Automatically include all dependencies when precompiling

In precompile.jl, precompile-no-run.jl and
precompile-makie-post-processing.jl, we can just use the default of
create_sysimage(), which is to include all packages associated with the
project.

For precompile_dependencies.jl where we explicitly want to exclude
moment_kinetics from the system image, we do need to pass a list of
packages, but we can read them from the Project.toml instead of
maintaing a separate, hard-coded list in the script.

precompile-makie-post-processing.jl

@@ -5,14 +5,11 @@ Pkg.activate(".")
 
 using PackageCompiler
 
-packages = [:moment_kinetics, :PackageCompiler, :ArgParse, :CairoMakie, :Combinatorics, :DelimitedFiles, :FFTW, :Glob, :HDF5, :IJulia, :LinearAlgebra, :LsqFit, :MPI, :NaturalSort, :NCDatasets, :OrderedCollections, :Primes, :Roots, :SHA, :SpecialFunctions, :Statistics, :TOML, :TimerOutputs]
-
 # Create the sysimage 'makie_postproc.so' in the base moment_kinetics source directory
 # with both moment_kinetics and the dependencies listed above precompiled.
 # Warning: editing the code will not affect what runs when using this .so, you
 # need to re-precompile if you change anything.
-create_sysimage(packages;
-                sysimage_path="makie_postproc.so",
+create_sysimage(; sysimage_path="makie_postproc.so",
                 precompile_execution_file="util/precompile_makie_plots.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
                 sysimage_build_args=`-O3`, # Assume if we are precompiling we want an optimized, production build. No `--check-bounds=no` because Makie doesn' like it https://github.com/MakieOrg/Makie.jl/issues/3132

precompile-no-run.jl

@@ -5,19 +5,11 @@ Pkg.activate(".")
 
 using PackageCompiler
 
-using TOML
-project_file = TOML.parsefile("Project.toml")
-deps = (Symbol(d) for d ∈ keys(project_file["deps"]))
-
-packages = [:moment_kinetics, :PackageCompiler, deps...]
-println("precompling $packages")
-
 # Create the sysimage 'moment_kinetics.so' in the base moment_kinetics source directory
 # with both moment_kinetics and the dependencies listed above precompiled.
 # Warning: editing the code will not affect what runs when using this .so, you
 # need to re-precompile if you change anything.
-create_sysimage(packages;
-                sysimage_path="moment_kinetics.so",
+create_sysimage(; sysimage_path="moment_kinetics.so",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
                 sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build
                )

precompile.jl

@@ -5,14 +5,11 @@ Pkg.activate(".")
 
 using PackageCompiler
 
-packages = [:moment_kinetics, :PackageCompiler, :ArgParse, :Combinatorics, :DelimitedFiles, :FFTW, :Glob, :IJulia, :LinearAlgebra, :LsqFit, :MPI, :NaturalSort, :NCDatasets, :OrderedCollections, :Plots, :Primes, :Roots, :SHA, :SpecialFunctions, :Statistics, :TOML, :TimerOutputs]
-
 # Create the sysimage 'moment_kinetics.so' in the base moment_kinetics source directory
 # with both moment_kinetics and the dependencies listed above precompiled.
 # Warning: editing the code will not affect what runs when using this .so, you
 # need to re-precompile if you change anything.
-create_sysimage(packages;
-                sysimage_path="moment_kinetics.so",
+create_sysimage(; sysimage_path="moment_kinetics.so",
                 precompile_execution_file="util/precompile_run.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
                 sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build

precompile_dependencies.jl

@@ -5,12 +5,13 @@ Pkg.activate(".")
 
 using PackageCompiler
 
-packages = [:PackageCompiler, :ArgParse, :Combinatorics, :DelimitedFiles, :FFTW, :Glob, :IJulia, :LinearAlgebra, :LsqFit, :MPI, :NaturalSort, :NCDatasets, :OrderedCollections, :Plots, :Primes, :Roots, :SHA, :SpecialFunctions, :Statistics, :TOML, :TimerOutputs]
+using TOML
+project_file = TOML.parsefile("Project.toml")
+packages = collect(Symbol(d) for d ∈ keys(project_file["deps"]))
 
 # create the sysimage 'dependencies.so' in the base moment_kinetics source directory
 # with the above pre-compiled packages
-create_sysimage(packages;
-                sysimage_path="dependencies.so",
+create_sysimage(packages; sysimage_path="dependencies.so",
                 precompile_execution_file="util/precompile_run_short.jl",
                 include_transitive_dependencies=false, # This is needed to make MPI work, see https://github.com/JuliaParallel/MPI.jl/issues/518
                 sysimage_build_args=`-O3 --check-bounds=no`, # Assume if we are precompiling we want an optimized, production build