rename scripts/ to sysimg/

Author: tfiers

ReadMe.md

@@ -15,7 +15,7 @@ Directories:
 - [`pkg/`](pkg) contains Julia packages, which define functions and data types that are reused in multiple notebooks.
 - [`web/`](web) contains config and code to build the [website](https://tfiers.github.io/phd) 
   where the notebooks are hosted (using [JupyterBook](https://jupyterbook.org/)).
-- [`scripts/`](scripts) contains scripts for updating dependencies and speeding up their imports.
+- [`sysimg/`](sysimg) contains instructions for building a custom Julia [system image](https://julialang.github.io/PackageCompiler.jl/dev/sysimages.html). It is not necessary to run the notebooks, but it speeds up package imports and first function calls.
 
 
 Files:
@@ -73,7 +73,7 @@ To reproduce results, *i.e.* to succesfully run one of the notebooks:
      which is included in the repository for the purpose of reproducibility.
    - Downloading and installing all these packages will take a while.
    - If you want to instead use newer versions of dependencies (maybe because you
-     already have them downloaded), run `julia scripts/update.jl` in the terminal, 
+     already have them downloaded), run `julia update.jl` in the terminal, 
      instead of `instantiate`.
    </details>
 

nb/2022-09-15__Two-pass_conntest_ptp-then-cor.ipynb

@@ -30,6 +30,8 @@ using VoltoMapSim
 
 # ## Params
 
+using ProfileView
+
 p = get_params(
     duration = 10minutes,
     p_conn = 0.04,
@@ -44,10 +46,16 @@ p = get_params(
 
 # ## Run sim
 
-s = cached(sim, [p.sim]);
+@time s = cached(sim, [p.sim]);
+
+@profview s = augment(s, p);
 
-s = augment(s, p);
+using PyPlot
+using VoltoMapSim.Plot
 
-plotSTA(23=>1,s,p);
+@profview plotSTA(1=>1,s,p);
+plotSTA(2=>2,s,p);
+plotSTA(801=>801,s,p);
+plotSTA(802=>802,s,p);
 
 

nb/2022-09-15__Two-pass_conntest_ptp-then-cor.jl

@@ -0,0 +1,30 @@
+# For use with PackageCompiler.jl, to generate a custom "system image", like here:
+# https://julialang.github.io/PackageCompiler.jl/stable/examples/plots.html.
+#
+# The goal is having to wait less long for package imports and first function calls in a
+# fresh Julia session.
+#
+# Commands to run, in the repo root:
+#=
+using PackageCompiler
+pkgs = [:Revise, :PyCall, :IJulia, :PyPlot, :DataFrames, :ComponentArrays]
+sysimage_path             = "sysimg/mysys.dll"
+precompile_execution_file = "sysimg/to_precompile.jl"
+script                    = "sysimg/pyplot_delay_init.jl"
+create_sysimage(pkgs; sysimage_path, precompile_execution_file, script)
+=#
+# To use this system image:
+# - On the command line: `julia --sysimg=sysimg/mysis.dll`
+# - As a 'kernel' in Jupyter:
+#     https://julialang.github.io/IJulia.jl/stable/manual/installation/#Installing-additional-Julia-kernels
+#   Make sure to also add the flag "--project=@.".
+#   For me, the generated kernel definition file is located at:
+#     C:\Users\tfiers\AppData\Roaming\jupyter\kernels\julia-preloaded-1.7\kernel.json
+
+using PyPlot, DataFrames, ComponentArrays
+
+df = DataFrame([(a=1, b=2), (a=2, b=2)])
+cv = ComponentVector(a=3, b=8)
+
+fig, ax = plt.subplots()
+ax.plot(df.a, collect(cv))