Merge branch 'main' into 225-ebook-situation

.github/workflows/release-book.yml

@@ -32,7 +32,7 @@ jobs:
           options: -v ${{ github.workspace }}:/app
           run: |
             cd /app/book
-            make bake
+            make -j bake
       - name: Release baked book to S3
         uses: shallwefootball/s3-upload-action@master
         with:

.github/workflows/validate-book-build.yml

@@ -29,4 +29,4 @@ jobs:
           options: -v ${{ github.workspace }}:/app
           run: |
             cd /app/book
-            make -j build_pdf build_ebook
+            make -j build_serif_pdf build_ebook

.gitignore

@@ -12,53 +12,31 @@
 *.run.xml
 *.html
 *.dlog
+*.bak
+*.opf
 book/book.out
 .vscode/
-book/book.synctex*
-book/tikz-cache/*
 book/bookch*
-book/content.opf
-book/output-epub
 book/figures/*.png
 book/figures/*.pdf
 book/figures/*.in
-book/tables/*.png
-book/tables/*.pdf
-book/release/*
 book/book*.4ct
 book/book*.4tc
-book/book*.aux
-book/book*.bbl
-book/book*.bcf
-book/book*.blg
 book/book*.css
 book/book*.dvi
-book/book*.html
 book/book*.idv
 book/book*.lg
-book/book*.log
-book/book*.mobi
-book/book*.azw3
-book/book*.epub
 book/book*.ncx
 book/book*.out
-book/book*.pdf
-book/book*.run.xml
 book/book*.tmp
-book/book*.toc
 book/book*.xref
-book/book*.html
 book/book*.svg
-book/book-epub/
+# Directories created during build
-book/book-mobi/
+book/book_sans_serif/*
-book/book-azw3/
+book/book_serif/*
-*.bak
-book_sans_serif/
-book_serif/
-release_sans_serif/
-book/book_sans_serif-epub/
 book/static_website_html/*
-book/bw-book-epub/*
-epub/
-*.opf
 website/static_website_html/*
+book/epub/
+book/book-epub/
+book/bw-book-epub/*
+book/release/*

README.md

@@ -33,7 +33,7 @@ make
 Then you can check out the file `book/book.pdf`
 
 If you want to 🍞 bake all the versions including ebook variants (.pdf, .epub
-in colour or size optimized Black&White), run:
+in colour and size optimized Black&White), run:
 
 ```console
 make bake
@@ -43,8 +43,9 @@ You can check the files in  the folder `book/release/`
 
 ## 🍞 Baking the book locally (LaTeX)
 
-Make sure you have `biber` and `latexmk` installed. Refer to your system's
+Make sure you have `biber`, `latexmk` and ``ImageMagick`` installed. Refer to
-installation instructions for LaTeX. To create the serif .pdf format, run:
+your system's installation instructions for LaTeX. To create the serif .pdf
+format, run:
 
 ```console
 cd book/
@@ -52,11 +53,11 @@ make
 ```
 
 If you want to 🍞 bake all the versions including ebook variants (.pdf, .epub
-in colour or size optimized Black&White), run:
+in colour and size optimized Black&White), run:
 
 ```console
 cd book/
-make bake
+make -j bake
 ```
 
 You can check the files in the folder `book/release/`
@@ -74,16 +75,16 @@ The below versions are automatically built on every push to the `main` branch.
 * [Download compiled .pdf version](https://www.the-bread-code.io/book.pdf)
 * [Download compiled .epub version](https://www.the-bread-code.io/book.epub)
 
-There's an additional enhanced accessibility version using a sans serif font:
+There's an additional enhanced accessibility version using a sans-serif font:
 
-* [Download compiled .pdf version](https://www.the-bread-code.io/book-sans-serif.pdf)
+* [Download compiled sans-serif .pdf version](https://www.the-bread-code.io/book-sans-serif.pdf)
 
-An additional black and white ebook is provided with a greatly reduced file size. This
+An additional black and white ebook is provided with a greatly reduced file
-shrinks the book from more than 50MB down to ~5MB:
+size. This shrinks the book from more than 50MB down to ~5MB:
 
-* [Download compiled .epub version](https://www.the-bread-code.io/bw-book.epub)
+* [Download compiled B&W .epub version](https://www.the-bread-code.io/bw-book.epub)
 
-## Online HTML version (WIP)
+## Online HTML version
 
 Head over to [https://www.the-sourdough-framework.com](https://www.the-sourdough-framework.com)
 

book/book_sans_serif.tex

@@ -1,4 +1,2 @@
 \def\isaccessible{1}
-% We have to use a symlink to book.tex to prevent tex4ebook to load book.ht4
+\input{book.tex}
-% before loading any other package and create conflicts 
-\input{sourdough_book.tex}

book/figures/fig-life-planet-sourdough-timeline.tex

@@ -0,0 +1,70 @@
+\begin{tikzpicture}
+  % Draw horizontal line
+  \draw[line width=1pt] (0,0) -- (\textwidth,0);
+
+  % Define the width of each segment
+  \pgfmathsetlengthmacro{\segmentwidth}{\textwidth/12}
+
+  % Draw lines for the events, higher up so that they don't overflow the text
+  % Placing the lines has been a bit manual work of trying different values
+  % Maritime bacteria.
+
+  \draw[line width=1pt] (2.8*\segmentwidth,1) -- (2.8*\segmentwidth,0.2);
+  % Eukaryotes
+  \draw[line width=1pt] (5.8*\segmentwidth,1.5) -- (5.8*\segmentwidth,0.2);
+  % First bacteria on land
+  \draw[line width=1pt] (9.1*\segmentwidth,-1.25) -- (9.1*\segmentwidth,-0.2);
+  % Maritime fungi ancestors
+  \draw[line width=1pt] (9.5*\segmentwidth,-2) -- (9.5*\segmentwidth,-0.2);
+  % Fungi on land
+  \draw[line width=1pt] (10.8*\segmentwidth,-2.75) -- (10.8*\segmentwidth,-0.2);
+  % Yeasts on land
+  \draw[line width=1pt] (11.1*\segmentwidth,-3.0) -- (11.1*\segmentwidth,-0.2);
+  % First dinosaurs
+  \draw[line width=1pt] (11.4*\segmentwidth,0.5) -- (11.4*\segmentwidth,0.2);
+  % Pangea begins to rift apart
+  \draw[line width=1pt] (11.6*\segmentwidth,1) -- (11.6*\segmentwidth,0.2);
+  % Dinosaur extinction
+  \draw[line width=1pt] (11.9*\segmentwidth,1.5) -- (11.9*\segmentwidth,0.2);
+
+  % Special lines for december events since they are so close togehter
+  \draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (12.0*\segmentwidth,0.2);  % Main branch
+  \draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (11.75*\segmentwidth,2.5); % Branch to first humans
+  \draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (11.75*\segmentwidth,3.0); % Branch to Jordan
+  \draw[line width=1pt] (12.0*\segmentwidth,3.0) -- (11.75*\segmentwidth,3.5); % Branch to Pasteur
+
+  % Draw months and month separators
+  \foreach \i/\month in {0/Jan, 1/Feb, 2/Mar, 3/Apr, 4/May, 5/Jun, 6/Jul, 7/Aug, 8/Sep, 9/Oct, 10/Nov, 11/Dec} {
+      % Separators
+      \draw[line width=1pt] (\i*\segmentwidth,0.1) -- (\i*\segmentwidth,-0.1);
+      % Month names
+      \node[timeline_event, below] at ({(\i+0.5)*\segmentwidth},-0.1) {\month};
+  }
+  \draw[line width=1pt] (\textwidth,0.1) -- (\textwidth,-0.1);
+
+  % Full timeline width for billion years
+  \draw[line width=1pt] (0,-3.8) -- node[midway, timeline_timespan] {5.45 billion years} (\textwidth,-3.8);
+  \draw[line width=1pt] (0,-3.7) -- (0,-3.9);
+  \draw[line width=1pt] (\textwidth,-3.7) -- (\textwidth,-3.9);
+
+  % Indicator for the period of 3 months = 1.1 billion years
+  \draw[line width=1pt] (0,-1.0) -- node[midway, timeline_timespan] {1.11 billion years} ({\segmentwidth * 3},-1.0);
+  \draw[line width=1pt] (0,-0.9) -- (0,-1.1);
+  \draw[line width=1pt] ({\segmentwidth * 3},-0.9) -- ({\segmentwidth * 3},-1.1);
+
+  % Place events on the timeline with dates using the timeline_event style
+  % As a calculation I used (4.54 billion years / 12 months = 0.3785 billion years/month.
+  \node[timeline_event, above] at (2.0*\segmentwidth,1) {Mar 25 - First maritime bacteria and archae};
+  \node[timeline_event, above] at (4.50*\segmentwidth,1.5) {June 25 - First organisms with nuklei (eukaryotes)};
+  \node[timeline_event, above] at (7.8*\segmentwidth,-1.5) {Oct 4 - First bacteria on land};
+  \node[timeline_event, above] at (8.0*\segmentwidth,-2.25) {Oct 15 - First maritime ancestors of fungi};
+  \node[timeline_event, above] at (9.7*\segmentwidth,-2.75) {Nov 24 - Fungi on land};
+  \node[timeline_event, above] at (10.5*\segmentwidth,-3.25) {Dec 3 - Yeasts on land};
+  \node[timeline_event, above] at (10.2*\segmentwidth,0.5) {Dec 14 - First dinosaurs};
+  \node[timeline_event, above] at (9.8*\segmentwidth,1) {Dec 17 - Pangea begins to rift apart};
+  \node[timeline_event, above] at (10.33*\segmentwidth,1.5) {Dec 29 - Dinosaurs go extinct};
+  \node[timeline_event, above, anchor=east, align=right] at (11.75*\segmentwidth,2.5) {Dec 31 - First humans};
+  \node[timeline_event, above, anchor=east, align=right] at (11.75*\segmentwidth,3.0) {Dec 31 - Sourdough in Jordan (23:59:55)};
+  \node[timeline_event, above, anchor=east, align=right] at (11.75*\segmentwidth,3.5) {Dec 31 - Louis Pasteur isolated yeast (23:59:59)};
+
+\end{tikzpicture}

book/figures/flowcharts_tikz.tex

@@ -25,3 +25,8 @@
                  decoration={calligraphic brace, amplitude=3mm, raise=1mm},
                  very thick, pen colour={black} ]
 \tikzstyle{loop} = [arc, draw=codeblack, line width=0.4mm]
+
+\tikzstyle{timeline_event}=[align=center, fill=white, inner sep=2pt]
+
+\tikzstyle{timeline_timespan} = [rectangle, draw=codeblack, fill=pinkpic,  text=black,
+    text centered, rounded corners, line width=0.4mm]

book/history/sourdough-history.tex

@@ -9,11 +9,78 @@
     lessons from the past.
 \end{quoting}
 
-Sourdough has been made since ancient times. The exact origins of fermented
+The story of sourdough bread begins in prehistoric oceans. These oceans were the
+birthplace of all life on Earth. To better envision the vast history of
+our planet, lets create a timeline in one~year/365~days. On this scale,
+January~1 signifies Earth's
+formation 4.54~billion years ago. Midnight on December~31 is the present.
+Each day represents roughly 12~million years. This technique simplifies the
+complexity of time but also renders the extraordinary expanse of our planet's
+history into a more graspable timeframe. We humans, are in fact a recent
+addition to our planet, so young that we made our first appearance on
+the evening of December~31.  It seems that humans managed to arrive just
+in time to join the celebration at the end of the year.
+
+The story of sourdough bread begins in ancient oceans. These oceans were the
+birthplace of all Earth's life. To better envision the vast history of
+our planet lets create a timeline of 1~year. On this scale, January~1 signifies Earth's
+formation 4.54~billion years ago. Midnight on December~31 is our present.
+Each day represents roughly 12~million years. This technique simplifies the
+complexity of time but also renders the extraordinary expanse of our planet's
+history into a more graspable frame. We humans are in fact a recent addition
+to our planet, so young that we made appearance on the evening of December~31.
+It seems that humans managed to arrive just in time to join
+the celebration at year's end.
+
+On March~25, the oceans birthed the first single-celled bacteria. In these
+waters, another single-celled life form, \emph{archaea}, also thrived. These
+organisms inhabit extreme environments, from boiling vents to icy waters.
+
+\begin{figure}[!htb]
+\begin{center}
+  \input{figures/fig-life-planet-sourdough-timeline.tex}
+  \caption[Sourdough microbiology timeline]{Timeline of significant events
+    starting from the first day of Earth's existence,
+    divided into months, and extending to the present day,
+    marked at midnight. This visualization shows the pivotal steps
+    of life and sourdough on earth.}%
+\end{center}
+\end{figure}
+
+Whoever comes first first, bacteria or archaea, remains debated. For three
+months (or approximately 1.1~billion years), these life forms dominated
+the oceans. Then, on June~25 in an highly unlikely event, an archaeon consumed a bacterium.
+Instead of digesting it, they formed a symbiotic relationship. This led to the
+first nucleated organisms, marking an evolutionary milestone. This event lead
+to the development of plants, fungi and also ultimately humans.
+
+Life stayed aquatic for another three months.
+On October~4, bacteria first colonized land. By October~15, the
+first aquatic fungi appeared. They adapted and, by November~24, had colonized
+land.
+
+By December~3rd, yeasts emerged on land. This laid groundwork for bread-making.
+Jump 140~million years to December~14, and dinosaurs arose. Just a couple
+of days after their appearance on December~17 the super continent pangea
+started to rift apart, reshaping the continents into their current form.
+The dinosaurs reigned until December~29 when they faced extinction.
+Another 25~million years later, or our timeline's 2~days after the dinosaur
+extinction, humans appeared.
+
+A few hours later after the arrival of humans, a more subtle culinary
+revolution was unfolding. By  \num{12000}~BC, just 5 seconds before our metaphorical
+midnight, the first sourdough breads were being baked in ancient Jordan. A blink of
+an eye later, or 4~seconds in our time compression, Pasteur's groundbreaking work
+with yeasts set the stage for modern bread-making. From the moment this book
+began to take shape to your current reading, only milliseconds have ticked by~\cite{Yong_2017}.
+
+Now delving deeper into the realm of sourdough, it can likely be traced to aforementioned
+Ancient Jordan~\cite{jordan+bread}. Looking at the earth's timeline sourdough
+bread can be considered a very recent invention.
+
+The exact origins of fermented
 bread are, however, unknown. One of the most ancient preserved
-sourdough breads has been excavated in Switzerland.
+sourdough breads has been excavated in Switzerland~\cite{switzerland+bread}.
-However, based on recent research, some scientists speculate that sourdough
-bread had already been made in \num{12000}~BC in ancient Jordan~\cite{jordan+bread}.
 
 \begin{figure}[ht]
   \includegraphics[width=\textwidth]{einkorn-crumb}
@@ -28,7 +95,7 @@ dough and at her return a few days later, she noticed that the dough had
 increased in size and smelled funky. She decided to bake
 the dough anyway and was rewarded with a much
 lighter, softer, better tasting bread dough. From that day
-on she continued to make bread this way.
+on she continued to make bread this way~\cite{egyptian+bread}.
 
 Little did the people back then know that tiny microorganisms
 were the reason the bread was better. It is not clear when

book/makefile

@@ -1,6 +1,6 @@
 # Macros for commands
 LATEX := latexmk -cd -pdflua -lualatex="lualatex -interaction=nonstopmode" -synctex=1 -use-make
-EBOOK := tex4ebook --lua -d epub -c tex4ebook.cfg
+EBOOK := tex4ebook --lua -d epub -f epub -c tex4ebook.cfg
 WEBSITE := make4ht --lua -c website.cfg -a debug -uf html5+tidy+common_domfilters+dvisvgm_hashes
 CLEAN := latexmk -cd -lualatex -c -use-make
 CHECK_1 := lacheck
@@ -87,32 +87,27 @@ book_serif/book.pdf: $(src_all)
 book_sans_serif/book_sans_serif.pdf: $(src_all)
 	$(LATEX) -output-directory=book_sans_serif book_sans_serif.tex
 
-.PHONY: bw_epub copy_ebook_files
+.PHONY: copy_ebook_files
 
 epub/%.epub: %.tex $(src_all) cover/cover-page.xbb
-	$(EBOOK) -f epub $<
+	$(EBOOK) $<
 
-bw-book-epub:
+copy_ebook_files: build_ebook
-	mkdir -p bw-book-epub
-
-copy_ebook_files: build_ebook | bw-book-epub
 	$(RSYNC) book-epub/ bw-book-epub/
 
 # We not convert SVG to B&W or lower res for now as they are super small
 # anyway
 bw-book-epub/OEBPS/%.jpg: %.jpg
+	mkdir -p $(dir $@)
 	$(CONVERT_PIC) $< $(REDUCE_PIC) $@
 
 bw-book-epub/OEBPS/%.png: %.png
+	mkdir -p $(dir $@)
 	$(CONVERT_PIC) $< $(REDUCE_PIC) $@
 
-bw_ebook.zip: copy_ebook_files $(bw_images)
+epub/bw_book.epub: copy_ebook_files $(bw_images)
-	zip -qXr9D bw_ebook.zip bw-book-epub
+	cd bw-book-epub; zip -q0X ../epub/bw_book.epub mimetype
-
+	cd bw-book-epub; zip -q9XrD ../epub/bw_book.epub ./
-epub/bw_book.epub: bw_ebook.zip
-	mv bw_ebook.zip epub/bw_book.epub
-
-bw_epub: epub/bw_book.epub | bw-book-epub
 
 # Now with the rules
 # Expected usual rules first
@@ -280,19 +275,22 @@ website: html ../website/_bundle_install_done $(ruby_src)
 	cd ../website && ruby modify_build.rb
 
 # Debug Stuff from now on
-.PHONY: quick show_tools_version printvars
+.PHONY: quick quick_ebook show_tools_version printvars
 
 # Those 2 targets allow fast debug cycles but not resolving references etc
+# They also ignore dependencies and run each time you call them.
 quick:  # run latex only once no biber, no references etc...
-	$(LATEX) -e '$$max_repeat=1' -output-directory=book_serif book.tex
+	$(LATEX) -e '$$max_repeat=1' -halt-on-error -output-directory=book_serif book.tex
 
 quick_ebook: cover/cover-page.xbb  # run latex only once no biber, ref etc...
-	$(EBOOK) --mode draft -f epub book.tex
+	$(EBOOK) --mode draft book.tex
 
 show_tools_version:  # Show version of tools used on the build machine
 	- git log -n 1
 	@echo ""
-	- ${SHELL} --version
+	- uname -a
+	@echo ""
+	- $(SHELL) --version
 	@echo ""
 	- latexmk --version
 	@echo ""
@@ -314,11 +312,10 @@ show_tools_version:  # Show version of tools used on the build machine
 	@echo ""
 	- ruby --version
 	@echo ""
-	- convert --version
+	- $(CONVERT_PIC) --version
 	@echo ""
 	- rsync --version
 
-
 # You can find the value of variable X with the following command:
 # make print-X
 print-%: ; @echo $* = $($*)  # Print a makefile variable

book/references.bib

@@ -98,6 +98,33 @@
   howpublished = {\url{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077754/}}
 }
 
+@article{switzerland+bread,
+  author    = {Pasquale Catzeddu},
+  title     = {Flour and Breads and their Fortification in Health and Disease Prevention},
+  pages     = {37--46},
+  year      = {2011}
+}
+
+@book{Yong_2017,
+  place     = {London},
+  title     = {I contain multitudes: The microbes within US and a grander view of life},
+  publisher = {Vintage},
+  author    = {Yong, Ed},
+  year      = {2017},
+  pages     = {5--9}
+}
+
+@article{egyptian+bread,
+  title     = {Investigation of ancient Egyptian baking and brewing methods by correlative microscopy},
+  volume    = {273},
+  DOI       = {10.1126/science.273.5274.488},
+  number    = {5274},
+  journal   = {Science},
+  author    = {Samuel, Delwen},
+  year      = {1996},
+  pages     = {488–490}
+}
+
 @article{vienna+breadrolls,
   author    = {Eben Norton Horsford},
   title     = {Report on Vienna bread},

book/sourdough_book.tex

@@ -1 +0,0 @@
-book.tex

book/style.css

@@ -62,6 +62,18 @@ main.main-content,main.titlepage,div.footnotes{
   padding:1rem;
 }
 
+.sectionHead a.permalink {
+  opacity: 0.5;
+  text-decoration: none;
+  font-size: 0.75rem;
+  vertical-align: top;
+  line-height: 0.8rem;
+  margin-left: 0.25rem;
+  padding-top: 0.2rem;
+  color: black;
+  display: inline-block;
+}
+
 p.indent, p.noindent{
   text-indent: 0;
   text-align: justify;

makefile

@@ -1,45 +1,45 @@
+.DEFAULT_GOAL := build_pdf
+
 DOCKER_IMAGE := ghcr.io/hendricius/the-sourdough-framework
+DOCKER_CMD := docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c
 
-.PHONY: build_pdf
+.PHONY: bake build_pdf build_docker_image push_docker_image validate website
-build_pdf: mrproper
+.PHONY: print_os_version start_shell printvars show_tools_version mrproper
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make"
 
-.PHONY: bake
+# Dockers targets
-bake: mrproper
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make bake"
-
-.PHONY: build_docker_image
 build_docker_image:
 	docker build -t $(DOCKER_IMAGE) -f Dockerfile --progress=plain .
 
-.PHONY: push_docker_image
+push_docker_image: build_docker_image
-push_docker_image:
 	docker push $(DOCKER_IMAGE):latest
 
-.PHONY: website
+# Books/website 
-website: mrproper
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make website"
 
-.PHONY: validate
+# Quicker run for each commit, shall catch most problems
-validate: mrproper
+validate:
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make -j build_pdf build_ebook"
+	$(DOCKER_CMD) "cd /opt/repo/book && make -j build_serif_pdf build_ebook"
+
+build_pdf:
+	$(DOCKER_CMD)  "cd /opt/repo/book && make"
+
+bake:
+	$(DOCKER_CMD) "cd /opt/repo/book && make -j bake"
+
+website:
+	$(DOCKER_CMD) "cd /opt/repo/book && make website"
 
-.PHONY: mrproper
 mrproper:
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make mrproper"
+	$(DOCKER_CMD) "cd /opt/repo/book && make mrproper"
 
-.PHONY: show_tools_version
+# Debug helpers
 show_tools_version:
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make show_tools_version"
+	$(DOCKER_CMD) "cd /opt/repo/book && make show_tools_version"
 
-.PHONY: printvars
 printvars:
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cd /opt/repo/book && make printvars"
+	$(DOCKER_CMD) "cd /opt/repo/book && make printvars"
 
-.PHONY: print_os_version
 print_os_version:
-	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash -c "cat /etc/*release"
+	$(DOCKER_CMD) "cat /etc/*release"
 
-.PHONY: start_shell
 start_shell:
 	docker run -it -v $(PWD):/opt/repo $(DOCKER_IMAGE) /bin/bash

website/assets/script.js

@@ -8,4 +8,14 @@ document.addEventListener('DOMContentLoaded', function() {
       });
     }
   });
+
+  // Add permalinks to headers
+  var heads = document.querySelectorAll('.sectionHead');
+  heads.forEach(function (head) {
+    let permalink = document.createElement("a");
+    permalink.href = '#' + head.id;
+    permalink.classList.add('permalink');
+    permalink.append('🔗');
+    head.append(permalink);
+  });
 });