Tests: resolve remaining deprecation warnings

[mgovers]

closes #325

• migrates old JSON format to new PGM JSON serialization format
• resolves pandas deprecation warning by not concatinating empty data frames

TODO:

• verify / test backwards compatibility (do-not-merge label)
  • the changes are indeed backwards compatible, because the "tricky" part only affects test code

To validate (reviewer):

• verify deprecation warnings on main
  • checkout main
  • editable install including dev dependencies
  • pytest does not result in deprecation warnings
  • pytest tests/validation results in deprecation warnings
• verify deprecation warnings fixed on this branch
  • checkout this branch
  • editable install including dev dependencies
  • pytest does not result in deprecation warnings
  • pytest tests/validation does not result in deprecation warnings

[mgovers]

Backwards compatibility only affects tests. removing do-not-merge label

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud