Load equilibrium data into summary IDS during parsing

.github/workflows/format_check.yml

@@ -16,8 +16,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.9.3]
-        julia-arch: [x86]
+        julia-version: [1.x]
+        julia-arch: [x64]
         os: [ubuntu-latest]
     steps:
       - uses: julia-actions/setup-julia@latest

.github/workflows/make_docs.yml

@@ -4,7 +4,7 @@ on:
     branches: ["master", "dev"]
     paths:
       - '.github/workflows/make_docs.yml'
-      - 'src/'
+      - 'src/**'
       - 'docs/**'
   push:
     branches:
@@ -13,7 +13,7 @@ on:
       - docs
     paths:
       - '.github/workflows/make_docs.yml'
-      - 'src/'
+      - 'src/**'
       - 'docs/**'
     tags: '*'
   workflow_dispatch:
@@ -25,7 +25,12 @@ jobs:
       contents: write
       statuses: write
     name: Documentation
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.x]
+        julia-arch: [x64]
+        os: [ubuntu-latest]
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
@@ -36,7 +41,7 @@ jobs:
         id: extract_branch
       - name: Install dependencies
         run: |
-          julia --project=docs/ -e 'using Pkg; Pkg.add(; url="https://github.com/ProjectTorreyPines/IMASDD.jl.git"); Pkg.add(; url="https://github.com/ProjectTorreyPines/GGDUtils.jl.git", rev="${{ steps.extract_branch.outputs.branch }}");  Pkg.add(; url="https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl.git", rev="${{ steps.extract_branch.outputs.branch }}"); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+          julia --project=docs/ -e 'using Pkg; Pkg.add(; url="https://github.com/ProjectTorreyPines/IMASDD.jl.git"); Pkg.add(; url="https://github.com/ProjectTorreyPines/Fortran90Namelists.jl.git"); Pkg.add(; url="https://github.com/ProjectTorreyPines/GGDUtils.jl.git", rev="${{ steps.extract_branch.outputs.branch }}");  Pkg.add(; url="https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl.git", rev="${{ steps.extract_branch.outputs.branch }}"); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yml

@@ -5,21 +5,21 @@ on:
     branches: ["master", "dev", "autotest"]
     paths:
       - '.github/workflows/test.yml'
-      - 'src/'
-      - 'test/'
+      - 'src/**'
+      - 'test/**'
   pull_request:
     branches: ["master", "dev"]
     paths:
       - '.github/workflows/test.yml'
-      - 'src/'
-      - 'test/'
+      - 'src/**'
+      - 'test/**'
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.9.3]
-        julia-arch: [x86]
+        julia-version: [1.x]
+        julia-arch: [x64]
         os: [ubuntu-latest]
     steps:
       - uses: julia-actions/setup-julia@latest
@@ -46,7 +46,7 @@ jobs:
         id: extract_branch
       - name: Install dependencies
         run: |
-          julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "GGDUtils", "SOLPS2IMAS", "EFIT"]); Pkg.add(; url="https://github.com/ProjectTorreyPines/IMASDD.jl.git"); Pkg.add(; url="https://github.com/ProjectTorreyPines/GGDUtils.jl.git", rev="${{ steps.extract_branch.outputs.branch }}");  Pkg.add(; url="https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl.git", rev="${{ steps.extract_branch.outputs.branch }}"); Pkg.add(; url="https://github.com/JuliaFusion/EFIT.jl.git")'
+          julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "Fortran90Namelists", "GGDUtils", "SOLPS2IMAS", "EFIT"]); Pkg.add(; url="https://github.com/ProjectTorreyPines/IMASDD.jl.git"); Pkg.add(; url="https://github.com/ProjectTorreyPines/Fortran90Namelists.jl.git"); Pkg.add(; url="https://github.com/ProjectTorreyPines/GGDUtils.jl.git", rev="${{ steps.extract_branch.outputs.branch }}");  Pkg.add(; url="https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl.git", rev="${{ steps.extract_branch.outputs.branch }}"); Pkg.add(; url="https://github.com/JuliaFusion/EFIT.jl.git")'
       - uses: julia-actions/julia-runtest@v1
       # Not set up yet
       # - uses: julia-actions/julia-processcoverage@v1

Project.toml

@@ -7,6 +7,7 @@ version = "1.0.0"
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 Contour = "d38c429a-6771-53c6-b99e-75d170b6e991"
 EFIT = "cda752c5-6b03-55a3-9e33-132a441b0c17"
+Fortran90Namelists = "8fb689aa-71ff-4044-8071-0cffc910b57d"
 GGDUtils = "b7b5e640-9b39-4803-84eb-376048795def"
 IMASDD = "06b86afa-9f21-11ec-2ef8-e51b8960cfc5"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"

makefile

@@ -15,14 +15,15 @@ env_with_cloned_repo r:
 	-git clone "git@github.com:ProjectTorreyPines/IMASDD.jl.git" ../IMASDD; \
 	git clone "git@github.com:ProjectTorreyPines/GGDUtils.jl.git" ../GGDUtils; \
 	git clone "git@github.com:ProjectTorreyPines/SOLPS2IMAS.jl.git" ../SOLPS2IMAS; \
-	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "GGDUtils", "SOLPS2IMAS", "EFIT"]); Pkg.develop(path="../IMASDD"); Pkg.develop(path="../GGDUtils"); Pkg.develop(path="../SOLPS2IMAS"); Pkg.add(url="git@github.com:JuliaFusion/EFIT.jl.git", rev="master"); Pkg.instantiate()'
+	git clone "git@github.com:ProjectTorreyPines/Fortran90Namelists.jl.git" ../Fortran90Namelists; \
+	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "Fortran90Namelists", "GGDUtils", "SOLPS2IMAS", "EFIT"]); Pkg.develop(path="../IMASDD"); Pkg.develop(path="../Fortran90Namelists"); Pkg.develop(path="../GGDUtils"); Pkg.develop(path="../SOLPS2IMAS"); Pkg.add(url="git@github.com:JuliaFusion/EFIT.jl.git", rev="master"); Pkg.instantiate()'
 
 env_with_git_url u:
 	@echo "Pulling sample files using dvc"
 	-dvc pull
 	@echo "Creating Julia environment with the git urls without creating local clones"
 	@echo "Generating Project.toml and Manifest.toml"
-	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "GGDUtils", "SOLPS2IMAS", "EFIT"]); Pkg.add(url="git@github.com:ProjectTorreyPines/IMASDD.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/GGDUtils.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/SOLPS2IMAS.jl.git", rev="master"); Pkg.add(url="git@github.com:JuliaFusion/EFIT.jl.git", rev="master"); Pkg.instantiate()'
+	julia --project=. -e 'using Pkg; Pkg.rm(["IMASDD", "Fortran90Namelists", "GGDUtils", "SOLPS2IMAS", "EFIT"]); Pkg.add(url="git@github.com:ProjectTorreyPines/IMASDD.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/Fortran90Namelists.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/GGDUtils.jl.git", rev="master"); Pkg.add(url="git@github.com:ProjectTorreyPines/SOLPS2IMAS.jl.git", rev="master"); Pkg.add(url="git@github.com:JuliaFusion/EFIT.jl.git", rev="master"); Pkg.instantiate()'
 
 clean:
 	@echo "Deleting Manifest.toml"

src/SD4SOLPS.jl

@@ -83,6 +83,7 @@ function geqdsk_to_imas!(
 )
     # https://github.com/JuliaFusion/EFIT.jl/blob/master/src/io.jl
     g = EFIT.readg(eqdsk_file; set_time=set_time)
+    gfilename = split(eqdsk_file, "/")[end]
     # Copying ideas from OMFIT: omfit/omfit_classes/omfit_eqdsk.py / to_omas()
     eq = dd.equilibrium
     if IMASDD.ismissing(eq, :time)
@@ -95,6 +96,8 @@ function geqdsk_to_imas!(
     eqt = eq.time_slice[time_index]
     eqt.time = g.time
 
+    source_for_summary = "gEQDSK file $gfilename loaded during SD4SOLPS workflow."
+
     # 0D
     gq = eqt.global_quantities
     gq.magnetic_axis.r = g.rmaxis
@@ -107,6 +110,17 @@ function geqdsk_to_imas!(
     b0[time_index] = g.bcentr
     eq.vacuum_toroidal_field.b0 = b0
 
+    if IMASDD.ismissing(dd.summary, :time)
+        dd.summary.time = Array{Float64}(undef, time_index)
+    end
+    dd.summary.time[time_index] = g.time
+    ip = Array{Float64}(undef, time_index)
+    ip[time_index] = g.current
+    dd.summary.global_quantities.ip.value = ip
+    dd.summary.global_quantities.r0.value = g.rcentr
+    dd.summary.global_quantities.b0.value = b0
+    summarize = ["ip", "r0", "b0"]
+
     # 1D
     p1 = eqt.profiles_1d
     nprof = length(g.pres)
@@ -141,6 +155,10 @@ function geqdsk_to_imas!(
         gq.q_min.rho_tor_norm = g.rhovn[qmin_idx]
     end
 
+    dd.summary.global_quantities.q_95.value = Array{Float64}(undef, time_index)
+    dd.summary.global_quantities.q_95.value[time_index] = gq.q_95
+    summarize = [summarize; "q_95"]
+
     # X-points
     xrs, xzs, xpsins, xseps = EFIT.x_points(g; within_limiter_only=false)
     if length(xrs) > 0
@@ -187,6 +205,11 @@ function geqdsk_to_imas!(
     resize!(limiter.unit, 1)
     limiter.unit[1].outline.r = g.rlim
     limiter.unit[1].outline.z = g.zlim
+
+    for s ∈ summarize
+        getproperty(dd.summary.global_quantities, Symbol(s)).source = source_for_summary
+    end
+
     return
 end
 

test/runtests.jl

@@ -10,6 +10,8 @@ using ArgParse: ArgParse
 using GGDUtils: GGDUtils, get_grid_subset
 
 function parse_commandline()
+    # Define newARGS = ["--yourflag"] to run only tests on your flags when including runtests.jl
+    localARGS = @isdefined(newARGS) ? newARGS : ARGS  # Thanks https://stackoverflow.com/a/44978474/6605826
     s = ArgParse.ArgParseSettings(; description="Run tests. Default is all tests.")
 
     ArgParse.add_arg_table!(s,
@@ -35,7 +37,7 @@ function parse_commandline()
         Dict(:help => "Test only preparation",
             :action => :store_true),
     )
-    args = ArgParse.parse_args(s)
+    args = ArgParse.parse_args(localARGS, s)
     if !any(values(args)) # If no flags are set, run all tests
         for k ∈ keys(args)
             args[k] = true
@@ -355,6 +357,10 @@ if args["geqdsk_to_imas"]
             @test gq.magnetic_axis.r > 0
             @test dd.equilibrium.vacuum_toroidal_field.r0 > 0
 
+            # Summary
+            @test dd.equilibrium.time[tslice] == dd.summary.time[tslice]
+            @test dd.summary.global_quantities.r0.value > 0
+
             # 1d
             p1 = eqt.profiles_1d
             nprof = length(p1.psi)