement already satisfied, skipping upgrade: numpy>=1.9.3 in /usr/local/lib64/python3.7/site-packages (from seaborn) (1.17.1)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.6.1 in /usr/lib/python3.7/site-packages (from pandas>=0.15.2->seaborn) (2.8.0)
Requirement already satisfied, skipping upgrade: kiwisolver>=1.0.1 in /usr/local/lib64/python3.7/site-packages (from matplotlib>=1.4.3->seaborn) (1.1.0)
Requirement already satisfied, skipping upgrade: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.4.3->seaborn) (2.4.2)
Requirement already satisfied, skipping upgrade: cycler>=0.10 in /usr/local/lib/python3.7/site-packages (from matplotlib>=1.4.3->seaborn) (0.10.0)
Requirement already satisfied, skipping upgrade: six>=1.5 in /usr/lib/python3.7/site-packages (from python-dateutil>=2.6.1->pandas>=0.15.2->seaborn) (1.12.0)
Requirement already satisfied, skipping upgrade: setuptools in /usr/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=1.4.3->seaborn) (41.0.0)
Requirement already up-to-date: pandas in /usr/local/lib64/python3.7/site-packages (0.25.1)
Requirement already satisfied, skipping upgrade: numpy>=1.13.3 in /usr/local/lib64/python3.7/site-packages (from pandas) (1.17.1)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.6.1 in /usr/lib/python3.7/site-packages (from pandas) (2.8.0)
Requirement already satisfied, skipping upgrade: pytz>=2017.2 in /usr/local/lib/python3.7/site-packages (from pandas) (2019.2)
Requirement already satisfied, skipping upgrade: six>=1.5 in /usr/lib/python3.7/site-packages (from python-dateutil>=2.6.1->pandas) (1.12.0)
Requirement already up-to-date: dabest in /usr/local/lib/python3.7/site-packages (0.2.5)

[josesho]

Hi,

which version of pandas are you using?

Thanks,
Joses

[heikostark]

Requirement already up-to-date: pandas in /usr/local/lib64/python3.7/site-packages (0.25.1)
Requirement already satisfied, skipping upgrade: numpy>=1.13.3 in /usr/local/lib64/python3.7/site-packages (from pandas) (1.17.1)
Requirement already satisfied, skipping upgrade: pytz>=2017.2 in /usr/local/lib/python3.7/site-packages (from pandas) (2019.2)
Requirement already satisfied, skipping upgrade: python-dateutil>=2.6.1 in /usr/lib/python3.7/site-packages (from pandas) (2.8.0)
Requirement already satisfied, skipping upgrade: six>=1.5 in /usr/lib/python3.7/site-packages (from python-dateutil>=2.6.1->pandas) (1.12.0)

Best regards,
Heiko

[josesho]

Hi,

As seen in #52 and #60 (my bad, I shouldn't have closed these unresolved issues), dabest doesn't play properly with pandas=0.25. For now, I would advise using pandas='0.24.

Thanks,
Joses

PS the easiest way to get any package's version is to run

pandas.__version__

in a Jupyter cell.

[lrq3000]

I get the same error, and probably for the same reason. Any hint on how to fix the issue with pandas >= 0.25?

[mje-nz]

@lrq3000 It should be fixed in pandas v0.26.0.dev0, which you can install from source. Why not just downgrade (pip install "pandas<0.25" --force-reinstall) or use a venv for now though?

[lrq3000]

Yes thank you, apparently it's going to be fixed with 0.25.2 minor revision but no ETA, so I'll downgrade meanwhile.

[josesho]

@BioinfoTongLI I think you should do what @mje-nz suggests: set up a conda env or venv, and either install pandas==0.26.0.dev0 from source, or downgrade to pandas=0.24. Hope this solves your problem!

[josesho]

Closed with #89