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@kahaaga kahaaga commented Aug 17, 2025

The documentation build in #400 was failing due to cross-reference and external cross reference issues that I did not manage to debug. The solution was to completely re-do how cross-referencing is done in the docs, according to the standards in the latest versions of Documenter.jl.

  • The documentation now is completely stand-alone. It does not build the documentation from other packages. Previously, the docs for Associations.jl also built part of the docs for ComplexityMeasures.jl and StateSpaceSets.jl, which caused cross-reference issues and dead links with the latest versions of Documenter.jl)
  • All types and methods references in the docs belonging to other packages (e.g. ComplexityMeasures.jl) are now referenced using an explicit @extref (e.g. [`OutcomeSpace`](@extref ComplexityMeasures.OutcomeSpace)). This eliminates all documentation cross-reference errors.
  • Docs are now shorter (arguably cleaner), because of the external references. I'd prefer to maintain this way of documenting external references going forward, so we don't need to do double maintenance when it comes to docs (i.e. keeping the docs manually up to date in Associations.jl AND updating the docs in ComplexityMeasures.jl).
  • Un-collapse all docstrings by default (since many pages are now shorter)
  • Use checkout action v5.
  • Set minimum julia version to long term stable release (1.10.10).

@kahaaga kahaaga merged commit 0836c15 into fix_complexitymeasure_3.8 Aug 17, 2025
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@kahaaga kahaaga deleted the useextref branch August 17, 2025 14:30
kahaaga added a commit that referenced this pull request Aug 17, 2025
* up complexitymeasures

* quick fix: move GroupSlices.jl code from ComplexityMeasures.jl here

* Better check for agreement between transfer operator and visitation frequency estimates

Use reasonable number of points and percentage discrepancy

* use package-internal groupslices

* Use StableRNG for test that sometimes fails due to random data generation

* up version

* Fix and clean up documentation build by using @extref (#401)

* set version of complexitymeasures

* use @extref

* update style

* formatting

* formatting and extref

* extref

* extref

* always use links

* formatting

* up to julia long term release version

* reintroduce references

* Properly use extrefs

* extref for statespaceset

* fix last doc errors and set collapse = false

* up minimum julia version to latest LTS

* Don't build StateSpaceSets.

* Remove temp dep

* Force higher versions for packages

DynamicalSystems.jl v2 is loaded during tests??

* Update checkout

* explicitly add complexitymeasures to test deps

* remove direct reference to statespaceset

* Some more fixes to docs + version (#402)

* set version of complexitymeasures

* use @extref

* update style

* formatting

* formatting and extref

* extref

* extref

* always use links

* formatting

* up to julia long term release version

* reintroduce references

* Properly use extrefs

* extref for statespaceset

* fix last doc errors and set collapse = false

* up minimum julia version to latest LTS

* Don't build StateSpaceSets.

* Remove temp dep

* Force higher versions for packages

DynamicalSystems.jl v2 is loaded during tests??

* Update checkout

* explicitly add complexitymeasures to test deps

* remove direct reference to statespaceset

* Up versions

* remove collapse info

* less strict dsp requirement
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