Merge remote-tracking branch 'origin' into study_TGLFdb_update

Author: tomneiser

Project.toml

@@ -5,6 +5,7 @@ version = "0.9.2"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 BalanceOfPlantSurrogate = "001e48cb-5a1e-4e3c-a5d4-cdc3aa14f3de"
 BoundaryPlasmaModels = "2da5b0d0-c5e5-4f14-9caf-62d0020df410"
 CHEASE = "40781a8e-f1bb-11ec-24ef-0f6bc40c1567"
@@ -79,6 +80,7 @@ WeaveExt = "Weave"
 
 [compat]
 AbstractTrees = "0.4"
+ArgParse = "1.2.0"
 BalanceOfPlantSurrogate = "3"
 BoundaryPlasmaModels = "1"
 CHEASE = "1"

README.md

@@ -12,6 +12,7 @@ The figure below is a sneakpeak of the models implemented in FUSE:
 
 Here are some key resources for getting started with FUSE:
 
+* 📨 **[Sign up for more info](https://forms.gle/iQGYKWfgeNkw2fCZ7)**
 * 📚 **[Online documentation](https://fuse.help)**
 * 🎓 **[Intro tutorial](https://fuse.help/dev/tutorial.html)**
 * 🎤 **[Recent presentation](https://github.com/ProjectTorreyPines/FUSE_extra_files/raw/master/2025_D3D/SET_mar_2025.pdf)**

deploy/omega/base.lua

@@ -15,6 +15,12 @@ local base_depot = envdir .. "/.julia"
 setenv("FUSE_HOME", basedir)
 setenv("FUSE_ENVIRONMENT", fuse_env)
 
+-- Environment variables for data fetching
+setenv("FUSE_OMFIT_HOST", "localhost")
+setenv("FUSE_OMFIT_ROOT", "/fusion/projects/theory/fuse/d3d_data_fetching/OMFIT-source")
+setenv("FUSE_OMAS_ROOT", "/fusion/projects/theory/fuse/d3d_data_fetching/omas")
+
+
 -- We put the user depot first so their own packages get installed there,
 --   then the FUSE environment's depot after so it can find packages for the
 --   precompiled sysimage
@@ -33,4 +39,4 @@ setenv("JULIA_CPU_TARGET", "generic")
 prepend_path("JUPYTER_PATH", envdir .. "/.jupyter")
 
 prepend_path("PATH", basedir .. "/miniconda3/bin")
-prepend_path("PATH", envdir)
+prepend_path("PATH", envdir)

deploy/perlmutter/base.lua

@@ -30,6 +30,12 @@ else
    )
 end
 
+-- Environment variables for data fetching
+setenv("FUSE_OMFIT_HOST", "localhost")
+setenv("FUSE_OMFIT_ROOT", "/global/common/software/m3739/perlmutter/OMFIT-CAKE")
+setenv("FUSE_OMAS_ROOT", "/global/common/software/m3739/perlmutter/FUSE_OMAS")
+setenv("FUSE_RESULT_ARCHIVE", pathJoin("/global/cfs/cdirs/m3739/FUSE/d3d-time-dependent", os.getenv("USER")))
+
 -- The FUSE sysimage enviornment is the last place julia looks for packages
 --   when a user does `using <package>`, but this allows Julia to automatically
 --   find FUSE, Plots, and IJulia.

deploy/perlmutter/deploy.sh

@@ -2,6 +2,11 @@
 command -v module >/dev/null 2>&1 || source /usr/share/lmod/lmod/init/bash
 module load julia/1.11.4
 
+# Set up OMFIT and OMAS which is needed for the DIII-D study
+export FUSE_OMFIT_HOST="localhost"
+export FUSE_OMFIT_ROOT="/global/common/software/m3739/perlmutter/OMFIT-CAKE"
+export FUSE_OMAS_ROOT="/global/common/software/m3739/perlmutter/FUSE_OMAS"
+
 basedir="/global/common/software/m3739/perlmutter/fuse"
 
 fuse_env=`curl -s https://api.github.com/repos/ProjectTorreyPines/FUSE.jl/releases/latest | jq -r .name`

docs/src/cases_docs.jl

@@ -25,7 +25,7 @@ pushfirst!(
 CurrentModule = FUSE
 ```
 
-FUSE comes with a set of pre-cookes used cases.
+FUSE comes with a set of pre-cooked use cases.
 The `case_parameters(:use_case, ...)` method returns the `ini` and `act` parameters for that specific `use_case`.
 These `ini` and `act` can then be further customized before running a FUSE simulation.
 

docs/src/install.md

@@ -68,9 +68,9 @@ For installation start your Julia interpreter by typing `julia` at the terminal,
    !!! note
        The WebIO jupyter-lab extension is needed for the [`Interact.jl`](https://github.com/JuliaGizmos/Interact.jl?tab=readme-ov-file#usage) package to work.
 
-       Make sure WebIO is working with `jupyter labextension list`.
+       Make sure WebIO is working with `jupyter labextension list`. If it is working properly, you should see something like: webio-jupyterlab-provider v0.1.0 enabled OK (python, webio_jupyter_extension). This can also be checked with `jupyter nbextension list`, which should show something like: webio-jupyter-nbextension/nbextension  enabled.
 
-       If the extension has compatibility issues, consider installing an older verision of Jupyter (eg. `conda install jupyterlab=3.6.7`).
+       If the extension has compatibility issues, consider installing an older verision of Jupyter (eg. `conda install jupyterlab=3.6.7`). Also ensure that the WebIO and Interact packages are fully up-to-date, and restart the notebook session before testing that it works. Finally, it may be necessary to downgrade your system's version of Python - the recommended version for compatibility with Interact is 3.11.11. 
 
 1. Start a new Jupyter-lab session (this should open a web-browser page with Jupyter running)
 

knowledge/how_to_use_fuse.md

@@ -820,7 +820,7 @@ Studies use a `sty` (study parameters) structure similar to `act` (actor paramet
 
 ```julia
 # Get study parameters - similar to case_parameters but for studies
-sty, act = FUSE.study_parameters(:TGLFdb)
+sty = FUSE.study_parameters(:TGLFdb)
 
 # Common study parameters
 sty.server = "localhost"           # Distributed computing server  
@@ -841,7 +841,7 @@ sty.custom_tglf_models = ["sat3_em_d3d_azf-1_withnegD"]  # Custom TGLF models to
 using Distributed
 
 # 1. Setup study parameters
-sty, act = FUSE.study_parameters(:TGLFdb)
+sty = FUSE.study_parameters(:TGLFdb)
 sty.server = "localhost"
 sty.n_workers = 4
 sty.database_folder = "/path/to/database"
@@ -951,7 +951,7 @@ ylabel!("Probability")
 
 ```julia
 # Get study parameters for database generation
-sty, _ = FUSE.study_parameters(:DatabaseGenerator)
+sty = FUSE.study_parameters(:DatabaseGenerator)
 
 # Configure distributed computing
 sty.server = "localhost"
@@ -1120,7 +1120,7 @@ ini.requirements.coil_stress_margin = 0.1   # 10% stress margin
 
 ```julia
 # Get study parameters for multi-objective optimization
-sty, _ = FUSE.study_parameters(:MultiObjectiveOptimizer)
+sty = FUSE.study_parameters(:MultiObjectiveOptimizer)
 
 # Configure distributed computing
 sty.server = "localhost"  # Can be "saga", "omega", or cluster name

src/FUSE.jl

@@ -178,6 +178,7 @@ include("studies.jl")
 include(joinpath("studies", "database_generator.jl"))
 include(joinpath("studies", "multi_objective_optimization.jl"))
 include(joinpath("studies", "TGLF_database.jl"))
+include(joinpath("studies", "study_database.jl"))
 include(joinpath("studies", "experiment_postdictive.jl"))
 
 #= ========= =#