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Draft: Update PanTools dependencies

Workum, Dirk-Jan van requested to merge update_dependencies_pantools into develop

There are quite some dependencies of PanTools that need updating, doing that here:

TODO:

  • Clean up conda dependencies
  • Add conda dependency test to pre-commit hooks & CI/CD
  • Clean up pom.xml
  • Update java 8 -> java 17
  • Update neo4j 3.5.30 -> neo4j 5
  • Update other maven dependencies
  • Update kmc version
  • Make sure kmc runs identically to original version
  • Update aster version
  • Update with changes to neo4j 5 API (homology group nodes, feature nodes, function nodes)
  • Final check graph is identical to previous versions

This merge request resolves #31, #8

Edited by Workum, Dirk-Jan van

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