[corrections]

Author: derpycode

muffin.pdf

@@ -2743,7 +2743,7 @@ \chapter{Marine ecosystems and dynamics}
 
 \hfill \break
 
-\noindent \textit{The following is based on workshop material originally devised by Ben Ward <b.a.ward@bristol.ac.uk>}
+\noindent \textit{The following is based on workshop material originally devised by Ben Ward <b.a.ward@soton.ac.uk>}
 
 \section*{Stuff to keep in mind\dots}
 \begin{itemize}
@@ -2754,7 +2754,7 @@ \section*{Stuff to keep in mind\dots}
 
 \section*{Background reading}
 \begin{itemize}
-\item \href{http://www.seao2.info/pubs/EcoGEnIE.pdf}{\textit{Ward et al.} [2017]} -- manuscript submitted to GMD.
+\item \href{https://doi.org/10.5194/gmd-2017-258}{\textit{Ward et al.} [2017]} -- Ward, B. A., Wilson, J. D., Death, R. M., Monteiro, F. M., Yool, A., and Ridgwell, A.: EcoGEnIE 0.1: Plankton Ecology in the cGENIE Earth system model, \textit{Geosci. Model Dev. Discuss.}, https://doi.org/10.5194/gmd-2017-258, 2017.
 \end{itemize}
 
 %------------------------------------------------
@@ -6655,7 +6655,7 @@ \section{HOW-TO ... macOS muffin}\label{how-to-macos}
 \noindent\rule{4cm}{0.1mm}
 \vspace{2mm}
 
-\noindent To install the \textbf{muffin} release of cGENIE on a Mac you will need a number of software packages, including Fortran, C++ and NetCDF. The best way to get hold of these is via a package management system, such as Homebrew (\href{}{https://brew.sh}) or MacPorts (\href{}{https://www.macports.org}). This guide is based on Homebrew, because it is slightly more user friendly than MacPorts, and is kept more up-to-date with changes in the Apple operating system. (If you are already a MacPorts user, please see Appendix~A.)
+\noindent To install the \textbf{muffin} release of cGENIE on a Mac you will need a number of software packages, including Fortran, C++ and NetCDF. The best way to get hold of these is via a package management system, such as Homebrew (\href{}{https://brew.sh}) or MacPorts (\href{}{https://www.macports.org}). This guide is based on Homebrew, because it is slightly more user friendly than MacPorts, and is kept more up-to-date with changes in the Apple operating system. (If you are already a MacPorts user, please see Section \ref{how-to-macports}).
 
 \begin{enumerate}
 
@@ -6665,9 +6665,12 @@ \section{HOW-TO ... macOS muffin}\label{how-to-macos}
 
 % I think XCode automatically comes with Homebrew and command line tools enabled
 \item Get Homebrew by pasting the following at the terminal command line...
-\\ \texttt{/usr/bin/ruby -e "\$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"}
-\\ Next, type `\texttt{brew doctor}'. This should tell you ``\texttt{your system is ready to brew}''. If it doesn't, see Appendix~B. 
-
+\\ \texttt{/usr/bin/ruby -e 
+\small
+\\"\$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+\normalsize}
+(\uline{all one line})
+\\Next, type `\texttt{brew doctor}'. This should tell you ``\texttt{your system is ready to brew}''. If it doesn't, see Section \ref{how-to-macports-errors}. 
 \item Install Fortran, C++, NetCDF and some other useful libraries at the command line (using Homebrew) as follows:
 
 % brew tap homebrew/science % deprecated in homebrew
@@ -6692,7 +6695,7 @@ \section{HOW-TO ... macOS muffin}\label{how-to-macos}
 \end{verbatim}\vspace{-5pt}
 (This was from my most recent install, with version \texttt{4.6.1\_2})
 
-\item Adjust the cGENIE environment variables for your machine and netcdf installation by editing
+\item Finaly, adjust the cGENIE environment variables for your machine and netcdf installation by editing
 \\\texttt{cgenie.muffin/genie-main/user.mak}, setting:
 \vspace{-5pt}\begin{verbatim}
 MACHINE=OSX
@@ -6703,18 +6706,6 @@ \section{HOW-TO ... macOS muffin}\label{how-to-macos}
 \end{verbatim} \vspace{-5pt}
 to reflect your netcdf path (Step 5).
 
-\item Finally, in cgenie.muffin/genie-main/makefile.arc, comment out:
-\vspace{-5pt}\begin{verbatim}
-#NETCDF=
-   $(LIB_SEARCH_FLAG)$(PATH_QUOTE)$(NETCDF_DIR)/lib$(PATH_QUOTE) $(LIB_FLAG)$(NETCDF_NAME)
-\end{verbatim}\vspace{-5pt}
-and un-comment 
-\vspace{-5pt}\begin{verbatim}
-NETCDF_NAMEF=$(NETCDF_NAME)f
-NETCDF=$(LIB_SEARCH_FLAG)$(PATH_QUOTE)$(NETCDF_DIR)/lib$(PATH_QUOTE) 
-   $(LIB_FLAG)$(NETCDF_NAME) $(LIB_FLAG)$(NETCDF_NAME) $(LIB_FLAG)$(NETCDF_NAMEF)
-\end{verbatim}
-
 \item To test the code installation -- change directory to \texttt{cgenie.muffin/genie-main} and type:
 \vspace{-5pt}\begin{verbatim}
 make testbiogem
@@ -6728,11 +6719,9 @@ \section{HOW-TO ... macOS muffin}\label{how-to-macos}
 
 \noindent That is is for the basic installation.
 
-\newpage
-
 %------------------------------------------------
 %
-\subsection*{MacPorts}
+\subsection{MacPorts}\label{how-to-macports}
 
 You are here because you have already installed MacPorts, presumably by following the instructions here:
 \\\href{https://www.macports.org/install.php}{https://www.macports.org/install.php}.
@@ -6798,7 +6787,7 @@ \subsubsection*{Option 2: Install required packages through MacPorts and precomp
 
 %------------------------------------------------
 %
-\subsection*{Errors}
+\subsection{Errors}\label{how-to-macports-errors}
 
 Errors identified by `\texttt{brew doctor}' are most likely associated with some incompatible files in your software libraries, perhaps from a previous installation of MacPorts. Try to follow the suggestions given to you by `\texttt{brew doctor}', deleting any problematic files (using \texttt{sudo rm} to overcome any permission issues). Note that you may wish to do a system backup first.
 
@@ -6808,6 +6797,19 @@ \subsection*{Errors}
 
 %------------------------------------------------
 
+\section{HOW-TO ... Windows(!) muffin}\label{how-to-redhat}
+\vspace{2mm}
+
+%------------------------------------------------
+
+TBA ...
+
+%------------------------------------------------
+
+\newpage
+
+%------------------------------------------------
+
 \section{HOW-TO ... (general)}\label{how-to-1}
 \vspace{2mm}