Scientific Writing and Publishing for the Future

Hans Petter Langtangen


Sep 24, 2015










Challenges with tools for scientific writing









Scientific writing = LaTeX 

\def\FrameCommand{\colorbox{shadecolor}}\FrameRule0.6pt
\MakeFramed {\FrameRestore}\vskip3mm}{\vskip0mm\endMakeFramed}
\providecommand{\shadedquoteBlue}{}
\renewenvironment{shadedquoteBlue}[1][]{
\bgroup\rmfamily\fboxsep=0mm\relax
\begin{shadedskip}
\list{}{\parsep=-2mm\parskip=0mm\topsep=0pt\leftmargin=2mm
\rightmargin=2\leftmargin\leftmargin=4pt\relax}
\relax}{\endlist\end{shadedskip}\egroup}\begin{shadedquoteBlue}
\fontsize{9pt}{9pt}
\begin{Verbatim}
print 'Hello, World!'
\end{Verbatim}

Big late 1990s question: Will MS Word replace LaTeX? It never did!









LaTeX PDF is mostly suboptimal for the new devices









The book will survive (LaTeX is ideal)









The classical report/paper will survive (LaTeX is ideal)









But there is an explosion of new platforms for digital learning systems!

MOOCs, Kahn Academy, ndla, H5P, Haiku Learning, Opigno, ...









My headache: How to write scientific material that can be easily published through old and new media?

LaTeX-for-paper and HTML-for-screen are two very different writing styles and technology platforms.









Scope: documents with much math and computer code

Key question:

What tools should I use for scientific writing?









There is a jungle of outlets your scientific writings should address









Can I assemble lots of different writings to a new future document (book)?

Suppose I write various types of scientific material,

and later want to collect the pieces into a larger document, maybe some book - is that at all feasible?

Probably not, but I have a solution









Pros and cons of various tools









Popular tools anno 2014 and their math support









LaTeX is very rich; other tools support much less









LaTeX is very rich; other tools support much less









LaTeX is very rich; other tools support much less

Highly non-trivial to translate from/to LaTeX!









My colleagues face fundamental problem with going from LaTeX to IPython notebook (=Markdown)

Plan.

I am used to write LaTeX paper/book-style with lots of cross-references and floating figures, code snippets, tables, algorithms, but now I want to convert to IPython notebooks.

Problem.

Must have fixed figures, code snippets, tables. No algorithm environment, cross-referencing, equation referencing. All code needed for a snippet to run must be included. It's a different writing style, but lots of new opportunities.









Examples on typesetting concerns (1)









Examples on typesetting concerns (2)









Examples on typesetting concerns (3)









Solution I: Use a format that translates to many









Solution II: Use DocOnce

DocOnce offers minimalistic typing, great flexibility wrt format, especially for scientific writing with much math and code.









DocOnce: Write once, include anywhere









DocOnce demos

http://hplgit.github.com/teamods/writing_reports/









DocOnce disclaimer

DocOnce divorce.

At any time one can divorce from DocOnce and marry one of the output formats, such as LaTeX or Sphinx. The generated code is clean.









DocOnce experience









A tour of DocOnce









Title, authors, date, toc 

TITLE: Some Title
AUTHOR: name1 at institution1, with more info & institution2
AUTHOR: name2 email:name2@web.com at institution
DATE: today

# A table of contents is optional:
TOC: on

Notice.

Title and authors must have all information on a single line!









Abstract 

__Abstract.__
Here goes the abstract...

Or: 

__Summary.__
Here goes the summary...









Section headings

Headings are surrounded by = signs: 

======= This is an H1/chapter heading =======

===== This is an H2/section heading =====

===== This is an H3/subsection heading =====

=== This is an H4/paragraph heading ===

__This is a paragraph heading.__

Result:

This is an H1/chapter heading

This is an H2/section heading

This is an H3/subsection heading

This is an H4/paragraph heading

This is a paragraph heading.









Markup and lists 

 * Bullet list items start with `*`
   and may span several lines
 * *Emphasized words* are possible
 * _Boldface words_ are also possible
 * color{red}{colored words} too
 * `inline verbatim code` is featured
   o and sublists with enumerated items starting with `o`
   o items are just indented as you would do in email

This gets rendered as









Labels, references, index items 

# Insert index items in the source
idx{key word1} idx{key word2}

# Label
===== Some section =====
label{this:section}

# Make reference
As we saw in Section ref{this:section}, references, index
items and labels follow a syntax similar to LaTeX
but without backslashes.

# Make reference to equations
See (ref{eq1})-(ref{myeq}).

# Make hyperlink
"some link text": "https://github.com/hplgit/doconce"

# Hyperlink with complete URL as link text
URL: "https://github.com/hplgit/doconce"









Figures and movies

Important:

Figures with HTML and LaTeX size info, and caption: everything on one line 

FIGURE: [figdir/myfig, width=300 frac=1.2] My caption. label{fig1}

Movies are also supported: 

MOVIE: [http://youtu.be/IDeGDFZSYo8, width=420 height=315]

and rendered as









Math

Inline math as in LaTeX: 

...where $a=\int_{\Omega}fdx$ is an integral.

gets rendered as ...where \( a=\int_{\Omega}fdx \) is an integral.

An equation environment is surrounded by !bt and !et tags, the rest is plain LaTeX: 

!bt
\begin{align}
\frac{\partial u}{\partial t} &= \nabla^2 u,
label{a:eq}\\ 
\nabla\cdot\pmb{v} & = 0
label{b:eq}
\end{align}
!et

which is rendered as $$ \begin{align} \frac{\partial u}{\partial t} &= \nabla^2 u, \label{a:eq}\\ \nabla\cdot\pmb{v} & = 0 \label{b:eq} \end{align} $$









Math flexibility

Limit math environments to 

\[ ... \]

\begin{equation*}
\end{equation*}

\begin{equation}
\end{equation}

\begin{align*}
\end{align*}

\begin{align}
\end{align}

DocOnce fix of shortcomings.









Displaying code

Code is enclosed in !bc and !ec tags: 

!bc pycod
def solver(I, a, T, dt, theta):
    """Solve u'=-a*u, u(0)=I, for t in (0,T] with steps of dt."""
    dt = float(dt); N = int(round(T/dt)); T = N*dt
    u = zeros(N+1); t = linspace(0, T, N+1)

    u[0] = I
    for n in range(0, N):
        u[n+1] = (1 - (1-theta)*a*dt)/(1 + theta*dt*a)*u[n]
    return u, t
!ec

This gets rendered as 

def solver(I, a, T, dt, theta):
    """Solve u'=-a*u, u(0)=I, for t in (0,T] with steps of dt."""
    dt = float(dt); N = int(round(T/dt)); T = N*dt
    u = zeros(N+1); t = linspace(0, T, N+1)

    u[0] = I
    for n in range(0, N):
        u[n+1] = (1 - (1-theta)*a*dt)/(1 + theta*dt*a)*u[n]
    return u, t









Copying code from source files

We recommend to copy as much code as possible directly from the source files: 

@@@CODE path/to/file
@@@CODE path/to/file   fromto: start-regex@end-regex

For example, copying a code snippet starting with def solver( and ending with (line not included) def next(x, y, is specified by start and end regular expressions: 

@@@CODE src/somefile.py  fromto: def solver\(@def next\(x,\s*y,









Typesetting of code is implied by the file extension









Demonstrating code execution; Online Python Tutor

With !bc pyoptpro or a file *.pyopt, the code applies the Online Python Tutor for displaying program flow and state of variables:









Demonstrating code execution; Sage Cell Server

With !bc pyscpro or a file *.pysc, the code is typeset in a sage cell:

Warning.

Works only in Sphinx documents (but HTML support is possible).









Demonstrating code execution; IPython notebook

Can take a DocOnce source and transform to an IPython notebook with source









Tables 

  |--------------------------------|
  |time  | velocity | acceleration |
  |---r-------r-----------r--------|
  | 0.0  | 1.4186   | -5.01        |
  | 2.0  | 1.376512 | 11.919       |
  | 4.0  | 1.1E+1   | 14.717624    |
  |--------------------------------|

Gets rendered as

time velocity acceleration
0.0 1.4186 -5.01
2.0 1.376512 11.919
4.0 1.1E+1 14.717624









Newcommands for math









Labels, citations, index, bibliography

Lables, citations, index, and bibliography follow the ideas of LaTeX, but without backslashes: 

===== My Section =====
label{sec:mysec}

idx{key equation} idx{$\u$ conservation}

We refer to Section ref{sec:yoursec} for background material on
the *key equation*. Here we focus on the extension


!bt
\begin{equation}
\Ddt{\u} = \mycommand{v} label{mysec:eq:Dudt}
\end{equation}
!et
Equation (ref{mysec:eq:Dudt}) is important, see
cite{Larsen_et_al_2002,Johnson_Friedman_2010a}.
Also, cite{Miller_2000} supports such a view.

Figure ref{mysec:fig:myfig} displays the features.

FIGURE: [fig/myfile, width=600] My figure. label{mysec:fig:myfig}

===== References =====

BIBFILE: papers.pub

The papers.pub file must be in Publish format (easy to make from BibTeX).









Exercises

DocOnce offers a special format for exercises, problems, projects, and examples: 

===== Problem: Flip a Coin =====
label{demo:ex:1}
files=flip_coin.py, flip_coin.pdf
solutions=mysol.txt, mysol_flip_coin.py
keywords = random numbers; Monte Carlo simulation

!bsubex
Make a program that simulates flipping a coin $N$ times.

!bhint
Use `r = random.random()` and define head as `r <= 0.5`.
!ehint
!esubex

!bsubex
Compute the probability of getting heads.

!bans
0.5.
!eans
!esubex









Rendering of the previous page

Problem 1: Flip a Coin

a) Make a program that simulates flipping a coin \( N \) times.

Hint. Use r = random.random() and define head as r <= 0.5.

b) Compute the probability of getting heads.

Answer. 0.5.

Filenames: flip_coin.py, flip_coin.pdf.









Exercises

All exercises, problems, and projects in a document are parsed and available in a data structure (list of dicts) for further processing (e.g., making a book of problems). 

[{'answer': '',
  'closing_remarks': '',
  'file': ['flip_coin.py', 'flip_coin.pdf'],
  'hints': [],
  'keywords': ['random numbers', 'Monte Carlo simulation'],
  'label': 'demo:ex:1',
  'solution_file': ['mysol.txt', 'mysol_flip_coin.py'],
  'subex': [{'answer': '',
             'file': None,
             'hints': ['Use `r = random.random()` ...'],
             'solution': '',
             'text': 'Make a program that simulates ...'},],
  'title': 'Flip a Coin',
  'type': 'Problem'}]









Use of preprocessors









DocOnce admonitions

Use with caution!

Such environments may light up the document, but can be disturbing too. Some admon styles have icons.

Going deeper.

More details can be separated from the rest.

Time for review!

Tasks:

Conclusion:









Generalized references 

ref[internal][latex cite][external]


...as shown in ref[Section ref{sec:eqs}][ in cite{math_eqs_2020}][
the document "Mathematical Equations":
"http://some.net/doc/matheqs.html" cite{math_eqs_2020}].









Slides

Very effective way to generate slides from running text:









Example on slide code 

!split
===== Headline =====

 * Key point 1
 * Key point 2
 * Key point 3: Although long
   bullet points are not recommended in general, we need
   it here for demonstration purposes to investigate
   what happens with the slide layout where there is
   so much text under one point

FIGURE: [fig/teacher1, width=100 frac=0.4]

Key equation:

!bt
\[ -\nabla^2 u = f \quad\hbox{in }\Omega \]
!et

And maybe a final comment?

!split
===== Next slide... =====









Example on slide code

Last page gets rendered to

Headline

Key equation: $$ -\nabla^2 u = f \quad\hbox{in }\Omega $$

And maybe a final comment?









Grid layout of slide: MxN cells

Example with a bullet list to the left and a figure to the right (two cells: 00 and 01): 

!split
===== Headline =====

!bslidecell 00
!bpop
 * Key point 1
 * Key point 2
 * Key point 3
!epop

!bpop
!bt
\[ -\nabla^2 u = f \quad\hbox{in }\Omega \]
!et
!epop

!eslidecell

!bslidecell 01
FIGURE: [fig/broken_pen_and_paper, width=400 frac=0.8]
!eslidecell

!split
===== Next slide... =====









Grid layout of slide: MxN cells

Last page gets rendered to

Headline

$$ -\nabla^2 u = f \quad\hbox{in }\Omega $$









Classic slide types









HTML5 slide types









DocOnce to HTML

Run in terminal window: 

doconce format html doconcefile

# Solarized HTML style
doconce format html doconcefile --html_solarized

# Control pygments typesetting of code
doconce format html doconcefile --pygments_html_style=native

# Or use plain <pre> tag for code
doconce format html doconcefile --no_pygments_html

# Further making of slides
doconce slides_html doconcefile reveal --html_slide_theme=darkgray









Output for blog posts

Two formats of blog posts are supported:

For wordpress, add --wordpress: 

doconce format html doconcefile --wordpress

and paste the code into the text area.









DocOnce to pdfLaTeX 

doconce format pdflatex doconcefile --latex_code_style=lst

pdflatex doconcefile
bibtex doconcefile
pdflatex doconcefile









DocOnce to Sphinx 

doconce format sphinx doconcefile

# Autocreate sphinx directory
doconce sphinx_dir theme=pyramid doconcefile

# Copy files and build HTML document
python automake-sphinx.py

google-chrome sphinx-rootdir/_build/html/index.html

Much easier than running the Sphinx tools manually!









Output for wiki

Only MediaWiki supports math. 

doconce format mwiki doconcefile

Recommended site:

Publishing of "official" documents:







DocOnce to other formats 

doconce format pandoc doconcefile  # (Pandoc extended) Markdown
doconce format gwiki  doconcefile  # Googlecode wiki
doconce format cwiki  doconcefile  # Creole wiki (Bitbucket)
doconce format rst    doconcefile  # reStructuredText
doconce format plain  doconcefile  # plain, untagged text for email









Installation









Writing tips for LaTeX writers who want to convert to DocOnce and generate other formats









DocOnce writing tips

Figures and movies:









DocOnce writing tips









Writing tips for sphinx and other formats

For output formats different from latex, pdflatex, and html:

© 2015, Hans Petter Langtangen