Problems with matplotlib version 2.2.3

[ixicrom]

The newest versions of matplotlib no longer includes support for axes.color_cycle as an rc parameter. Apparently this was deprecated in matplotlib 1.5

It seems that the solution to this is to use the cycler package, as in this example: https://matplotlib.org/1.5.1/examples/color/color_cycle_demo.html

The problem in in file base.py line 104, but I'm currently not sure how exactly this needs to be updated.

[briandleahy]

Thanks for raising this issue. The solution is probably to stop importing peri.viz.base on the initial import, as well as fixing that line in base.py. Can you tell me when you got the error? I'll try to fix it tonight.

[ixicrom]

I got the error while trying to test the example code from the walkthrough:
from peri import util
from peri.viz.interaction import OrthoViewer
im = util.RawImage('small_confocal_image.tif')
OrthoViewer(im.get_image())

I have managed to fix it on my machine by replacing line 104 in base.py with 'axes.prop_cycle': cycler.cycler('color', COLORS + ['#FF7F00', '#D0D033','#A65628','#F781BF','#999999']),
and adding import cycler to the start of that file too (although I imagine there may be somewhere better to do this).

[briandleahy]

Hmm.... I'm on matplotlib 3.1.1 and I have no problems with the tutorial on master.

Can I ask you, what version of peri are you running and how did you install it? Can you try to install it from master and see if it works? I think this problem may have already been fixed on master. If so, it may be that the version on pypi is out of date and needs to be updated.

[ixicrom]

I installed it using pip, I'll try and install from master and will report back!

[ixicrom]

Everything works fine for me on the master version, so looks like that update is all that's needed to solve my issue!

[briandleahy]

Should be fixed with new version on pypi