Layer Selected in Coverage Layer Dropdown Ignored
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Trying Atlas for the first time, and kept getting maps as if a different layer were set as the coverage layer. Coverage layer dropdown displays all visible layers in the order that they appear in the Layers pane. Eventually I realized that the Atlas plugin was using the first-listed (i.e., "top" layer) layer, regardless of which layer I selected in the Coverage layer dropdown. I then reordered the layers in the QGIS Layers pane, and was able to get the maps that I wanted.
Obviously, you may not always want the coverage layer as the top layer of each map. Since Atlas allows you to suppress display of the coverage layer, a workaround is to always have a copy of the desired coverage layer as the top layer of your project, and suppress display. But I'm assuming this is a bug because the Coverage layer dropdown seems to have no effect.