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Major overhaul of documentation - #84

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bgroenks96 merged 152 commits into

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bg/update-docs

Apr 7, 2026

Commits on Mar 19, 2026
- Add initial version of AGENTS.md
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- Add more docs for soil types/method interfaces
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- Add getter for soil thermal properties
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- Move soil process abstract types into separate files
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- Add process interface stubs for soil energy/hydrology
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- Initial rewrite of doc pages (still WIP)
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- Minor update to abstract type interfaces
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- Minor tweaks to headings in energy/hydrology docs
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- Add force = true to example notebook `mv`
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- Minor clean up of soil stratigraphy types
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- Initial version of doc page on soil stratigraphy
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Commits on Mar 20, 2026
- Add initial version of docs for photosynthesis
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Commits on Mar 21, 2026
- Minor refactoring of photosynethsis code
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Commits on Mar 22, 2026
- Minor refactoring of phenology
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- Add initial drafts of vegetation docs
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- Update include for vegetation_carbon.jl
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- Add missing docstrings and fix errors in docs
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- Fix outdated tests
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- Fix tests
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- Add RingGrids and CUDA to docs deps
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- More docs/test fixes
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- Add more rules to AGENTS.md
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- Add initial drafts of doc pages for SEB
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  82b057b
- Update time units on variables for autotrophic respiration
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- Minor formatting changes in SEB code
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  d39294c
- Fix issues in SEB doc pages
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  87d5351
- Fix constructors in doc example blocks
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  d995d54
- Fix inconsistent unit for NPP in carbon dynamics
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  8a1fc69
- Remote notebook doc pages form source control
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- Add initial doc pages drafts for surface hydrology
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- Fix issues with surface hydrology docs
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- Add initialization and timestepping sections to basic concepts
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- Fix timestepper ctor in doc example
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Commits on Mar 23, 2026
- Add initial version of soil model doc page
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- Update docs/src/extending/core_interfaces.md
  
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- Update docs/src/extending/core_interfaces.md
  
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  ff73697
- Update docs/src/introduction/basic_concepts.md
  
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  7994987
- Update docs/src/introduction/basic_concepts.md
  
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- Fix typos
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  83e4ad9
- Update docs/src/extending/core_interfaces.md
  
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- Change 'early prototype' to 'prototype'
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- Fix incorrect branch name in git hook
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- Update README
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- Fix more typos and add note about interfaces
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Commits on Mar 24, 2026
- Update docs/src/introduction/basic_concepts.md
  
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Commits on Mar 25, 2026
- Fix yet more typos
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  73e84bb
- Make var summary string more compact
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  c6ad51a
- Restructure soil hydrology doc page
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- Merge branch 'main' into bg/update-docs
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- Fix doc build issues
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  ae0ceb3
- Improve initialization section in intro doc page
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Commits on Mar 26, 2026
- Fix draft mode for docs
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  5be9679
- Rewrite documentation for photosynthesis
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  6a78eb5
- Reorganize sections
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Commits on Mar 27, 2026
- More improvements to soil docs
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  c5b18e8
- Add missing setup block to photosynthesis doc page
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  f8b3727
- Improve SEB docs
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  9e9544e
- Add section on building the docs
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  b669600
- Re-order models and processes in nav bar
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- More tweaks to soil docs
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  90a9de3
- Add missing docstrings and fix crossrefs
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- Add doc pages for atmosphere and physics utils
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  151e133
- Add table of constants to PhysicalConstants doc page
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  17cb788
- Update table of contents and move examples
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  4db4ee3
- Update surface hydrology docs
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  6fbb129
- Remove process pages from ToC
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Commits on Mar 30, 2026
- Rewrite stomatal conductance documentation
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  e239dda
- Fix phototsynthesis docs
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  28fb9a0
- Rewrite autotrophic respiration documentation
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  2e2d127
- Add missing setup block to stomatal conductance doc page
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- Rewrite phenology documentation
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- Update photosynthesis docs
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- Restructure paw and root_dist docs
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Commits on Apr 1, 2026
- Update docs/src/index.md
  
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- Update docs/src/index.md
  
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  12fa277
- Update docs/src/introduction/basic_concepts.md
  
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Commits on Apr 2, 2026
- Update docs/src/processes/soil/soil_stratigraphy.md
  
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- Restructure veg_dynamics + carbon_dynamics docs
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- Rewrite carbon dynamics docs
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  30fe3b0
- Update docs/src/processes/surface_hydrology/surface_hydrology.md
  
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  5e75e0a
- Update docs/src/processes/vegetation/photosynthesis.md
  
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- Update docs/src/processes/surface_hydrology/canopy_interception.md
  
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  74009b7
- Update docs/src/processes/vegetation/photosynthesis.md
  
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  4802aee
- Update docs/src/processes/vegetation/photosynthesis.md
  
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  ea50b66
- Remove kernel reference in veg dynamics doc page
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  7c58016
- Update docs/src/processes/vegetation/photosynthesis.md
  
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- Fix incorrect docstrings
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  9d2856c
- Replace unfinished sentence in basic_concepts.md doc page
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  74931ef
- Fix incorrect rendering of admonitiions
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  32fe2c4
- More minor docs improvements
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  c82f9ca
- Update docstrings for `initialize`
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  33fd8a0
- Fix include order
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  f0e4e14
- Update docs/src/processes/atmosphere/aerodynamics.md
  
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  e4edc8e
- Update docs/src/processes/atmosphere/prescribed_atmosphere.md
  
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- Fix typo in cross-ref
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  f57cca2
- Add more details to core interfaces doc page
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  676c2ad
- Update docstrings for closure! and invclosure!
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- Initial draft of doc page on setting up Simulations
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  9a71621
- Use unique identifiers for doc example blocks
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  9bf4628
- Fix `show` for variables printing to wrong output stream
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  fdcef75
- Fix docstrings for input sources
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- Fix typos in README
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- Add doc page for input sources
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  f2581ab
- Split intro sections on initialization and time stepping into separate pages
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- Update doc build and add more page stubs
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- Fix process doc file names
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Commits on Apr 3, 2026
- Fix typo in make.jl
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- Rewrite veg dynamics docs
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  fe12b31
- Re-organize example scripts and doc pages
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  c871d97
- Update veg dynamics tendency test
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  2a79ee9
- Update AGENTS.md
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  cf1b2a1
- Add implementation example with linear heat conduction
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  46bb175
- Update doc page on implementing processes
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  cdec726
- Minor fixes in snow ddm example
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  53f5848
- Fix typos and link issues in docs/make.jl
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  00a47fd
- Fix more broken or incorrect links
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  3b49d1a
- Fix another typo
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- Minor improvements to soil and SEB docs
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Commits on Apr 4, 2026
- Add more headings to DDM example
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- Fix incorrect variable name in PAW
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- Add dedicated doc page for state variables
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  42d777c
- Minor docs tweaks
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  3a07bdb
- Add initial draft of page on process coupling
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  4a2e09c
- Minor changes to AGENTS.md
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  7db3382
- Update page on process coupling
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  04017c1
- Fix typo in SEB doc page
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  de4fbb8
- Merge sections on process coupling
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  a8bff93
- Make link check optional in doc build
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  767d1c7
- Minor tweaks to model/process interface docs
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Commits on Apr 5, 2026
- Revise formatting of units and symbol declarations in some doc pages
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  83da404
- Update docs for PAW and root distribution
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  0d57384
- Add citation management with DocumenterCitations.jl
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- Add references page + citation CSS
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- Add more references
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- Add more citations and in-page bibs
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- Add more refs to bibliography
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- Update yet more citations
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- Fix unit inconsistencies in canopy interception
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Commits on Apr 6, 2026
- More improvements to doc pages
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  50bc1ed
- More docs fixes and improvements
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  2dd9d85
- Fix ambiguous naming of process abstraction levels
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  e12d657
- Fix formatting error
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  03d4260
- Update doc pages on atmosphere interface
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- Add process interface section for all processes
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Commits on Apr 7, 2026
- Use SoilInitializer by default in soil model
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- Improve soil heat examples
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- Add more example doc pages
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  812b15b
- Fix issue with input file path in global example
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  b1efde4
- Create example output dirs prior to file copy
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  3e03d2f
- Fix inconsistencies in linear heat conduction example
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  3c5c67b
- Fix incorrect path in docs/make.jl
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  f4b6442
- Reduce default simulation time in global example
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Commits

Commits on Mar 19, 2026

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