Name change: SOLPS2IMAS -> SOLPS2imas

All occurences of SOLPS2IMAS have been replaced with SOLPS2imas. Also, in anticipation of successful registration with Julia general registry, the installation instructions have been modified.
ProjectTorreyPines · Oct 3, 2024 · c1abdec · c1abdec
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diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,4 @@
-name = "SOLPS2IMAS"
+name = "SOLPS2imas"
 uuid = "09becab6-0636-4c23-a92a-2b3723265c31"
 authors = ["David Eldon <[email protected]>"]
 version = "1.0.3"

diff --git a/README.md b/README.md
@@ -1,38 +1,15 @@
-# SOLPS2IMAS.jl
+# SOLPS2imas.jl
 
-![Format Check](https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl/actions/workflows/format_check.yml/badge.svg)
-![Docs](https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl/actions/workflows/make_docs.yml/badge.svg)
-![Tests](https://github.com/ProjectTorreyPines/SOLPS2IMAS.jl/actions/workflows/test.yml/badge.svg)
+![Format Check](https://github.com/ProjectTorreyPines/SOLPS2imas.jl/actions/workflows/format_check.yml/badge.svg)
+![Docs](https://github.com/ProjectTorreyPines/SOLPS2imas.jl/actions/workflows/make_docs.yml/badge.svg)
+![Tests](https://github.com/ProjectTorreyPines/SOLPS2imas.jl/actions/workflows/test.yml/badge.svg)
 
 Utility for loading data from existing SOLPS runs, including custom data in b2time.nc,
-from native SOLPS output format into IMAS. For installation and usage instructions, see the [online documentation](https://projecttorreypines.github.io/SOLPS2IMAS.jl/stable). For documentation on under development branch, see [dev online documentation](https://projecttorreypines.github.io/SOLPS2IMAS.jl/dev).
+from native SOLPS output format into IMAS. For installation and usage instructions, see the [online documentation](https://projecttorreypines.github.io/SOLPS2imas.jl/stable). For documentation on under development branch, see [dev online documentation](https://projecttorreypines.github.io/SOLPS2imas.jl/dev).
 
 ## Installation
 
-SOLPS2IMAS is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). For installation:
-
 ```
 using Pkg
-Pkg.Registry.add(RegistrySpec(url="https://github.com/ProjectTorreyPines/FuseRegistry.jl.git"))
-Pkg.Registry.add("General")
-Pkg.add("SOLPS2IMAS")
-```
-
-## Running tests:
-
-Following code ensures it uses the enviroment described in ./Project.toml:
-
-```bash
-% julia --project test/runtests.jl
-Test Summary:          | Pass  Total  Time
-Test index conversions |    1      1  0.0s
-Test Summary:              | Pass  Total  Time
-Test file parsing in depth |    6      6  0.4s
-Test Summary:       | Pass  Total  Time
-Test read_b2_output |   19     19  1.9s
-solps2imas() time:  49.510687 seconds (154.81 M allocations: 10.512 GiB, 8.27% gc time, 96.47% compilation time)
-Test Summary:                        | Pass  Total   Time
-Test solps2imas() (overall workflow) |    4      4  50.4s
-Test Summary:                                   |  Pass  Total  Time
-Test triangular mesh generation from fort files | 23479  23479  3.7s
+Pkg.add("SOLPS2imas")
 ```
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,15 +1,15 @@
 using Documenter
-using SOLPS2IMAS
+using SOLPS2imas
 
 makedocs(;
-    modules=[SOLPS2IMAS],
+    modules=[SOLPS2imas],
     format=Documenter.HTML(),
-    sitename="SOLPS2IMAS",
+    sitename="SOLPS2imas",
     checkdocs=:none,
 )
 
 deploydocs(;
-    repo="github.com/ProjectTorreyPines/SOLPS2IMAS.jl.git",
+    repo="github.com/ProjectTorreyPines/SOLPS2imas.jl.git",
     target="build",
     branch="gh-pages",
     devbranch="master",

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,5 +1,5 @@
 
-# SOLPS2IMAS.jl 
+# SOLPS2imas.jl 
 
 ```@contents
 Pages = ["index.md"]
@@ -8,13 +8,11 @@ Depth = 5
 
 ## Installation
 
-SOLPS2IMAS is registered with public repository [FuseRegistry](https://github.com/ProjectTorreyPines/FuseRegistry.jl/). For installation:
+For installation:
 
 ```
 using Pkg
-Pkg.Registry.add(RegistrySpec(url="https://github.com/ProjectTorreyPines/FuseRegistry.jl.git"))
-Pkg.Registry.add("General")
-Pkg.add("SOLPS2IMAS")
+Pkg.add("SOLPS2imas")
 ```
 
 ## solps2imas
@@ -44,37 +42,37 @@ read_b2_boundary_parameters
 ## SOLPS Mesh Tools
 
 ```@docs
-SOLPS2IMAS.xytoc
-SOLPS2IMAS.ctoxy
-SOLPS2IMAS.data_xytoc
-SOLPS2IMAS.search_point
-SOLPS2IMAS.search_edges
-SOLPS2IMAS.distance_between_nodes
-SOLPS2IMAS.neighbour_inds
-SOLPS2IMAS.get_neighbour_inds
-SOLPS2IMAS.attach_neightbours!
+SOLPS2imas.xytoc
+SOLPS2imas.ctoxy
+SOLPS2imas.data_xytoc
+SOLPS2imas.search_point
+SOLPS2imas.search_edges
+SOLPS2imas.distance_between_nodes
+SOLPS2imas.neighbour_inds
+SOLPS2imas.get_neighbour_inds
+SOLPS2imas.attach_neightbours!
 ```
 
 ## Subset Identification Tools
 
 These functions provide a way to identify if a linear cell index in SOLPS notation belongs to a grid subset.
 
 ```@docs
-SOLPS2IMAS.in_core
-SOLPS2IMAS.in_sol
-SOLPS2IMAS.in_idr
-SOLPS2IMAS.in_odr
-SOLPS2IMAS.is_x_aligned
-SOLPS2IMAS.is_y_aligned
-SOLPS2IMAS.is_core_cut
-SOLPS2IMAS.is_pfr_cut
-SOLPS2IMAS.is_outer_throat
-SOLPS2IMAS.is_inner_throat
-SOLPS2IMAS.is_outer_midplane
-SOLPS2IMAS.is_inner_midplane
-SOLPS2IMAS.is_outer_target
-SOLPS2IMAS.is_inner_target
-SOLPS2IMAS.is_core_boundary
-SOLPS2IMAS.is_separatrix
-SOLPS2IMAS.get_xpoint_nodes
+SOLPS2imas.in_core
+SOLPS2imas.in_sol
+SOLPS2imas.in_idr
+SOLPS2imas.in_odr
+SOLPS2imas.is_x_aligned
+SOLPS2imas.is_y_aligned
+SOLPS2imas.is_core_cut
+SOLPS2imas.is_pfr_cut
+SOLPS2imas.is_outer_throat
+SOLPS2imas.is_inner_throat
+SOLPS2imas.is_outer_midplane
+SOLPS2imas.is_inner_midplane
+SOLPS2imas.is_outer_target
+SOLPS2imas.is_inner_target
+SOLPS2imas.is_core_boundary
+SOLPS2imas.is_separatrix
+SOLPS2imas.get_xpoint_nodes
 ```
diff --git a/src/SOLPS2IMAS.jl b/src/SOLPS2IMAS.jl
@@ -1,4 +1,4 @@
-module SOLPS2IMAS
+module SOLPS2imas
 
 using IMASdd: IMASdd
 using NCDatasets: Dataset, dimnames
@@ -795,4 +795,4 @@ function solps2imas(
     return ids
 end
 
-end # module SOLPS2IMAS
+end # module SOLPS2imas
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,9 +1,9 @@
-using SOLPS2IMAS: SOLPS2IMAS
+using SOLPS2imas: SOLPS2imas
 using Test
 using YAML: load_file as YAML_load_file
 using ArgParse: ArgParse
 using IMASdd: IMASdd
-import SOLPS2IMAS: get_grid_subset, read_b2_boundary_parameters
+import SOLPS2imas: get_grid_subset, read_b2_boundary_parameters
 
 allowed_rtol = 1e-4
 
@@ -52,9 +52,9 @@ if args["ind"]
         success = true
         for iy ∈ 1:ny
             for ix ∈ 1:nx
-                cxy = SOLPS2IMAS.ctoxy(SOLPS2IMAS.xytoc(ix, iy; nx=nx); nx=nx)
+                cxy = SOLPS2imas.ctoxy(SOLPS2imas.xytoc(ix, iy; nx=nx); nx=nx)
                 if cxy != (ix, iy)
-                    ic = SOLPS2IMAS.xytoc(ix, iy; nx=nx)
+                    ic = SOLPS2imas.xytoc(ix, iy; nx=nx)
                     println(
                         "ic: ",
                         ic,
@@ -71,9 +71,9 @@ if args["ind"]
         end
 
         for ic ∈ 1:nx*ny
-            cic = SOLPS2IMAS.xytoc(SOLPS2IMAS.ctoxy(ic; nx=nx)...; nx=nx)
+            cic = SOLPS2imas.xytoc(SOLPS2imas.ctoxy(ic; nx=nx)...; nx=nx)
             if cic != ic
-                ix, iy = SOLPS2IMAS.ctoxy(ic; nx=nx)
+                ix, iy = SOLPS2imas.ctoxy(ic; nx=nx)
                 println(
                     "ic: ",
                     ic,
@@ -99,7 +99,7 @@ if args["parser"]
         ]
         always_required_keys = ["b2mndr_ntim", "b2mndr_dtim"]
         for b2mn_sample ∈ b2mn_samples
-            b2mn_data = SOLPS2IMAS.read_b2mn_output(b2mn_sample)
+            b2mn_data = SOLPS2imas.read_b2mn_output(b2mn_sample)
             for ark ∈ always_required_keys
                 @test ark in keys(b2mn_data)
             end
@@ -111,7 +111,7 @@ end
 
 if args["b2"]
     @testset "Test read_b2_output" begin
-        contents = SOLPS2IMAS.read_b2_output("$(@__DIR__)/../samples/b2fstate")
+        contents = SOLPS2imas.read_b2_output("$(@__DIR__)/../samples/b2fstate")
         nt = contents["dim"]["time"]
         nx = contents["dim"]["nx"]
         ny = contents["dim"]["ny"]
@@ -121,7 +121,7 @@ if args["b2"]
         @test size(contents["data"]["fna"]) == (nt, ns, 2, ny, nx)
         @test size(contents["data"]["fhe"]) == (nt, ns, ny, nx)
 
-        contents = SOLPS2IMAS.read_b2_output("$(@__DIR__)/../samples/b2fgmtry")
+        contents = SOLPS2imas.read_b2_output("$(@__DIR__)/../samples/b2fgmtry")
         nt = contents["dim"]["time"]
         nxg = contents["dim"]["nx"]
         nyg = contents["dim"]["ny"]
@@ -130,7 +130,7 @@ if args["b2"]
         @test nyg == ny
         @test nxg == nx
 
-        contents = SOLPS2IMAS.read_b2_output("$(@__DIR__)/../samples/b2time_red.nc")
+        contents = SOLPS2imas.read_b2_output("$(@__DIR__)/../samples/b2time_red.nc")
         nx = contents["dim"]["nx"]
         ny = contents["dim"]["ny"]
         nybl = contents["dim"]["nybl"]
@@ -156,10 +156,10 @@ if args["solps2imas"]
         b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
         b2output = "$(@__DIR__)/../samples/b2time.nc"
         b2mn = "$(@__DIR__)/../samples/b2mn.dat"
-        b2t = SOLPS2IMAS.read_b2_output(b2output)
+        b2t = SOLPS2imas.read_b2_output(b2output)
         nx = b2t["dim"]["nx"]
         print("solps2imas() time: ")
-        @time dd = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn=b2mn, load_bb=false)
+        @time dd = SOLPS2imas.solps2imas(b2gmtry, b2output; b2mn=b2mn, load_bb=false)
         # Check time stamp 3 at iy=4, ix=5
         it = 3
         iy = 4
@@ -174,15 +174,15 @@ if args["solps2imas"]
         # as using a brute force definition which is too dependent
         # on the correct ordering of nodes in SOLPS data files.
         cut_keys = ["leftcut", "rightcut", "bottomcut", "topcut"]
-        gmtry = SOLPS2IMAS.read_b2_output(b2gmtry)
+        gmtry = SOLPS2imas.read_b2_output(b2gmtry)
         ny = gmtry["dim"]["ny"]
         cuts = Dict([(Symbol(key), gmtry["data"][key][1]) for key ∈ cut_keys])
         subset_pfrcut =
-            SOLPS2IMAS.get_grid_subset(dd.edge_profiles.grid_ggd[1], 8)
+            SOLPS2imas.get_grid_subset(dd.edge_profiles.grid_ggd[1], 8)
         subset_corebnd =
-            SOLPS2IMAS.get_grid_subset(dd.edge_profiles.grid_ggd[1], 15)
+            SOLPS2imas.get_grid_subset(dd.edge_profiles.grid_ggd[1], 15)
         subset_separatrix =
-            SOLPS2IMAS.get_grid_subset(dd.edge_profiles.grid_ggd[1], 16)
+            SOLPS2imas.get_grid_subset(dd.edge_profiles.grid_ggd[1], 16)
         cells = dd.edge_profiles.grid_ggd[1].space[1].objects_per_dimension[3].object
         subset_pfrcut_element_list =
             [ele.object[1].index for ele ∈ subset_pfrcut.element]
@@ -197,12 +197,12 @@ if args["solps2imas"]
             for ix ∈ 1:nx
                 for boundary_ind ∈ 1:4
                     edge_ind =
-                        cells[SOLPS2IMAS.xytoc(ix, iy; nx)].boundary[boundary_ind].index
-                    if SOLPS2IMAS.is_pfr_cut(; ix, iy, cells, nx, boundary_ind, cuts...)
+                        cells[SOLPS2imas.xytoc(ix, iy; nx)].boundary[boundary_ind].index
+                    if SOLPS2imas.is_pfr_cut(; ix, iy, cells, nx, boundary_ind, cuts...)
                         append!(brute_force_pfrcut_list, edge_ind)
-                    elseif SOLPS2IMAS.is_core_boundary(; ix, iy, boundary_ind, cuts...)
+                    elseif SOLPS2imas.is_core_boundary(; ix, iy, boundary_ind, cuts...)
                         append!(brute_force_corebnd_list, edge_ind)
-                    elseif SOLPS2IMAS.is_separatrix(; iy, boundary_ind, cuts...)
+                    elseif SOLPS2imas.is_separatrix(; iy, boundary_ind, cuts...)
                         append!(brute_force_separatrix_list, edge_ind)
                     end
                 end
@@ -213,7 +213,7 @@ if args["solps2imas"]
         @test Set(brute_force_separatrix_list) == Set(subset_separatrix_element_list)
 
         # Test loading of magnetic field data from b2fgmtry to equilibrium IDS
-        @time ddbb = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn=b2mn, load_bb=true)
+        @time ddbb = SOLPS2imas.solps2imas(b2gmtry, b2output; b2mn=b2mn, load_bb=true)
         btor = ddbb.equilibrium.time_slice[1].ggd[1].b_field_tor[1].values
         bz = ddbb.equilibrium.time_slice[1].ggd[1].b_field_z[1].values
         br = ddbb.equilibrium.time_slice[1].ggd[1].b_field_r[1].values
@@ -232,7 +232,7 @@ if args["fort"]
         b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
         b2output = "$(@__DIR__)/../samples/b2time.nc"
         b2mn = "$(@__DIR__)/../samples/b2mn.dat"
-        ids = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn=b2mn, fort=fort)
+        ids = SOLPS2imas.solps2imas(b2gmtry, b2output; b2mn=b2mn, fort=fort)
         grid_ggd = ids.edge_profiles.grid_ggd[1]
         space = grid_ggd.space[1]
 
@@ -253,7 +253,7 @@ if args["fort"]
         edges = grid_ggd.space[1].objects_per_dimension[2].object
         cells = grid_ggd.space[1].objects_per_dimension[3].object
 
-        gmtry = SOLPS2IMAS.read_b2_output(b2gmtry)
+        gmtry = SOLPS2imas.read_b2_output(b2gmtry)
         nx = gmtry["dim"]["nx"]
         ny = gmtry["dim"]["ny"]
         extra_nodes = 2 * (nx + ny)
@@ -276,7 +276,7 @@ if args["fort"]
                         cells[cells[tricell_ind].boundary[bnd_ind].neighbours[1]].nodes,
                     )
                     vert_no = Tuple(indexin(common_nodes, cells[tricell_ind].nodes))
-                    @test SOLPS2IMAS.chosen_tri_edge_order[bnd_ind][2] == vert_no
+                    @test SOLPS2imas.chosen_tri_edge_order[bnd_ind][2] == vert_no
                 end
             end
         end
@@ -287,7 +287,7 @@ if args["namelist"]
     @testset "Test parsing of namelists" begin
         # Basic parameters namelist parsing
         testfile = "$(@__DIR__)/../samples/b2.boundary.parameters"
-        boundary_params = SOLPS2IMAS.read_b2_boundary_parameters(testfile)
+        boundary_params = SOLPS2imas.read_b2_boundary_parameters(testfile)
         println(boundary_params)
         @test boundary_params["power_electrons"] > 0.0
         @test boundary_params["power_ions"] > 0.0
@@ -296,7 +296,7 @@ if args["namelist"]
 
         # Using parameters namelist to populate summary data
         ids = IMASdd.dd()
-        SOLPS2IMAS.load_summary_data!(ids, (testfile, "", "", ""))
+        SOLPS2imas.load_summary_data!(ids, (testfile, "", "", ""))
         @test !(ismissing(ids.summary.heating_current_drive.power_ec, :value))
     end
 end
diff --git a/test/speedtest.jl b/test/speedtest.jl
@@ -1,4 +1,4 @@
-using SOLPS2IMAS: SOLPS2IMAS
+using SOLPS2imas: SOLPS2imas
 
 println("-----------------------------------------------------------------------------")
 b2gmtry = "$(@__DIR__)/../samples/b2fgmtry"
@@ -9,6 +9,6 @@ fort = (
     "$(@__DIR__)/../samples/fort.34",
     "$(@__DIR__)/../samples/fort.35")
 print("solps2imas(b2gmtry, b2output; b2mn, fort) time with compilation: ")
-@time dd = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn, fort);
+@time dd = SOLPS2imas.solps2imas(b2gmtry, b2output; b2mn, fort);
 print("solps2imas(b2gmtry, b2output; b2mn, fort) time (true runtime): ")
-@time dd = SOLPS2IMAS.solps2imas(b2gmtry, b2output; b2mn, fort);
+@time dd = SOLPS2imas.solps2imas(b2gmtry, b2output; b2mn, fort);