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The following script illustrates the issue:
importmatplotlib.pyplotaspltfig=plt.figure()ax=fig.add_subplot(1,1,1)ax.scatter([1,2,3], [3,4,5],c=[3,2,1],edgecolor='k',cmap=plt.cm.viridis)fig.savefig('scatter.png')
Matplotlib 1.5.1
Matplotlib 2.0.0b3
In the Matplotlib 2.0.0b3 version, the scatter markers are missing edges.