From: Eric S Fraga <esflists@gmail.com>
To: Julius Dittmar <Julius.S.Mueller@eureca.de>
Cc: emacs-orgmode@gnu.org
Subject: Re: Help with sharing emacs-org presentation
Date: Wed, 31 Oct 2018 07:21:42 +0000 [thread overview]
Message-ID: <878t2elgxl.fsf@gmail.com> (raw)
In-Reply-To: <35f49038-76f2-8573-09b3-6ab2055b9aba@eureca.de> (Julius Dittmar's message of "Tue, 30 Oct 2018 20:43:33 +0100")
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On Tuesday, 30 Oct 2018 at 20:43, Julius Dittmar wrote:
> Am 30.10.18 um 20:01 schrieb Martin Schöön:
>> My own mantra for preparing slide-packs is to minimize text. I want
>> the audience to listen to me rather than reading text on my slides.
>> My 2 cents...
>
> please don't overdo that.
>
> People have quite different ways of taking in information. Some memorize
> best if they hear something. Others memorize best if they have visual
> input. Others memorize best if they somehow take that information into
> their hands (for example by writing).
>
> If all you give is auditory input, you will leave a lot of interested
> persons in your auditory in the cold.
There is always a balance to be achieved, in my experience. The trick
is to have slides that support you but do not compete. If there is too
much text, the audience will be tempted to read and will not be paying
attention to what you say. I tend towards Martin's view with little or
no text on many slides but slides with text will be limited to 3-4
bullet points and each bullet point having 5-6 words maximum. But, of
course, this all depends on your intended audience.
In any case, in the spirit of this thread, please find attached a
presentation (both PDF and original org file) I gave earlier this year
to an academic audience consisting mostly of mathematicians and
numerical analysts. The topic was literate programming but it was
really about org and Emacs. Lot of interest from the audience and I
hope I converted some to this eco-system.
--
Eric S Fraga via Emacs 27.0.50, Org release_9.1.13-783-g97fac4
[-- Attachment #2: talk.pdf --]
[-- Type: application/pdf, Size: 637187 bytes --]
[-- Attachment #3: talk.org --]
[-- Type: text/x-org, Size: 19535 bytes --]
#+title: Literate programming and reproducible research
#+author: Professor Eric S Fraga, UCL
#+macro: lastchange 2018.06.06 10:36
* Introduction
** The aim & challenge
*** Reproducible research
To ensure that our research is *reproducible* both by ourselves and by others.
*** Coding, processing, writing
In doing research,
1. we all *write* programs ...
2. which generate *results* ...
3. which need to be *processed* ...
4. and which should be *disseminated*.
Currently, we use different tools for each step.
*** Tools
Workflow:
- coding :: IDE, MATLAB editor, ~vi~, ~notepad~, ...
- results :: ~.txt~, ~.xls~, ~.dat~
- processing :: spreadsheet, ~R~
- dissemination :: ~Word~, ~PowerPoint~, LaTeX, ~beamer~
- project management :: ?
leading to constant *transfer* of data from one place to another.
** Literate programming
*** Definition
#+begin_quote
Literate programming is a programming paradigm introduced by Donald Knuth in which a program is given as an explanation of the program logic in a natural language, such as English, interspersed with snippets of macros and traditional source code, from which a compilable source code can be generated.
#+end_quote
https://en.wikipedia.org/wiki/Literate_programming
*** Code and documentation
#+attr_latex: :width 0.8\textwidth
[[file:literate-programming-tangling.png]]
[[http://howardism.org/Technical/Emacs/literate-programming-tutorial.html][Source]]
*** Example: the Strawberry algorithm
[[file:strawberry-outline-withborder.png]]
[[https://www.ucl.ac.uk/~ucecesf/strawberry.html]]
** Emacs
*** Editor
- originally written in 1976
- content aware editing
- fully extensible in ~Emacs LISP~
- self-documenting with comprehensive help system
- large eco-system of packages
https://www.gnu.org/software/emacs/
*** org mode
Text (*it's all text*) based mode for
- writing & dissemination
- project management
- literate programming
https://orgmode.org/
* org mode
** Programming
*** Example objective function
\begin{align*}
\min_x z &= \sum_{i=1}^{n} x_i^4 + x_i^3 - 2x_i^2 \\
x & \in [a,b]\cap\mathbb{R}^n
\end{align*}
*** Plot of objective function
#+results: plot-f
[[file:f.png]]
:plotcode:
#+name: plot-f
#+header: :term "png crop"
#+begin_src gnuplot :file f.png :exports results
reset
set cntrparam levels 40 bspline
set contour base
set hidden3d
unset key
set view 60,326
set xrange [-2:2]
set yrange [-2:2]
unset xtics
unset ytics
unset ztics
unset zlabel
splot x**4+y**4+x**3+y**3-2*x*x-2*y*y
#+end_src
:end:
*** Tangling
Create an ~octave~ file with the objective function using *tangling*:
#+name: octave-f
#+begin_src octave :tangle "f.m"
function [z g] = f(x)
z = sum(x.^4 + x.^3 - 2*x.^2);
g = 0; % unconstrained
endfunction
#+end_src
*** Code segments
Specify the parameters for the optimisation problem:
#+name: problem-setup
#+begin_src octave :noweb yes
n = 2;
x0 = rand(n,1);
a = -2*ones(n,1);
b = 2*ones(n,1);
#+end_src
*** Bringing bits together
The code to include the problem setup directly and solve the problem:
#+name: strawberry
#+begin_src octave :results value :noweb yes
clear
format short
<<problem-setup>>
[x y] = strawberry(x0, a, b, @f, 10, 10);
[x;y]'
#+end_src
:results:
#+name: strawberry-results
#+results: strawberry
| -1.42716504443494 | -1.443856778049211 | -5.66531336687728 | 0 |
| -1.42716504443494 | -1.443856778049211 | -5.66531336687728 | 0 |
| -1.342508585413797 | -1.55250372785845 | -5.529004698055015 | 0 |
| -1.360506726205515 | -1.372263538977069 | -5.598345289891352 | 0 |
| -1.468158011926931 | -1.544415421188739 | -5.594381839388814 | 0 |
| -1.339213003233875 | -1.36422094977677 | -5.569697214609254 | 0 |
| -1.364417892433951 | -1.491553912171922 | -5.615971023198005 | 0 |
| -1.463919469920687 | -1.450505968993437 | -5.663754045524612 | 0 |
| -1.445565121464613 | -1.420730525034394 | -5.663799364174422 | 0 |
| -1.525782025485549 | -1.5303639151147 | -5.571556830521184 | 0 |
| -1.40352725450047 | -1.472972377299925 | -5.651863813417487 | 0 |
| -1.410286649811288 | -1.414343225362287 | -5.655462642214252 | 0 |
| -1.52277571384937 | -1.446360898144175 | -5.62508035617786 | 0 |
| -1.584751338098946 | -1.373116848847318 | -5.500483131429339 | 0 |
| -1.243018966119808 | -1.476516324299424 | -5.449770831917819 | 0 |
| -1.444138322679675 | -1.666222711962772 | -5.304110381262799 | 0 |
| -1.370072015649149 | -1.525937116930233 | -5.590709124514991 | 0 |
| -1.576526755720007 | -1.530518104917815 | -5.494784345778852 | 0 |
| -1.507786501304049 | -1.37902437675949 | -5.615657626549971 | 0 |
| -1.450567499881924 | -1.408583920258332 | -5.659381058555995 | 0 |
| -1.535526266987041 | -1.456193641066952 | -5.609133134458752 | 0 |
| -1.238285464782562 | -1.25198387068423 | -5.254687157245281 | 0 |
| -1.321030271837289 | -1.420499018517368 | -5.580507706519432 | 0 |
| -1.457276546364113 | -1.510431969520121 | -5.636060671059006 | 0 |
| -1.386994515876665 | -1.452244319822924 | -5.647806776697823 | 0 |
| -1.455869791504375 | -1.446387391362544 | -5.665742757998999 | 0 |
| -1.62382235873763 | -1.442265536388754 | -5.436001199588198 | 0 |
| -1.455447362960834 | -1.404854864255555 | -5.657173423616351 | 0 |
| -1.352852883884089 | -1.468988859997606 | -5.615930658043434 | 0 |
| -1.316282451554356 | -1.481169331825285 | -5.568062394335248 | 0 |
| -1.346872171742821 | -1.559721739239854 | -5.52227606914515 | 0 |
| -1.392193082324921 | -1.540475777984804 | -5.588469535120524 | 0 |
| -1.358676764875123 | -1.533272203185758 | -5.572011634831901 | 0 |
| -1.430102855019641 | -1.499714214014829 | -5.645120932555698 | 0 |
| -1.375336252513826 | -1.351372446488072 | -5.591923631732472 | 0 |
| -1.323532458220509 | -1.344166563266232 | -5.531090335022149 | 0 |
| -1.493260210372538 | -1.448067147541937 | -5.650501934854817 | 0 |
| -1.497055854832323 | -1.437039672362705 | -5.647851947473225 | 0 |
:end:
*** Plotting results
Using data in table of results on previous slide:
#+results: plot-results
[[file:results.png]]
:plotcode:
#+name: plot-results
#+header: :term "png size 600,600 crop"
#+begin_src gnuplot :var data=strawberry-results :file results.png
reset
set contour base
set cntrparam levels 40
set xrange [-2:2]
set yrange [-2:2]
unset key
unset xtics
unset xlabel
unset ytics
unset xlabel
set view 0,0
splot data using 1:2:3 with points pt 6 ps 1, x**4+y**4+x**3+y**3-2*x*x-2*y*y
#+end_src
:end:
*** Processing results
Statistical analysis of results obtained above:
| Statistic | Value |
|--------------------+--------|
| Best | -5.666 |
| Average | -5.582 |
| Worst | -5.255 |
| Standard deviation | 0.094 |
#+TBLFM: @2$2=vmin(remote(strawberry-results,@<$>>..@>$>>));f3::@3$2=vsum(remote(strawberry-results,@<$>>..@>$>>))/vcount(remote(strawberry-results,@<$>>..@>$>>));f3::@4$2=vmax(remote(strawberry-results,@<$>>..@>$>>));f3::@5$2=vsdev(remote(strawberry-results,@<$>>..@>$>>));f3
** Writing
*** Outlines
Example (a recent paper):
[[file:impact-paper-outline.png]]
Can show, hide, and move individual sub-trees.
*** COMMENT Content
- export can handle mathematics:
\[ y = \sqrt{x} \]
- figures:
[[file:~/s/personal/avatar-australia-hat-sunglasses-64x64.png]]
- tables (as we have already seen) but with formatting:
| Item | Description |
| <l> | <r> |
|------+-------------|
| One | Interesting |
| Two | Boring |
*** COMMENT Inline LaTeX for full control
- We can include inline LaTeX directives.
- For instance, \fbox{in a box} would output as you expect.
*** Publishable output
~org~ will *export* to LaTeX (and hence to ~PDF~) or ~ODT~ (~MS Word~ compatible).
[[file:odt-export.png]]
*** Project management
Support for tasks, scheduling, appointments:
**** TODO [3/4] prepare and give presentation on literate programming
DEADLINE: <2018-06-06 Wed>
- [X] collect images
- [X] write slides
- [X] book hotel
- [ ] give presentation
*** Revision control
- A research project is a long term activity comprised of many individual tasks.
- Revision control should (*must*) be an integral element of project management.
- Think *track changes* but on steroids and which works for *data* as well.
- Excellent tools exist: ~git~, ~mercurial~, ~subversion~, ...
*** Example of revision control
[[file:hg-log-view.png]]
* Conclusions
** Summary
*** Emacs & org
Single tool for *writing*, *coding*, *data manipulation*, *data provenance*, *dissemination*, and *project management*.
*** Testimonial I
#+begin_quote
By the age of 35 you should have realized that Emacs is the One True Editor and should have embraced it. If that’s not the case - your life so far has been completely wasted.
#+end_quote
[[https://twitter.com/bbatsov/status/998217369204948992][@bbatsov, 04:02 pm May 20, 2018]]
*** Testimonial II
#+begin_quote
The advantages of plain text are hard to overstate, as is the advantage of having everything from plot notes to research material in a single (large) file under version control. And building up a novel from an outline is a natural process with org-mode.
#+end_quote
Bob Newell, =emacs.help= newsgroup, 2018-05-30.
*** Links
- Emacs :: https://www.gnu.org/software/emacs/
- Complete computing environment :: http://doc.rix.si/cce/cce.html
- org mode :: https://orgmode.org/
- reproducible research :: https://reproducibleresearch.net/links/
- blog :: [[https://dfeich.github.io/www/org-mode/emacs/reproducible-research/2018/05/20/reproducible-research-for-management.html][reproducible research for management]]
*** And finally
[[file:real_programmers.png]]
https://www.xkcd.com/378/
** COMMENT Revision log
#+begin_example
$Revision: 1.33 $
$Log: talk.org,v $
Revision 1.33 2018/06/04 08:14:55 ucecesf
Summary: reformatted (unfilled) second testimonial
Revision 1.32 2018/06/04 08:09:32 ucecesf
Summary: added another Emacs link
Revision 1.31 2018/05/30 17:09:48 ucecesf
Summary: added another testimonial
Revision 1.30 2018/05/28 16:08:22 ucecesf
Summary: some blank lines added for clearer slides
Revision 1.29 2018/05/26 09:46:24 ucecesf
Summary: more commentary and changed order of last two slides
Revision 1.28 2018/05/25 06:51:00 ucecesf
Summary: added slide on project management and one on links for further information
Revision 1.27 2018/05/22 09:15:09 ucecesf
Summary: added xkcd real programmers use Emacs slide
Revision 1.26 2018/05/22 06:12:37 ucecesf
Summary: updated objective function example with subscripts
Revision 1.25 2018/05/21 19:04:07 ucecesf
Summary: minor reformatting and added link to Strawberry
Revision 1.24 2018/05/21 18:58:01 ucecesf
Summary: added mercurial example
Revision 1.23 2018/05/21 18:52:08 ucecesf
Summary: added testimonial on Emacs from twitter
Revision 1.22 2018/05/21 16:28:25 ucecesf
Summary: added some commentary and removed superfluous screenshots
Revision 1.21 2018/05/21 16:14:49 ucecesf
Summary: added aim and LP figure from web
Revision 1.20 2018/05/20 14:01:41 ucecesf
Summary: updated the objective function to be more mathematically precise
Revision 1.19 2018/05/20 12:40:57 ucecesf
Summary: added ODT export image and reformatted conclusions
Revision 1.18 2018/05/20 12:32:19 ucecesf
Summary: minor formatting to make PDF export look good
Revision 1.17 2018/05/20 12:23:46 ucecesf
Summary: added impact paper outline as example
Revision 1.16 2018/05/20 12:09:36 ucecesf
Summary: added project management to summary
Revision 1.15 2018/05/20 12:06:29 ucecesf
Summary: moved plot of results and hid code
Also ensured that LaTeX fragments were displayed and text was scaled
appropriately.
Revision 1.14 2018/05/20 11:52:33 ucecesf
Summary: added plot of objective function and show results with contours
Revision 1.13 2018/05/18 22:45:25 ucecesf
Summary: added plotting of results slide
Revision 1.12 2018/05/18 17:46:33 ucecesf
Summary: added Strawberry folded example
For literate programming and for outlines in org.
Revision 1.11 2018/05/18 17:38:10 ucecesf
Summary: made literate programming slide top level
Revision 1.10 2018/05/18 17:37:16 ucecesf
Summary: customised page up/down for slide transitions
Revision 1.9 2018/05/18 17:04:19 ucecesf
Summary: added revision log
Revision 1.8 2018/05/18 17:00:28 ucecesf
Summary: added conclusions
revision 1.7 2018/05/18 16:57:44 ucecesf
Summary: added motivation section
revision 1.6 2018/05/18 08:03:39 ucecesf
Summary: settings for beamer export
revision 1.5 2018/05/17 17:44:07 ucecesf
Summary: started talking about writing
revision 1.4 2018/05/17 17:31:35 ucecesf
Summary: turn off beacon mode to avoid annoying
revision 1.3 2018/05/17 17:28:12 ucecesf
Summary: introduce noweb for code segments
revision 1.2 2018/05/16 19:30:09 ucecesf
Summary: added some octave code and tables
revision 1.1 2018/05/16 16:41:50 ucecesf
Initial revision
#+end_example
* settings :noexport:
** org
#+PROPERTY: cache yes
*** beamer settings
#+startup: beamer
Change this setting depending on whether there are sections for the talk or not, with 2 for sections, 1 for no sections and 3 for subsections as well.
#+options: H:3
The theme can be ~minimal~, ~progressbar~, or anything else.
#+beamer_theme: minimal
If links are used directly, colour them gray.
#+latex_header: \hypersetup{colorlinks=true,urlcolor=gray}
#+macro: actualdate 6 June 2018
#+macro: where EGL2018, Essex
#+institute: University College London
# +LATEX_HEADER: \institute{University College London (UCL)}
*** date formatting with version information :ignoreheading:
**** COMMENT git
#+NAME: mydateline
#+BEGIN_SRC emacs-lisp
(format "#+DATE: \\copyright{} %s\n" *this*)
#+END_SRC
src_shell[:post mydateline() :results raw]{echo -n $(date +%Y) '@@latex:\\ \vspace*{0.1cm} \tiny \color{gray}@@' version $(git log --format=format:"%ad %h" --date=short | head -1 )}
**** COMMENT mercurial
#+NAME: mydateline
#+BEGIN_SRC emacs-lisp
(format "#+DATE: \\copyright{} %s\n" *this*)
#+END_SRC
src_shell[:post mydateline() :results raw]{echo -n $(date +%Y) '@@latex:\\ \vspace*{0.1cm} \tiny \color{gray}@@' version $(hg log slides.org | head -1 | sed -e 's/^.* \([0-9]*\):.*$/\1/')}
**** rcs
#+latex_header: \usepackage{rcs}
#+latex_header: \RCS $Revision: 1.33 $
#+latex_header: \RCS $Date: 2018/06/04 08:14:55 $
#+date: @@latex:\ifdef{\institute}{@@ {{{actualdate}}} @@latex:\\@@ {{{where}}} @@latex:\\ \vfill\hfill{\tiny\color{gray}v\RCSRevision~\RCSDate}}{@@ @@latex:}@@
*** macros
**** calc: short better formatted version of calculate macro
If the second argument is not given, no variable is stored or shown in the output.
#+macro: calc src_emacs-lisp[:results latex]{(esf/calc-and-output "$1" "$2")}
The macro relies on the following code:
#+name: calc-and-output
#+begin_src emacs-lisp :results silent :exports none
(defun esf/calc-and-output (expression variable)
(let ((result (string-to-number (calc-eval (format "evalv(%s)" expression)))))
(message "Expression %s results in %s" expression result)
(if (string= "" variable)
(format "%s = \\fbox{%s}" expression result)
(progn
(eval (format "(setq var-%s %s)" variable result))
(format "\\texttt{%s} \\(\\gets\\) %s = \\fbox{%s}" variable expression result))
)
))
#+end_src
**** calculate: use emacs calc to evaluate expressions and assign variables
# use listings to export the code evaluated
#+latex_header: \lstdefinelanguage{calc}{}
# evaluate the code and format the output
#+macro: calculate $2 \(\gets\) src_calc[:exports code]{$1} = @@latex:\fbox{@@ src_emacs-lisp{(setq var-$2 (string-to-number (calc-eval "evalv($1)")))} @@latex:}@@
**** cite: macro for citing work and url to actual source
# +macro: cite @@latex:\vfill\Citation{$1}@@@@html:<p style="text-align: right; color: gray;">@@[[$2][$1]]@@html:</p>@@
# alternative cite macro for LaTeX only but with working link
#+macro: cite [[$2][@@latex:\vfill\Citation{$1}@@]]
#+latex_header: \newcommand{\Citation}[1]{\hfill{\scriptsize{\color{gray}#1}}}
**** overlay: for absolute positioning of images etc.
#+latex_header: \usepackage[overlay]{textpos} \TPGrid[0pt,0pt]{20}{20}
#+macro: overlay @@latex:\begin{textblock}{$4}($2,$3)@@[[file:$1]]@@latex:\end{textblock}@@
*** org startup on file visit
#+name: startup
#+begin_src emacs-lisp :results none
(defun esf/next-slide-or-page-up ()
(interactive)
(if (and (boundp 'org-tree-slide-mode) org-tree-slide-mode)
(org-tree-slide-move-next-tree)
(scroll-up-command)))
(local-set-key (kbd "<next>") 'esf/next-slide-or-page-up)
(defun esf/previous-slide-or-page-down ()
(interactive)
(if (and (boundp 'org-tree-slide-mode) org-tree-slide-mode)
(org-tree-slide-move-previous-tree)
(scroll-down-command)))
(local-set-key (kbd "<prior>") 'esf/previous-slide-or-page-down)
(add-hook 'org-tree-slide-play-hook
#'(lambda ()
(setq display-line-numbers nil)
(beacon-mode -1)
(setq evil-normal-state-cursor 'bar)
;; (evil-emacs-state)
(hl-line-mode 0)
(text-scale-set 2)
(org-toggle-latex-fragment)
(org-toggle-inline-images)))
(add-hook 'org-tree-slide-stop-hook
#'(lambda ()
(setq display-line-numbers 'visual)
(beacon-mode 1)
;; (evil-normal-state)
(setq evil-normal-state-cursor 'box)
(hl-line-mode 1)
(text-scale-set 0)
(org-toggle-latex-fragment)
(org-toggle-inline-images)))
(org-content 2)
(setq-local org-confirm-babel-evaluate nil)
(setq-local org-export-allow-bind-keywords t)
(setq-local org-fontify-quote-and-verse-blocks t)
(setq-local org-format-latex-options '(:background default :foreground default :scale 4))
(setq-local org-latex-image-default-height "5cm")
(setq-local org-latex-image-default-width nil)
(setq-local org-latex-pdf-process '("pdflatex -interaction nonstopmode %f"))
(setq-local org-tree-slide-breadcrumbs " ‣ ")
;; (setq-local org-tree-slide-cursor-init nil)
(setq-local org-tree-slide-fold-subtrees-skipped nil)
(setq-local org-tree-slide-skip-outline-level 4)
;; (setq-local sentence-highlight-mode nil)
(setq-local time-stamp-line-limit 1000)
(setq-local time-stamp-format "%04y.%02m.%02d %02H:%02M")
(setq-local time-stamp-active t)
(setq-local time-stamp-start "#\\+macro:[ \t]* lastchange[ \t]* ")
(setq-local time-stamp-end "$")
#+end_src
** local variables
# Local Variables:
# org-confirm-babel-evaluate: nil
# eval: (esf/execute-startup-block)
# End:
next prev parent reply other threads:[~2018-10-31 7:22 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-10-25 19:14 Help with sharing emacs-org presentation Feiming Chen
2018-10-30 8:42 ` Grant Rettke
2018-10-30 19:01 ` Martin Schöön
2018-10-30 19:43 ` Julius Dittmar
2018-10-31 7:21 ` Eric S Fraga [this message]
2018-11-01 18:51 ` Joseph Vidal-Rosset
2018-10-31 6:39 ` Jens Lechtenboerger
2018-11-03 2:30 ` Feiming Chen
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