Merge branch 'master' into spatial_poissons_equation

.github/workflows/debug_checks.yml

@@ -15,14 +15,11 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: 'openmpi'
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
           arch: x64
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Debug test
         run: |
           # Hard code the debug level so that we can run without using the

.github/workflows/documentation.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Install dependencies
         run: |
           # Version 3.9.0 of matplotlib causes an error with PyPlot.jl, so pin

.github/workflows/examples.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Test examples
         run: |
           touch Project.toml

.github/workflows/longtest.yml

@@ -22,7 +22,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         with:
           project: 'moment_kinetics/'

.github/workflows/parallel_test.yml

@@ -14,14 +14,11 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: 'openmpi'
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
           arch: x64
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - run: |
           touch Project.toml
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
@@ -47,15 +44,11 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: 'openmpi'
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - run: |
-          export MPILIBPATH=$(find /opt/homebrew/Cellar/open-mpi/ -name libmpi.dylib)
           touch Project.toml
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
           julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'

.github/workflows/test.yml

@@ -21,7 +21,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
         with:
           project: 'moment_kinetics/'

.github/workflows/test_scripts.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v2
       - name: Test test_scripts
         run: |
           touch Project.toml

makie_post_processing/makie_post_processing/src/makie_post_processing.jl

@@ -675,39 +675,37 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
     animate_log_options_1d = Tuple(Symbol(:animate_log_vs_, d) for d ∈ one_dimension_combinations_no_t)
     animate_options_2d = Tuple(Symbol(:animate_vs_, d2, :_, d1) for (d1, d2) ∈ two_dimension_combinations_no_t)
     animate_log_options_2d = Tuple(Symbol(:animate_log_vs_, d2, :_, d1) for (d1, d2) ∈ two_dimension_combinations_no_t)
-    if dfns
-        for variable_name ∈ all_dfn_variables
-            set_defaults_and_check_section!(
-                this_input_dict, variable_name;
-                check_moments=false,
-                (o=>false for o ∈ plot_options_1d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ plot_log_options_1d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ plot_options_2d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ plot_log_options_2d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ animate_options_1d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ animate_log_options_1d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ animate_options_2d if String(o) ∉ keys(section_defaults))...,
-                (o=>false for o ∈ animate_log_options_2d if String(o) ∉ keys(section_defaults))...,
-                plot_unnorm_vs_vpa=false,
-                plot_unnorm_vs_vz=false,
-                plot_unnorm_vs_vpa_z=false,
-                plot_unnorm_vs_vz_z=false,
-                plot_log_unnorm_vs_vpa=false,
-                plot_log_unnorm_vs_vz=false,
-                plot_log_unnorm_vs_vpa_z=false,
-                plot_log_unnorm_vs_vz_z=false,
-                animate_unnorm_vs_vpa=false,
-                animate_unnorm_vs_vz=false,
-                animate_unnorm_vs_vpa_z=false,
-                animate_unnorm_vs_vz_z=false,
-                animate_log_unnorm_vs_vpa=false,
-                animate_log_unnorm_vs_vz=false,
-                animate_log_unnorm_vs_vpa_z=false,
-                animate_log_unnorm_vs_vz_z=false,
-                OrderedDict(Symbol(k)=>v for (k,v) ∈ section_defaults)...)
-            # Sort keys to make dict easier to read
-            sort!(this_input_dict[variable_name])
-        end
+    for variable_name ∈ all_dfn_variables
+        set_defaults_and_check_section!(
+            this_input_dict, variable_name;
+            check_moments=false,
+            (o=>false for o ∈ plot_options_1d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ plot_log_options_1d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ plot_options_2d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ plot_log_options_2d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ animate_options_1d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ animate_log_options_1d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ animate_options_2d if String(o) ∉ keys(section_defaults))...,
+            (o=>false for o ∈ animate_log_options_2d if String(o) ∉ keys(section_defaults))...,
+            plot_unnorm_vs_vpa=false,
+            plot_unnorm_vs_vz=false,
+            plot_unnorm_vs_vpa_z=false,
+            plot_unnorm_vs_vz_z=false,
+            plot_log_unnorm_vs_vpa=false,
+            plot_log_unnorm_vs_vz=false,
+            plot_log_unnorm_vs_vpa_z=false,
+            plot_log_unnorm_vs_vz_z=false,
+            animate_unnorm_vs_vpa=false,
+            animate_unnorm_vs_vz=false,
+            animate_unnorm_vs_vpa_z=false,
+            animate_unnorm_vs_vz_z=false,
+            animate_log_unnorm_vs_vpa=false,
+            animate_log_unnorm_vs_vz=false,
+            animate_log_unnorm_vs_vpa_z=false,
+            animate_log_unnorm_vs_vz_z=false,
+            OrderedDict(Symbol(k)=>v for (k,v) ∈ section_defaults)...)
+        # Sort keys to make dict easier to read
+        sort!(this_input_dict[variable_name])
     end
 
     set_defaults_and_check_section!(

moment_kinetics/test/restart_interpolation_tests.jl

@@ -104,8 +104,8 @@ function run_test(test_input, base, message, rtol, atol; tol_3V, args...)
         name = string(name, "_", (stringify_arg(k, v) for (k, v) in args)...)
     end
     # Make sure name is not too long
-    if length(name) > 90
-        name = name[1:90]
+    if length(name) > 80
+        name = name[1:80]
     end
     if parallel_io
         name *= "parallel-io"