Coll_krook heat flux closure, updated PI_controller for density, and added PI_controller for temperature

docs/src/post_processing_notes.md

@@ -19,6 +19,11 @@ julia> makie_post_process("runs/example-run1/", "runs/example-run2/", "runs/exam
 What this function does is controlled by the settings in an input file, by
 default `post_processing_input.toml`.
 
+!!! note "Example input file"
+    You can generate an example input file, with all the options shown (with
+    their default values) but commented out, by running
+    `makie_post_processing.generate_example_input_file()`.
+
 To run from the command line
 ```julia
 julia --project run_makie_post_processing.jl dir1 [dir2 [dir3 ...]]

machines/shared/add_dependencies_to_project.jl

@@ -151,31 +151,38 @@ end
 
 println("\n** Setting up to use system HDF5\n")
 
+function get_hdf5_lib_names(dirname)
+    if Sys.isapple()
+        libhdf5_name = joinpath(dirname, "libhdf5.dylib")
+        libhdf5_hl_name = joinpath(dirname, "libhdf5_hl.dylib")
+    else
+        libhdf5_name = joinpath(dirname, "libhdf5.so")
+        libhdf5_hl_name = joinpath(dirname, "libhdf5_hl.so")
+    end
+    return libhdf5_name, libhdf5_hl_name
+end
+
 if machine_settings["hdf5_library_setting"] == "system"
     hdf5_dir = joinpath(ENV["HDF5_DIR"], "lib") # system hdf5
     using HDF5
-    HDF5.API.set_libraries!(joinpath(hdf5_dir, "libhdf5.so"),
-                            joinpath(hdf5_dir, "libhdf5_hl.so"))
+    HDF5.API.set_libraries!(get_hdf5_lib_names(hdf5_dir)...)
 elseif machine_settings["hdf5_library_setting"] == "download"
     artifact_dir = joinpath(repo_dir, "machines", "artifacts")
     hdf5_dir = joinpath(artifact_dir, "hdf5-build", "lib")
     using HDF5
-    HDF5.API.set_libraries!(joinpath(hdf5_dir, "libhdf5.so"),
-                            joinpath(hdf5_dir, "libhdf5_hl.so"))
+    HDF5.API.set_libraries!(get_hdf5_lib_names(hdf5_dir)...)
 elseif machine_settings["hdf5_library_setting"] == "prompt"
     # Prompt user to select what HDF5 to use
     if mk_preferences["build_hdf5"] == "y"
         local_hdf5_install_dir = joinpath("machines", "artifacts", "hdf5-build", "lib")
         local_hdf5_install_dir = realpath(local_hdf5_install_dir)
         # We have downloaded and compiled HDF5, so link that
         hdf5_dir = local_hdf5_install_dir
-        hdf5_lib = joinpath(local_hdf5_install_dir, "libhdf5.so")
-        hdf5_lib_hl = joinpath(local_hdf5_install_dir, "libhdf5_hl.so")
+        hdf5_lib, hdf5_lib_hl = get_hdf5_lib_names(hdf5_dir)
     elseif !prompt_for_lib_paths
         hdf5_dir = mk_preferences["hdf5_dir"]
         if hdf5_dir != "default"
-            hdf5_lib = joinpath(hdf5_dir, "libhdf5.so")
-            hdf5_lib_hl = joinpath(hdf5_dir, "libhdf5_hl.so")
+            hdf5_lib, hdf5_lib_hl = get_hdf5_lib_names(hdf5_dir)
         end
     else
         println("\n** Setting up to use system HDF5\n")
@@ -206,8 +213,7 @@ elseif machine_settings["hdf5_library_setting"] == "prompt"
             if isdir(hdf5_dir)
                 hdf5_dir = realpath(hdf5_dir)
             end
-            hdf5_lib = joinpath(hdf5_dir, "libhdf5.so")
-            hdf5_lib_hl = joinpath(hdf5_dir, "libhdf5_hl.so")
+            hdf5_lib, hdf5_lib_hl = get_hdf5_lib_names(hdf5_dir)
             if isfile(hdf5_lib) && isfile(hdf5_lib_hl)
                 break
             else

machines/shared/machine_setup_stage_two.jl

@@ -11,7 +11,7 @@ batch_system = mk_preferences["batch_system"]
 if mk_preferences["use_plots"] == "y"
     python_venv_path = joinpath(repo_dir, "machines", "artifacts", "mk_venv")
     activate_path = joinpath(python_venv_path, "bin", "activate")
-    run(`bash -c "python -m venv --system-site-packages $python_venv_path; source $activate_path; PYTHONNOUSERSITE=1 pip install matplotlib"`)
+    run(`bash -c "/usr/bin/env python3 -m venv --system-site-packages $python_venv_path; source $activate_path; PYTHONNOUSERSITE=1 pip install matplotlib"`)
     if batch_system
         open("julia.env", "a") do io
             println(io, "source $activate_path")

makie_post_processing/makie_post_processing/src/makie_post_processing.jl

@@ -826,7 +826,7 @@ function _setup_single_input!(this_input_dict::OrderedDict{String,Any},
         include_patterns=String[],
         exclude_patterns=String[],
         ranks=mk_int[],
-        figsize=(600,800)
+        figsize=[600,800]
        )
 
     # We allow top-level options in the post-processing input file
@@ -8492,7 +8492,7 @@ function timing_data(run_info::Tuple; plot_prefix=nothing, threshold=nothing,
 
     if figsize === nothing
         if input !== nothing
-            figsize = input.figsize
+            figsize = Tuple(input.figsize)
         else
             figsize = (600,800)
         end
@@ -8602,7 +8602,7 @@ function timing_data(run_info; plot_prefix=nothing, threshold=nothing,
 
     if figsize === nothing
         if input !== nothing
-            figsize = input.figsize
+            figsize = Tuple(input.figsize)
         else
             figsize = (600,800)
         end