add nm_psn nm_pharmpy nlmixr example workflows

[JordanBrooks33]

Adds example luna workflows for: NONMEM + PsN, NONMEM + PharmPy, and nlmixr2.

[Copilot]

Pull request overview

Adds three end-to-end example workflows (NONMEM+PharmPy, NONMEM+PsN, nlmixr2) for a busulfan popPK model-building sequence, and makes a few supporting changes in core luna functions around cache loading, config access, and syntax checking.

Changes:

• Added example project folders, model files, and workflow scripts for NONMEM+PharmPy, NONMEM+PsN, and nlmixr2.
• Updated luna_load_project(), get_luna_config(), luna_check(), and luna_run() to adjust cache/config behavior and (for luna_check) switch to Pharmpy parsing.
• Updated .gitignore and generated documentation for luna_check().

Reviewed changes

Copilot reviewed 26 out of 29 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
vignettes/example-3-nlmixr2/project/run1.R	Adds nlmixr2 run1 (1-cmt) model function for the example workflow
vignettes/example-3-nlmixr2/project/run2.R	Adds nlmixr2 run2 (2-cmt) model function
vignettes/example-3-nlmixr2/project/run3.R	Adds nlmixr2 run3 (WT allometry) model function
vignettes/example-3-nlmixr2/project/run4.R	Adds nlmixr2 run4 (SEX on CL test) model function
vignettes/example-3-nlmixr2/project/run5.R	Adds nlmixr2 run5 (IOV on CL) model function
vignettes/example-3-nlmixr2/project/busulfan.yaml	Adds luna project YAML describing the nlmixr2 model-building runs
vignettes/example-3-nlmixr2/luna_workflow_nlmixr2.R	Adds an nlmixr2-focused workflow script demonstrating modeling + luna annotations
vignettes/example-2-nm-psn/project/run1.mod	Adds NONMEM run1 control stream for PsN example
vignettes/example-2-nm-psn/project/run2.mod	Adds NONMEM run2 control stream for PsN example
vignettes/example-2-nm-psn/project/run3.mod	Adds NONMEM run3 control stream for PsN example
vignettes/example-2-nm-psn/project/run4.mod	Adds NONMEM run4 control stream for PsN example
vignettes/example-2-nm-psn/project/run5.mod	Adds NONMEM run5 control stream for PsN example
vignettes/example-2-nm-psn/project/busulfan.yaml	Adds luna project YAML for PsN example
vignettes/example-2-nm-psn/luna_workflow_nm_psn.R	Adds PsN-backed luna workflow script
vignettes/example-1-nm-pharmpy/project/run1.mod	Adds NONMEM run1 control stream for Pharmpy example
vignettes/example-1-nm-pharmpy/project/run2.mod	Adds NONMEM run2 control stream for Pharmpy example
vignettes/example-1-nm-pharmpy/project/run3.mod	Adds NONMEM run3 control stream for Pharmpy example
vignettes/example-1-nm-pharmpy/project/run4.mod	Adds NONMEM run4 control stream for Pharmpy example
vignettes/example-1-nm-pharmpy/project/run5.mod	Adds NONMEM run5 control stream for Pharmpy example
vignettes/example-1-nm-pharmpy/project/busulfan.yaml	Adds luna project YAML for Pharmpy example
vignettes/example-1-nm-pharmpy/luna_workflow_nm_pharmpy.R	Adds Pharmpy-backed luna workflow script
R/luna_run.R	Updates model execution to pass nmfe and attempt nmfe resolution via config
R/luna_load_project.R	Adjusts cache folder detection and cache reloading behavior
R/luna_check.R	Changes syntax check to use Pharmpy parsing + dataset load, updates messaging
R/get_luna_config.R	Fixes project config lookup to read YAML from cached project object
R/create_cache.R	Removes unused caching of Pharmpy settings
man/luna_check.Rd	Updates generated documentation to match new luna_check() behavior
.gitignore	Ignores data-raw/ and .claude artifacts

Files not reviewed (1)

• man/luna_check.Rd: Language not supported

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[roninsightrx]

Few minor things.

[roninsightrx]

is there a reason why this was removed? I don't know exactly if this was important, but not sure it can just be removed.

[JordanBrooks33]

Yes, this was actually an intentional choice (though maybe should have highlighted the issue to get your sense of best path proactively.,

The issue I found when building the vignettes was that since pharmr is the R interface to pharmpy, any user calling luna_load_project() (PsN and nlmixr2 users who never touch pharmpy) would fail at cache creation if pharmpy wasn't installed.

The fix: remove the eager pharmpy config read from create_cache(). Pharmpy is now only called from functions that actually need it (luna_run(), luna_check(), luna_info(), etc.), so PSN/nlmixr2 users can load projects just fine.

I think PsN workflows here still use pharmpy some, but may want detangle in future. This will also be helpful for building in FeRx so we are necessarily dependent on pharmpy dependency if not using their workflow.

[JordanBrooks33]

I will add a comment to the code for better traceability.

[roninsightrx]

lgtm