retest fails on MacOS about recentrifuge HOT 5 CLOSED

Thank you very much for the bug report. Recentrifuge is developed and tested on my mac:

Darwin Kernel Version 15.6.0: Wed May  2 21:04:22 PDT 2018; root:xnu-3248.73.10~1/RELEASE_X86_64

So, I will try to reproduce your issue with conda. Anyway, it may be a problem with the matplotlib backend (like in this SO question). In the meantime, could you please set the environment variable MPLBACKEND to PDF before running retest to check if something changes? Thanks!

from recentrifuge.

There are some well-known (not for me) issues with matplotlib/conda/osx (see matplotlib docs for example) so that some fine-tuning is required. I found two ways to get retest properly ending under conda/bash/osx on my mac:

1. Setting the matplotlib backend to PDF:

$ conda create -n recentrifuge python=3.7
$ conda activate recentrifuge
(recentrifuge)$ git clone https://github.com/khyox/recentrifuge.git
(recentrifuge)$ cd recentrifuge
(recentrifuge)$ conda install --file=requirements.txt
(recentrifuge)$ export MPLBACKEND=PDF
(recentrifuge)$ ./retest -d -l -r

2. Using use pythonw rather than python as suggested on matplotlib docs:

$ conda create -n rcf python=3.7
$ source activate rcf
(rcf)$ git clone https://github.com/khyox/recentrifuge.git
(rcf)$ cd recentrifuge
(rcf)$ conda install python.app
(rcf)$ conda install --file=requirements.txt
(rcf)$ pythonw retest -d -l -r

Please, confirm me if any of these works for you. If so, I will update the docs with instructions for conda users. Thanks!

from recentrifuge.

Thanks @khyox, that fixed it!

I ran

conda create -n recentrifuge python=3.7 pandas openpyxl xlrd matplotlib
source activate recentrifuge
export MPLBACKEND=PDF
pip install recentrifuge
retest -d -r

and got

$ echo $?
0

Note that using pythonw isn't really a fix, because it jumps outside the conda environment:

$ which pythonw
/usr/local/bin/pythonw

from recentrifuge.

Thanks for the feedback @BenKaehler!

That's interesting. In my mac, pythonw is executed inside the conda enviroment where I installed the python framework build with conda install python.app:

(rcf)$ which pythonw
/anaconda3/envs/rcf/bin/pythonw

Anyway, I think I will hardwire the matplotlib PDF backend in the retest code to avoid future problems.

from recentrifuge.

Thanks @khyox. I would guess that's because I didn't install python.app.

from recentrifuge.