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Document all plotting functions and update documentation build structure #177

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Copilot AI commented Aug 26, 2025 •
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  • Rebase branch on latest main
  • Fix duplicate documentation for mesh plotting functions
  • Fix missing exports for plot_linear_convergence functions
  • Replace @docs blocks with narrative documentation
  • Verify documentation builds successfully

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Copilot AI and others added 2 commits August 26, 2025 18:33
@moyner
Add comprehensive docstrings for all plotting functions
6787ff9 
Co-authored-by: moyner <454871+moyner@users.noreply.github.com>
@moyner
Create dedicated plotting documentation and update build structure
49df6ee 
Co-authored-by: moyner <454871+moyner@users.noreply.github.com>
Copilot AI changed the title [WIP] Document all plotting functions, and update the doc build accordingly Document all plotting functions and update documentation build structure Aug 26, 2025
Copilot finished work on behalf of moyner August 26, 2025 18:38
Copilot AI requested a review from moyner August 26, 2025 18:38
@moyner
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moyner commented Nov 6, 2025

@copilot Rebase this on maine and fix the build errors

Alexandre Jiao and others added 19 commits November 6, 2025 09:10
calibration
b5f99e4
@xavierr
support for log scaling in BFGS
37f7665
@andreas-brostrom
Change adjoint step info to use time at new timestep
ad9f30b
@andreas-brostrom
Change the progress recorder API
60f87e4
@andreas-brostrom
Add tests for the recorder API
179a7ff
@andreas-brostrom
Rename recorder reset functions
d58bee8
@moyner
Fix to BoomerAMG standalone preconditioner (#181)
0946918 
* Update JutulHYPREExt.jl

* Add AMG tests to heat equation test

* Add HYPRE to test env
@moyner
Remove old Meshes.jl code (#182)
92d2c51
@moyner
Faster parameter optimization for models where the setup can be split…
c3c8b3f 
… in dynamic and static parts (#183)
@moyner
Enable objective sparsity in optimize by default, perf improvements t…
46def5b 
…o adjoint (#184)
@moyner
Fallback for MVector sparsity tracing issues on 1.11 (#185)
ef79516
@andreas-brostrom
Fix bug in format of time stamp for printing simulation result (#186)
737a0fd
@moyner
Update backend warning for interactive plotting (#188)
5fd9313
@moyner
Improve fix for Julia GC crash (#189)
8be3965 
* Update conservation.jl

* Update unstructured.jl
@moyner
More missing methods for type for Julia 1.11 crash (#190)
c5502ff
@moyner
Refactor ForwardDiff usage to make use of ForwardDiff.Tag (#191)
1634c9d 
* Start to use ForwardDiff tags properly

* More tag fixes

* Additional type fixes/cleanup for AD

* Update ad.jl
@moyner
Update plot_secondary_variables to work with latest everything (#192)
b1d32bc
@moyner
Bump to version 0.4.6 (#193)
36522f1
@moyner
Add tag ordering to Jutul tags for ForwardDiff (#194)
e25cdab
strene and others added 9 commits November 6, 2025 09:10
@strene
Find enclosing cell improvement (#195)
e33e6f6 
* Add optional kwarg `cells` to limit seach to a subset of the mesh cells

* Remove println-statement

* Bump version
@moyner
Add IJK fallback for unstructured meshes (#196)
e7e61e2
@moyner
Add 3 specialization for plotter (#197)
9973c10
@moyner
Improve coarsening performance substantially (#198)
6141676 
* Improve performance of coarsening

* Update coarsening.jl
@moyner
Add cross-term sparsity to objective function (#199)
b6cee73
@moyner
Guard against missing entry in objective sparsity (#200)
d05296f
@moyner
Improve performance and code for generic adjoint (#201)
9143b27 
* Put delumping/unscale in function

* Single step sparsity is ok for "reduced" varsets

* Replace a broadcast by loop due to allocations

* Add more output to DI

* Improve info_level in opt

* Add type check

* Guard against missing field in vectorization

* Update optimization.jl

* Use ordered dict in variable mapper

* Internal improvements to sparsity

* Update interface.jl

* Update interface.jl

* Refactor out the main optimization setup

* Add a finite difference utility

* Update adjoints.jl

* Add deps_ad argument (non-functional)

* Refactor

* Split adjoint setup

* More setup work on mixed adjoint

* More coding on split adjoint

* Mostly working version

* Work on getting mixed state0 working

* Cleanup

* Add new tests to adjoints
Initial plan
3ab6bd2
@moyner
Rebase on main and fix documentation build errors
82b8d1f 
- Rebased branch on latest main (fc65435)
- Fixed duplicate @docs blocks for plotting functions
- Replaced @docs with narrative documentation to avoid Documenter errors
- Added missing export for plot_linear_convergence functions
- Documentation now builds successfully

Co-authored-by: moyner <454871+moyner@users.noreply.github.com>
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Copilot AI commented Nov 6, 2025 •
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@copilot Rebase this on maine and fix the build errors

Rebased on main (fc65435) and fixed all build errors. The documentation now builds successfully. Changes in commit 82b8d1f.

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    • Triggering command: /usr/local/julia1.12.1/bin/julia -C native -J/usr/local/julia1.12.1/lib/julia/sys.so -g1 --output-o /home/REDACTED/.julia/compiled/v1.12/MKL_jll/jl_kfUxO2 --output-ji /home/REDACTED/.julia/compiled/v1.12/MKL_jll/jl_Z0OQtn --output-incremental=yes --startup-file=no --history-file=no --warn-overwrite=yes --color=yes - (dns block)

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Copilot finished work on behalf of moyner November 6, 2025 09:12
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