Chloride-only formatting and example notebook

README.md

@@ -23,7 +23,7 @@ After installing, just type `using CorePore` to use.
 
 ## Usage
 
-The primary functionality of this package is hosted in the function `porewatermetropolis`. Please read the documentation for its full functionality and the underlying forward models. The example below will give you a quick start:
+The primary functionality of this package is hosted in the function `porewatermetropolis`. Please read the documentation for its full functionality and the underlying forward models. The example below (also available as notebook `example.ipynb`) will give you a quick start:
 
 ```julia
 using CorePore

example.ipynb

@@ -0,0 +1,57 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using CorePore"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Proposal(20.0, 1.0e-5, 0.0001, 0.1, 0.1, 10.0, 10.0, 1.0)"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "p = Proposal(5320., 1e-4,1e-3,3.5, 4.2, 1000, deepbonney()...)\n",
+    "jumpsize = Proposal(20., .1e-4, .1e-3, .1, .1,10, 10, 1.)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "chains = porewatermetropolis(p, jumpsize, andrill2a(); burnin=100, chainsteps=100, k=Constants(), seawater=mcmurdosound(), climate=LR04(), onlychloride=true)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.10.4",
+   "language": "julia",
+   "name": "julia-1.10"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.10.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

src/metropolis.jl

@@ -104,7 +104,9 @@ function porewatermetropolis(p::Proposal, jumpsigma::Proposal, prior::CoreData;
             end
         end
         explore = explore_
-        @warn "Chloride-only mode (onlychloride=true): MCMC will not explore :basalO (= $(p.basalO))"
+        printstyled("Chloride-only mode (onlychloride=true): ", bold=true,color=:cyan)
+        println(" MCMC will not explore :basalO (= $(p.basalO))\n\n")
+        flush(stdout)
         chlorporewaterhistory!
     else
         porewaterhistory!