I generate dependency graphmls (of components, assemblies, jenkins jobs and such) and use yEd to layout it. I usually do the following:
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Open the file
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Run "Fit Node to label"
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Run "Hierarchical Layout"
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Observe that it does not render something readable, as there are too many edges
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Remove transitive edges
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Tools -> Select ("Elemente auswählen" in german) -> Edges
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Run Transitive reduction
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Transitively "redundant" edges are selected
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Delete selection
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Run "Hierarchical Layout"
The problem arises in step 5.3. In versions 3.17 as well as 3.17.1, no transitive edges are selected. If I run the very same file and steps in version 3.16, it works as expected.
I can provide example files if necessary. I double checked that in step 5.2, no other tabs (nodes, labels, ...) have any tickmarks.