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Resolve "Periodically extract and store network structure and meta-data"

Yunus Sevinchan requested to merge 8-extract-nw into master

This MR adds periodic network extraction (using the thresholding by Allhoff et al., described in #8 (closed)) and computes a set of network characteristics.

Can this MR be accepted?

  • Implementation ready
    • Network extraction
      • Structure
      • Vertex and edge properties, configurable
    • Network storage
      • ... via action and trigger
      • default: at end of simulation (in epilog), but easily configurable
    • frontend-side graph building and computation of topological characteristics from that
      • Create nx.DiGraph from GraphGroup
      • Annotating graph with network measures (a few are not yet implemented, but that can be done later on...)
    • Tweaks and other notable changes
      • Disabled armadillo runtime checks for Release builds; should speed things up a bit 🚀
      • Set write mode to manual to have full control in model itself
  • Tests added or adjusted
    • Basic output writing tests
    • network plots run as part of CI
  • Plots added
    • ... for all written vertex properties
    • ... for network measures (overview plot)
  • Documentation extended or updated
  • Code quality
    • Changes follow coding guidelines
    • Checked code coverage on new and adjusted code

Related issues

Closes #8 (closed)

Edited by Yunus Sevinchan

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