Merge dba0296939 into 3e602fa71f

Michal will update tex4ht ditribution... this will eventually make it to
texlive then to the CI server and it will break.  Adding his comment in
the code so we know.

book/book.tex

@@ -12,6 +12,7 @@
 \input{cover/cover.tex}
 \titlepage
 
+\frontmatter
 {%
 \hypersetup{hidelinks}
 \ifdefined\HCode\else\tableofcontents\fi
@@ -20,89 +21,43 @@
 \input{intro/preface}
 \input{intro/acknowledgments}
 
-\begin{flowchart}[!htb]
-\begin{center}
-  \input{figures/fig-dutch-oven-process.tex}
-  \caption[Baking process with a dutch oven]{A visualization of the baking
-      process using a dutch oven (DO). The dough is steamed for the first half
-      of the bake and then baked without cover for the second half of the
-      bake. The desired darkness and thickness of the crust depends on your
-      personal preference. Some bakers prefer a lighter crust and others a
-      darker.}%
-  \label{fig:dutch-oven-process}
-\end{center}
-\end{flowchart}
+\mainmatter
 
-At around  \qty{60}{\degreeCelsius} (\qty{140}{\degF}) the microbes in your
-dough start to die.  There are rumors that until this happens the microbes
-produce a lot of \ch{CO2}.
+\input{history/sourdough-history}
 
-% Does not work
-\begin{figure}[!htb]
-\begin{center}
-  \input{figures/fig-ethanol-oxidation.tex}
-  \caption[Acetic acid creation]{Oxygen is required to create acetic
-      acid~\cite{acetic+acid+production}.}%
-  \label{fig:ethanol-oxidation}
-\end{center}
-\end{figure}
+\input{basics/how-sourdough-works}
 
-%% Works
-%% Generate first with: cd figures && pdflatex fig-ethanol-oxidation-external.tex
-%\begin{figure}[!htb]
-%  \begin{center}
-%    \includegraphics{figures/fig-ethanol-oxidation-external.png}
-%    \caption[Acetic acid creation]{Oxygen is required to create acetic
-%        acid~\cite{acetic+acid+production}.}%
-%  \end{center}
-%\end{figure}
-%
-%% Does not work
-%\begin{figure}[!htb]
-%\begin{center}
-%  \input{figures/fig-life-planet-sourdough-timeline.tex}
-%  \caption[Sourdough microbiology timeline]{Timeline giberrish on website}%
-%\end{center}
-%\end{figure}
-%
-%% Works
-%% Generate first with: cd figures && pdflatex fig-life-planet-sourdough-timeline-external.pdf
-%\begin{figure}[!htb]
-%  \includegraphics{figures/fig-life-planet-sourdough-timeline-external.png}
-%  \caption[Sourdough microbiology timeline]{Timeline works embedded as png}%
-%\end{figure}
-%
-%\begin{figure}[!htb]
-%  \includegraphics[width=\textwidth]{baking-experiment-temperatures.png}
-%  \caption[Surface temperature for different steaming methods]{png file}
-%\end{figure}
+\input{sourdough-starter/sourdough-starter}
 
-\begin{figure}[!htb]
-  \includegraphics[width=\textwidth]{baking-process-steam.jpg}
-  \caption[Steam building with inverted tray]{jpg file}%
-      \label{flc:inverted-tray}
-\end{figure}
-If you're a hobby brewer, you'll know that it's important to keep your beer at
-certain temperatures to allow the different amylases to convert the contained
-starches into sugar~\cite{beer+amylase}.
-This test, called the \emph{Iodine Starch Test}, involves mixing iodine into
-a sample of your brew and checking the color.
+\input{sourdough-starter/sourdough-starter-types}
 
-% https://github.com/hendricius/the-sourdough-framework/issues/358
-\begin{table}[!htb]
-    \begin{center}
-        \input{tables/table-starter-usage-activity.tex}
-        \caption[Different oven types]{An overview of different oven types and
-        eheir different baking methods.}
-    \end{center}
-\end{table}
+\input{flour-types/flour-types}
 
-\begin{table}[!htb]
-    \begin{center}
-        \input{tables/table-oven-baking-overview.tex}
-        \caption[Different oven types]{An overview of different oven types and their
-            different baking methods.}
-    \end{center}
-\end{table}
+\input{bread-types/bread-types}
+
+\chapter{Wheat sourdough}%
+\label{chapter:wheat-sourdough}
+\input{wheat-sourdough/wheat-sourdough}
+
+\input{non-wheat-sourdough/non-wheat-sourdough}
+
+\input{mix-ins/mix-ins.tex}
+
+\input{baking/baking}
+
+\input{storing-bread/storing-bread}
+
+\chapter{Troubleshooting}
+\input{troubleshooting/misc}
+
+\backmatter
+\input{glossary/glossary}
+{%
+\hypersetup{hidelinks}
+\listofflowcharts
+\listoftables
+\listoffigures
+}
+\printbibliography
 
 \end{document}

book/figures/export_figures.sh

@@ -10,7 +10,6 @@ if [ "$#" -ne 1 ]; then
     done
 else
     target=figures/`basename $1 .png.pdf`.png
-    echo ${target}
     echo "Converting: " $1 " to: " ${target}
     convert -density 900 -trim $1 -quality 100 ${target}
 fi

book/figures/fig-dutch-oven-process.tex

@@ -1,8 +1,32 @@
 \begin{tikzpicture}[node distance = 3cm, auto]
   \node [start] (heat_oven) {Preheat DO to \qty{230}{\degreeCelsius} (\qty{446}{\degF}) for 30~minutes};
-  \node [block, right of=heat_oven] (remove_oven) {Remove DO from oven ° \text{°}  \textup{°}};
-  \node [decision, below of=heat_oven, node distance=4cm] (is_ready_check) {Core temperature \qty{92}{\degreeCelsius} (\qty{197}{\degF})?};
-  \node [block, right of=is_ready_check, node distance=4cm] (remove_do_lid) {%
-Jörg bäckt quasi zwei Haxenfüße vom Wildpony .Dès Noël, où un zéphyr haï me
-vêt};
+  \node [block, right of=heat_oven] (remove_oven) {Remove DO from oven };
+  \node [block, right of=remove_oven] (open_load_dough) {Open DO \& load your dough};
+  \node [block, right of=open_load_dough] (score) {Score your dough};
+  \node [block, right of=score] (spritz) {Spritz dough with water};
+  \node [block, below of=spritz] (close) {Close DO};
+  \node [block, left of=close] (back_oven) {Place DO back in oven};
+  \node [block, left of=back_oven] (bake) {Bake 30~minutes at \qty{230}{\degreeCelsius} (\qty{446}{\degF})};
+  \node [decision, below right= 5cm and -1 cm of heat_oven]  (is_ready_check)
+        {Core temperature \qty{92}{\degreeCelsius} (\qty{197}{\degF})?};
+  \node [block, below of=is_ready_check, node distance=4cm] (wait_5_minutes) {Wait\\ 5 minutes};
+  \node [block, right of=is_ready_check, node distance=4cm] (remove_do_lid) {Remove DO lid};
+  \node [decision, right of=remove_do_lid, node distance=3.5cm] (dark_enough_decision) {Crust color dark enough?};
+  \node [success, below of=dark_enough_decision, node distance=4cm] (finish_baking) {Bread is finished};
+  \node [block, right of=dark_enough_decision, node distance=3.5cm] (bake_5_more_minutes) {Bake another 5~minutes};
+  \path [line] (heat_oven) -- (remove_oven);
+  \path [line] (remove_oven) -- (open_load_dough);
+  \path [line] (open_load_dough) -- (score);
+  \path [line] (score) -- (spritz);
+  \path [line] (spritz) -- (close);
+  \path [line] (close) -- (back_oven);
+  \path [line] (back_oven) -- (bake);
+  \path [line] (bake.west) -- node{} ++(-2, 0) -| (is_ready_check.north);
+  \path [line] (is_ready_check) -- node{Yes} (remove_do_lid);
+  \path [line] (is_ready_check) -- node{No} (wait_5_minutes);
+  \path [line] (wait_5_minutes.west) -- node{} ++(-1.5, 0) |- (is_ready_check.west);
+  \path [line] (remove_do_lid) -- (dark_enough_decision);
+  \path [line] (dark_enough_decision) -- node{Yes} (finish_baking);
+  \path [line] (dark_enough_decision) -- node{No} (bake_5_more_minutes);
+  \path [line] (bake_5_more_minutes.east) -- node{} ++(1, 0) -- node{} ++(0, 2.3) -| (dark_enough_decision.north);
 \end{tikzpicture}

book/history/sourdough-history.tex

@@ -204,7 +204,7 @@ the process of alcoholic fermentation. He would prove that
 yeast microorganisms are the reason for alcoholic fermentation
 and not other chemical catalysts. He continued with his research and
 was the first person to isolate and grow pure yeast strains.
-Soon later in \num{1868} in the Fleischmann brothers Charles
+Soon later in \num{1868} the Fleischmann brothers Charles
 and Maximilian were the first to patent pure yeast strains
 for bread making. The yeasts offered
 were isolated from batches of sourdough. By \num{1879} the machinery was built

book/sourdough-starter/sourdough-starter.tex

@@ -1,6 +1,15 @@
 \chapter{Making a sourdough starter}%
 \label{chapter:sourdough-starter}
 \begin{quoting}
+
+\begin{figure}[!htb]
+  \centering
+  \includegraphics[width=\textwidth]{sourdough-starter-activity-indicators}
+  \caption[Very active sourdough]{A very active sourdough starter shown by the
+      bubbles in the dough.}%
+  \label{fig:sourdough-starter}
+\end{figure}
+
 In this chapter you will learn how to make your
 own sourdough starter, but before doing so you will
 quickly learn about baker's math. Don't worry,
@@ -12,6 +21,8 @@ your starter's readiness, as well as
 how to prepare your starter for long-term storage.
 \end{quoting}
 
+%\iffalse
+
 \section{Baker's math}%
 \label{section:bakers-math}
 
@@ -80,20 +91,23 @@ hungry family arrives. You are tasked with making pasta
 for \num{20} people. How would you calculate the amount of sauce
 you need? You go to the internet and check a recipe and then
 are completely lost when trying to scale it up.
+% \fi
 
 \section{The process of making a starter}
 
-\begin{figure}[!htb]
-  \centering
-  \includegraphics[width=\textwidth]{sourdough-starter-activity-indicators}
-  \caption[Very active sourdough]{A very active sourdough starter shown by the
-      bubbles in the dough.}%
-  \label{fig:sourdough-starter}
-\end{figure}
-
 Making a sourdough starter is very easy, all you need
 is a little bit of patience. It is in fact so easy that it can be summarized
-in a simple flowchart~\ref{fig:sourdough-starter-process} The flour you should
+in a simple flowchart~\ref{fig:sourdough-starter-process}.
+
+\begin{flowchart}[!htb]
+\centering
+  \input{figures/fig-starter-process.tex}
+  \caption[The full sourdough starter process]{The process of making a sourdough
+      starter from scratch.}%
+  \label{fig:sourdough-starter-process}
+\end{flowchart}
+
+The flour you should
 use to bootstrap your starter is ideally a whole flour.
 You could use whole-wheat, whole-rye, whole-spelt or
 any other flour you have. In fact gluten free flours such
@@ -131,14 +145,6 @@ not airtight. You still want some gas exchange to be possible.
 I~like to use a glass and place another
 inverted one on top.
 
-\begin{flowchart}[!htb]
-\centering
-  \input{figures/fig-starter-process.tex}
-  \caption[The full sourdough starter process]{The process of making a sourdough
-      starter from scratch.}%
-  \label{fig:sourdough-starter-process}
-\end{flowchart}
-
 Now an epic battle begins. In one study~\cite{yeasts+biocontrol+agent}
 scientists have identified more than \num{150}~different yeast species living
 on a single leaf of a plant.
@@ -147,6 +153,14 @@ the upper hand in this battle. Other pathogens such as mold
 are also being activated as we added water. Only the strongest
 most adaptable microorganisms will survive.
 
+\begin{figure}[!htb]
+  \includegraphics[width=\textwidth]{sourdough-starter-microbial-war-i}
+  \caption[Microbial warfare during sourdough early days]{A simple
+      visualization of the microbial warfare that happens during the early days of making of
+      a sourdough starter.}
+  \label{fig:sourdough-starter-microbial-war-i}
+\end{figure}
+
 By adding water to the
 flour the starches start to degrade. The seedling tries to
 sprout but it no longer can. Essential for this process is the
@@ -188,20 +202,6 @@ days my new starter seems to be quite alive already. This might
 be due to previous contamination of flour fermenting microbes in
 my kitchen.
 
-\begin{figure}[!htb]
-  \includegraphics[width=\textwidth]{sourdough-starter-microbial-war}
-  \caption[Microbial warfare during sourdough early days]{A simple
-      visualization of the microbial warfare that happens during the making of
-      a sourdough starter. The wild spores on the plant and flour become
-      activated the moment flour and water is mixed.  Only the most adapted
-      flour-fermenting microbes will survive. Because of unwanted microbial
-      fermentation it is advised to discard the feeding-leftovers of the first
-      days. The surviving yeast and bacteria continuously try to outcompete
-      each other for resources. New microbes have a hard time entering the
-      starter and are eliminated.}%
-  \label{fig:sourdough-starter-microbial-war}
-\end{figure}
-
 Wait for around 24~hours and observe what happens to your starter.
 You might see some early signs of fermentation already. Use your nose
 to smell the dough. Look for bubbles in the dough. Your dough
@@ -252,6 +252,14 @@ great option if the starter was accidentally depleted. A practical approach
 is to store all discard in a single jar in the fridge, adding new discard on
 top as needed and using it whenever required.}
 
+\begin{figure}[!htb]
+  \includegraphics[width=\textwidth]{sourdough-starter-microbial-war-ii}
+  \caption[Microbial warfare during sourdough later days]{A simple
+      visualization of the microbial warfare that happens during the later days of making of
+      a sourdough starter.}
+  \label{fig:sourdough-starter-microbial-war-ii}
+\end{figure}
+
 You should hopefully again see some bubbles, the starter increasing
 in size and/or the starter changing its smell. Some people give
 up after the second or third day, because the signs might no longer

book/tex4ebook.cfg

@@ -33,4 +33,13 @@
 }
 \makeatother
 
+% Warnig from Michal: Note that once you get the updated TeX Live with a new
+% `chemfig.4ht` file, you can remove this from the config file:
+%
+%```latex \pend:def\schemestart{\Picture+{}}
+%\append:def\CF_schemestop{\EndPicture} ```
+%
+%You could get an error otherwise, as there would be nested `\Picture+{}` and
+%`\EndPicture` commands.
+
 \EndPreamble