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This happened to me because I was using matplotlib 1.5 code, where this was actually not invisible.
Changing markeredgecolor='k' (which was the default before) fixes the problem. But that is a pretty surprising error and might hint at something going wrong somewhere?
In particular, png rendering works fine, only pdf errors.
Activity
anntzer commentedon Apr 23, 2018
Fixed by #8850 (AFAICT, please request a reopen if not).
amueller commentedon Apr 23, 2018
Fixed in 2.1.0 (or earlier).