Five lemma, ASCII art, and Unicode

A few days ago I wrote about creating ASCII art in Emacs using ditaa. Out of curiosity, I wanted to try making the Five Lemma diagram. [1]

The examples in the ditaa site all have arrows between boxes, but you don’t have to have boxes.

Here’s the ditaa source:

A₀ ---> A₁ ---> A₂ ---> A₃ ---> A₄
|       |       |       |       |            
| f₀    | f₁    | f₂    | f₃    | f₄    
|       |       |       |       |      
v       v       v       v       v      
B₀ ---> B₁ ---> B₂ ---> B₃ ---> B₄

and here’s the image it produces:

Five lemma diagram

It’s not pretty. You could make a nicer image with LaTeX. But as the old saying goes, the remarkable thing about a dancing bear is not that it dances well but that it dances at all.

The trick to getting the subscripts is to use Unicode characters 0x208n for subscript n. As I noted at the bottom of this post, ditaa isn’t strictly limited to ASCII art. You can use Unicode characters as well. You may or may not be able to see the subscripts in the source code they are not part of the most widely supported set of characters.

* * *

[1]  The Five Lemma is a diagram-chasing result from homological algebra. It lets you infer properties the middle function f from properties of the other f‘s.

ASCII art diagrams in Emacs org-mode

Yesterday I wrote about ASCII art diagrams and gave four reasons you might want to use this ancient approach to creating simple diagrams:

  • It could be quicker than creating a graphical image .
  • You can paste them into plain text documents like source code files.
  • They can be produced programmatically.
  • There is software to turn ASCII art into more polished images.

Today I’ll post a few notes about how to create graphical versions of ASCII diagrams in Emacs with org-mode.

Running code inside org-mode

You can embed and execute source code in org-mode files. I wrote a couple posts about this, one showing how to run Python and R inside org-mode and another showing how to mix languages in org-mode. The latter shows Perl calling R and Python, all in 14 lines of code.

There are currently 39 programming languages that org-mode can call by default. In addition to conventional programming languages like the ones listed above, org-mode also supports ditaa, the language that treats ASCII art as a specification language to produce graphics.

You can edit code blocks just as you would other text in an org-mode file. But if you’d like to edit a code block in its language’s mode, type C-c ' from inside the code block. If you’re editing Python code, for example, this will open a new window, in Python mode, containing just that code block. If you type C-c ' inside a ditaa code block, Emacs opens a new window in “artist mode,” a mode specifically for editing ASCII art.

You can run code inside org-mode two ways: interactively and for export. With your cursor inside a block of code, type C-c C-c to execute the code and report the results. You can also export an entire org-mode document and have the results of code execution embedded in the final document. This works much the same as “*weave” projects like Sweave, Pweave, and Hweave. But while each of these is specific to a particular programming language (R, Python, and Haskell respectively), org-mode works with dozens of languages, including ditaa.

Running ditaa inside org-mode

You embed ditaa code just like you’d embed any other code. In the first post mentioned above, I gave this example of calling R:

    #+begin_src R

Here’s the analogous code for ditaa:

    #+BEGIN_SRC ditaa :file foo.png
    | Hello |

The markers to begin and end a source code segment can be upper or lower case. I used lower case in my previous post, but it may be more readable to use upper case so that the markers stand out better from their arguments.

The R example above didn’t use any header arguments, though it could have. With ditaa, you must provide a header argument: the name of the file to save the graphics in.

If you run the ditaa code by navigating inside the code block and running C-c C-c, Emacs will add a couple lines after the code block:


This is the literal text, what you’d see if you opened the file in another editor. But org-mode uses the double brackets for links. You wouldn’t see the double brackets. Instead you’d see a hyperlink with text file:foo.png. Clicking on that link opens the image.

Hello image produce by ditaa

You can export the org-mode file with the command C-c C-e. This brings up a menu of export options: h for HTML, l for LaTeX, etc. Within each of these are further options. For example, you could type l for LaTeX and then type l again to select export to LaTeX or type p to have have org-mode run LaTeX on the file and produce a PDF. If you know you want a PDF, you could do this all in one command: C-c C-l l p.

You can control whether org-mode exports code or the results of running code (or both or neither). Org-mode exports the results of ditaa code, i.e. graphics files, by default. This makes sense: your PDF file will have a nice image version of your diagram, not the ASCII art used as its source code.

Configuration and troubleshooting

By default, the only programming language you can run inside org-mode is Emacs Lisp. This makes sense. You want to be deliberate about what code you run, but if you don’t want to run Emacs Lisp you’d better not run Emacs!

Inside your Emacs configuration file, you specify what languages org-mode is allowed to run. Here’s an example allowing Python and ditaa:

    (org-babel-do-load-languages 'org-babel-load-languages '(
        (python . t) 
        (ditaa . t))

Recent versions of Emacs are supposed to ship with ditaa, but the ditaa jar file was missing from the two computers I experimented with. Emacs complained

    org-babel-execute:ditaa: Could not find ditaa.jar at ...

and so I copied ditaa.jar to the place where Emacs said it was looking for it. That worked, but it’s kind of a kludge because now I had two copies of the jar file. A better solution is to tell Emacs where you already have ditaa.

I like to use the exact same init.el file on every machine I use and so I added a section where I put OS-specific and machine-specific configuration. Here I put a different path to ditaa for each OS.

    ;; OS specific
        ((string-equal system-type "windows-nt") ; Microsoft Windows
                (setq-default ispell-program-name "C:/bin/Aspell/bin/aspell.exe") 
                # etc.
                (setq org-ditaa-jar-path "c:/bin/ditaa/ditaa.jar")
        ((string-equal system-type "gnu/linux") ; Linux
                (setq x-select-enable-clipboard t)
                 # etc.
                (setq org-ditaa-jar-path "/usr/bin/ditaa")

Rare letter combinations and key chords

A bigram is a pair of letters. For various reasons—word games, cryptography, user interface development, etc.—people are interested in knowing which bigrams occur most often, and so such information is easy to find. But sometimes you might want to know which bigrams occur least often, and that’s harder to find. My interest is finding safe key-chord combinations for Emacs.

Peter Norvig calculated frequencies for all pairs of letters based on the corpus Google extracted from millions of books. He gives a table that will show you the frequency of a bigram when you mouse over it. I scraped his HTML page to create a simple CSV version of the data. My file lists bigrams, frequencies to three decimal places, and the raw counts: bigram_frequencies.csv. The file is sorted in decreasing order of frequency.

The Emacs key-chord module lets you bind pairs of letters to Emacs commands. For example, if you map a command to jk, that command will execute whenever you type j and k in quick succession. In that case if you want the literal sequence “jk” to appear in a file, pause between typing the j and the k. This may sound like a bad idea, but I haven’t run into any problems using it. It allows you to execute your most frequently used commands very quickly. Also, there’s no danger of conflict since neither basic Emacs nor any of its common packages use key chords.

The table below gives bigrams whose percentage frequency rounds to zero keeping three decimal places. See the data file for details.

Since Q is always followed by U in native English words, it’s safe to combine Q with any other letter. (If you need to type Qatar, just pause a little after typing the Q.) It’s also safe to use any consonant after J and most consonants after Z. (It’s rare for a consonant to follow Z, but not quite rare enough to round to zero. ZH and ZL occur with 0.001% frequency, ZY 0.002% and ZZ 0.003%.)

Double letters make especially convenient key chords since they’re easy to type quickly. JJ, KK, QQ, VV, WW, and YY all have frequency rounding to zero. HH and UU have frequency 0.001% and AA, XX, and ZZ have frequency 0.003%.

Note that the discussion above does not distinguish upper and lower case letters in counting frequencies, but Emacs key chords are case-sensitive. You could make a key chord out of any pair of capital letters unless you like to shout in online discussions, use a lot of acronyms, or write old-school FORTRAN.

Update (2 Feb 2015):

This post only considered ordered bigrams. But Emacs key chords are unordered, combinations of keys pressed at or near the same time. This means, for example, that qe would not be a good keychord because although QE is a rare bigram, EQ is not (0.057%). The file unordered_bigram_frequencies.csv gives the combined frequencies of bigrams and their reverse (except for double letters, in which case it simply gives the frequency).

Combinations of J and a consonant are still mostly good key chords except for JB (0.023%), JN (0.011%), and JD (0.005%).

Combinations of Q and a consonant are also good key chords except for QS (0.007%), QN (0.006%), and QC (0.005%). And although O is a vowel, QO still makes a good key chord (0.001%).

Managing Emacs windows

When you have Emacs split into multiple windows, how do you move your cursor between windows? How do you move the windows around?

Update (27 Jan 2015): You may want to skip the post below and use ace-window.  I plan to use it rather than my solution below. Also, see Sacha Chua’s video on window management, including using ace-window.

Moving the cursor between windows

You can use C-x o to move the cursor to the “other” window. That works great when you only have two windows: C-x o toggles between them.

When you have more windows, C-x o moves to the next window in top-to-bottom, left-to-right order. So if you have five windows, for example, you have to go to the “other” window up to four times to move to each of the windows.

The cursor is in the A window. Repeatedly executing C-x o will move the cursor to C, B, and D.

There are more direct commands:

  • windmove-up
  • windmove-down
  • windmove-left
  • windmove-right

You might map these to Control or Alt plus the arrow keys to have a memorable key sequence to navigate windows. However, such keybindings may conflict with existing keybindings, particularly in org-mode.

Moving windows

You can move windows around with the buffer-move. (Technically the windows stay fixed and the buffer contents moves around.)

Super and Hyper keys

Since the various Control arrow keys and Alt arrow keys are spoken for in my configuration, I thought I’d create Super and Hyper keys so that Super-up would map to windmove-up etc.

Several articles recommend mapping the Windows key to Super and the Menu key to Hyper on Windows. The former is problematic because so many of the Windows key combinations are already used by the OS. I did get the latter to work by adding the following to the branch of my init.el that runs on Windows.

        (setq w32-pass-apps-to-system nil
              w32-apps-modifier 'hyper)
        (global-set-key (kbd "<H-up>")    'windmove-up)
        (global-set-key (kbd "<H-down>")  'windmove-down)
        (global-set-key (kbd "<H-left>")  'windmove-left)
        (global-set-key (kbd "<H-right>") 'windmove-right)  

I haven’t figured out yet how to make Super or Hyper keys work on Linux. Suggestions for setting up Super and Hyper on Linux or Windows would be much appreciated.

Interview with Sacha Chua

I spoke with with Sacha Chua last week. We talked about entrepreneurship, Emacs, having eclectic interests, delegation, and more.

Navigation cons from Sacha's blog

J: I ran into you by searching on Emacs topics. When I look at your blog, I see that you do a lot of interesting things, but it’s a little hard to get a handle on exactly what you do.

S: Oh, the dreaded networking quirky question. What exactly do you do?

J: Yeah, people have said the same thing to me. Not to put you in a box, but I was curious. I see from your site that you do graphic art — sketching and such — and it doesn’t create the impression that you’re someone who would spend a lot of time in front of Emacs. So I’m curious how these things fit together, how you got started using Emacs and how you use it now.

Image by Sacha Chua

S: So my background is actually fairly technical. I’ve been doing computer programming for ages and ages. In high school I came across a book Unix Power Tools, which is how I got interested in Emacs. And because I was interested in programming, in open source, a little bit of wearable computing as well, I got to know Emacs and all these different modules it had. For example, Emacspeak is amazing! It’s been around since the 1990s and it’s a great way to use the computer while you’re walking around. Because I love programming and because I wanted to find a way to help out, I ended up maintaining PlannerMode and later EmacsWiki mode as well.

When I went to university, I took up computer science. After I finished, I taught. Then I took my masters in Toronto, where I am now. Emacs was super helpful — being able to do everything in one place. After I finished my masters, I did a lot of software consulting with IBM. I did business consulting as well. Then in 2012, after saving up, I decided to go on pretty much the same adventure you’re on. I’m completely unhirable for the next five years! Most businesses struggle for the first five years, so I saved up enough to not worry too much about my expenses for the next five years. I’m one year in, four years to go, and that’s where I am.

At networking events, I like to shake people up a bit by telling them I’m semi-retired. I’m in this five-year experiment to see how awesome life can be and what I can do to make things better. I’ve done technical consulting, business consulting, sketching, illustration, writing, all sorts of things. Basically, my job description is context-dependent.

J: I understand that.

S: I use Emacs across all the things I do. When I’m doing technical and business consulting, I use Emacs to edit code, to draft documents, even to outline comic strips. And when I’m doing illustration, Emacs — especially Org Mode — helps me keep track of clients and deliverables, things to do, agenda, calendar, deadlines.

J: I’m basically running my life through Org Mode right now. When you say you use Emacs to draft documents, are you using LaTeX?

S: I used LaTeX when I was working on my master’s thesis and other papers, I think. Now I mostly use org mode and export from there.

J: Are you using Emacs for email?

S: I used to. But I’m stuck on Windows to use drawing programs like Sketchbook Pro on my Tablet PC. So it’s harder to set up my email like I had it set up when I used Ubuntu. Back when I used Ubuntu, I was very happy with Gnus.

J: Do you work entirely on Windows, or do you go back and forth between operating systems?

S: I have a private server that runs Linux. On Windows I run Cygwin, but I miss some of the conveniences I had when I had a nicely set-up Linux installation.

J: When you’re running Emacs on Windows, I’m sure you run into things that don’t quite work. What do you do about that?

S: Most things work OK if they’re just Emacs Lisp, but some things call a shell command or use some library that hasn’t been ported over yet. Then I basically wail and gnash my teeth. Sometimes I get things working by using Cygwin, but sometimes it’s a bit of a mess. I don’t use Emacs under Cygwin because I prefer how it works natively. I don’t run into much that doesn’t work.

J: So what programming languages do you use when you’re writing code?

S: I do a lot of quick-and-dirty things in Emacs Lisp. When I need to do some XML parsing or web development, I’ll use Ruby because a lot of people can read it and there are a lot of useful gems. Sometimes I’ll do some miscellaneous things in Perl.

I love doing programming and putting together tools. And I quite enjoy drawing, helping people with presentation and design. So this is left brain plus right brain.

It does boggle people that you can have more than one passion, but others are, like, “Yeah, I know, I’m like that too.”

J: I think having an interest in multiple things is a healthier lifestyle, but it’s a little harder to market.

S: Actually, no. I finally figured out a name for my company, ExperiVis, after a year of playing with it. People reach out to me and we figure out whether it’s a good fit. I don’t need to necessarily guide people to just this aspect or another of my work. I like the fact that people bump into these different things.

J: When we scheduled this call, I went through your virtual assistant. How do you use a virtual assistant?

S: One of the things I don’t like to do is scheduling. I used to get stressed out about scheduling when I did it myself. I’ve always been interested in delegating and taking advantage of what other people enjoy and are good at. I work with an assistant — Criselda. She lives in the Philippines. I found her on oDesk. She works one to four hours a week, more or less, and keeps track of her time.

J: What else might you ask a VA to do?

S: I’ve asked people to do web research. I’ve had someone do a little bit of illustration for me. I’ve had someone do a little bit of programming for me because I want to learn how to delegate technical tasks. He does some Rails prototyping for me. I have someone doing data entry and transcription. It’s fascinating to see how you can swap money for time, especially for things that stress me out, or bore me, or things I can’t do.

Every week I go over my task list with my VA to see which of the tasks I should have delegated. Still working on it!

* * *

Later on in the conversation Sacha asked about my new career and had this gem of advice:

Treating this as a grand experiment makes it much easier for me to try different approaches and not be so scared, to not treat it as a personal rejection if something doesn’t work.

Related posts:

People I’ve interviewed and people who have interviewed me

Python / Emacs setup

When I got a new computer a few days ago, I installed the latest version of Emacs, 24.2, and broke my Python environment. I decided to re-evaluate my environment and start over. I asked a question on the Python Google+ group and here’s a summary of the Emacs packages recommended.

  • python-mode
  • rainbow-mode, rainbow-delimiters-mode
  • flymake-mode (hooked up to flymake-pyflakes)
  • linum-on
  • jedi
  • pycheckers + pyflakes
  • rope
  • electric-pair
  • show-paren
  • auto-complete
  • yassnippets

What recommendations do you have for packages? Links to relevant articles?

It might be better to leave your comments on Google+ rather than here so the answers will be in one place.

It’s not the text editor, it’s text

Vivek Haldar had a nice rant about editors a couple days ago. In response to complaints that some editors are ugly, he writes:

The primary factor in looking good should be the choice of a good font at a comfortable size, and a syntax coloring theme that you like. And that is not something specific to an editor. Editors like Emacs and vi have almost no UI!

To illustrate his point, here’s what my Emacs looks like without text:

There’s just not much there, not enough to say it’s pretty or ugly.

When people say that Emacs is not pretty, I think they mean that plain text is not pretty.

For better and for worse, everything in Emacs is text. The advantage of this approach is consistency. Everything uses the same commands for navigation and editing: source code, error messages, directory listings, … Everything is just text. The disadvantage is that you don’t have nicely designed special windows for each of these things, and it does get a little monotonous.

When people say they love their text editor, I think they love text. They prefer an environment that allows them to solve problems by editing text files rather than clicking buttons. And as Vivek says, that is not something specific to a particular editor.

Related posts:

Editing by semantic units

The most basic text editor commands operate on lines and characters: move up or down a line, delete the next or previous character, etc. More advanced commands operate on context-specific semantic units. In the context of English prose, this means words, sentences, and paragraphs. In the context of source code, it means blocks and functions, however these are delimited in a particular language. In the context of an outline, it means navigating the tree.

One way to become more proficient at using your editor of choice is to become fluent at working with larger semantic units. Of course this saves keystrokes, though as I argued here, I don’t think typing speed matters so much. However, working in larger semantic units reduces errors. It also improves the chances that you can act on an idea before you forget what you were doing. These factors matter more than typing speed per se.

The general principles above apply to any editor. Here I’ll sketch how these ideas work in Emacs.

As a general rule, commands that operate on physical units begin with Control and analogous commands that work on semantic units being with Meta (Alt). For example, C-f moves forward a character and M-f moves forward a word. C-e moves to the end of a line and M-e moves to the end of a sentence.

Emacs extends the meaning of prose units by analogy in other contexts. For example, in calendar mode, a “line” corresponds to a week, and a “paragraph” corresponds to a month.

Emacs has numerous commands to work on “balanced expressions,” i.e. text surrounded by parentheses, brackets, braces, quotation marks, etc. Often the default keybindings are consistent with those used for other units. For example, “f” means forward and “b” means backward in any context. C-f and C-b move by character, M-f and M-b move by word, and C-M-f and C-M-b move by balanced expression. Emacs also has commands for working with function definitions: selecting a function definition, moving to the beginning or end of a function definition, etc. In Lisp, function definitions are balanced expressions. In other languages, like C, these ideas are distinct.

This morning, Irreal points out an Emacs package expand-region that selects larger and larger semantic regions. The first time it is invoked, it selects the immediate context of the cursor. Each subsequent invocation selects a larger context, moving up the parse tree of the content. I look forwarding to trying it.

* * *

For daily tips on using Unix, follow @UnixToolTip on Twitter.

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How Emacs influenced Ruby

Ruby creator Yukihiro Matsumoto gave a presentation How Emacs changed my Life in which he explains how Emacs influenced him personally and how it influenced the programming language he created. Here is his summary:

  1. Emacs taught me freedom for software.
  2. Emacs taught me how to code.
  3. Emacs taught me the power of Lisp.
  4. Emacs taught me how to implement a core language.
  5. Emacs taught me how to implement a garbage collector.
  6. Emacs helped me to code and debug.
  7. Emacs helped me to write and edit text/mails/documents.
  8. Emacs helped me to be an effective programmer.
  9. Emacs made me a hacker.
  10. Emacs has changed my life.

Shuffling Emacs windows

Emacs lets you split your screen into windows, what other applications might call panels. This can be quite handy. However, I often want to move the windows around and I couldn’t find how to do that. I asked Xah Lee, he posted the question on G+, and Mark Hepburn answered with a pointer to code that does what I wanted: buffer-move.el

(Strictly speaking the windows don’t move; the buffers move between the windows. But I think of it as moving the windows around.)

Lucas Bonnet explains how his buffer-move works:

This file is for lazy people wanting to swap buffers without
typing C-x b on each window. This is useful when you have :

|              |             |
|    #emacs    |    #gnus    |
|              |             |
|                            |
|           .emacs           |
|                            |

and you want to have :

|              |             |
|    #gnus     |   .emacs    |
|              |             |
|                            |
|           #emacs           |
|                            |

This is exactly what I had in mind. I did have one problem, however, though it wasn’t with buffer-move per se. The file defines four functions for moving buffers between windows and suggests key bindings. The author says he uses the following.

(global-set-key (kbd "<C-S-up>")     'buf-move-up)
(global-set-key (kbd "<C-S-down>")   'buf-move-down)
(global-set-key (kbd "<C-S-left>")   'buf-move-left)
(global-set-key (kbd "<C-S-right>")  'buf-move-right)

This works fine, except when one of the windows contains an org-mode buffer. Org-mode has its own bindings for control-shift-up etc.

I learned that global-set-key does not globally set a key binding! Well, it does as long as there are no conflicts. But local bindings, i.e. bindings specific to a mode, have precedent. After some searching and trail-and-error, I added the following to my .emacs to override org-mode’s local bindings.

(add-hook 'org-mode-hook '(lambda ()
   (local-set-key [C-S-up]    'buf-move-up)
   (local-set-key [C-S-down]  'buf-move-down)
   (local-set-key [C-S-left]  'buf-move-left)
   (local-set-key [C-S-right] 'buf-move-right)))

Clipboard history

The Windows clipboard only remembers the most recent thing you copied [1]. This can be very disappointing. Maybe you cut a large block of text intending to paste it somewhere, but without thinking you cut something else, and then realize you’ve just wiped out your first cut. Here are a few possible alternatives for Windows, MS Office, and Emacs.

A few years ago I tried ClipX, a free clipboard history manager for Windows, based on Jeff Atwood’s recommendation. It worked OK at first, but then I had problems with it and stopped using it. It looks like the software hasn’t been updated since 2008. If you know of a better alternative, please let me know. Also, please let me know if you have suggestions for Ubuntu.

(Update: See the comments for numerous suggestions of ClipX-like products. Also, see PHenry’s comment about clipboard history in Visual Studio.)

MS Office has its own clipboard that will store 24 entries. It stores things that have been copied either inside or outside of Office applications, but you can only paste from the Office clipboard using an Office application.

Emacs has a “kill ring” which is essentially a clipboard. It also has “registers” which are like named clipboard items.

Yesterday Emacs Knight posted a handy little bit of code for viewing your kill ring.

(global-set-key "C-cy" '(lambda ()
    (interactive) (popup-menu 'yank-menu)))

If you add this to your .emacs file, you can type ctrl-c y to pull up a little GUI menu displaying the contents of your kill ring.

[1] I’ve heard that Windows actually keeps more clipboard history, but it doesn’t provide a user interface for accessing that history. I don’t know whether this is true. But if it is, you could access the history programmatically. Maybe Office isn’t maintaining its own clipboard but just exposing more of the system clipboard.

Playing with Eshell

I’ve been trying out Eshell lately. It’s a shell implemented in Emacs Lisp. Here I’ll mention a few features I’ve found interesting.

The command M-x shell lets you run a shell inside Emacs. This is quite handy, but it runs a different shell on each platform. For example, it might pull up bash on Linux and cmd.exe on Windows. Eshell provides a consistent shell across operating systems.

Eshell is one way to have a bash-like shell on Windows, so it’s an alternative to Cygwin. I haven’t used Eshell or Cygwin extensively, but Cygwin feels like some alien thing awkwardly grafted on to my Windows machine. Eshell feels more like cmd.exe with bash features added.

Of course Eshell is integrated with Emacs. One example of that is being able to run Emacs commands as shell commands. For example, you can run dired from the shell to open a directory in the Emacs directory editor.

Eshell has pseudo-devices. These act like Unix devices, but they’re implemented in Emacs and therefore run on non-Unix platforms. For example, you could direct command output to /dev/clip to send it to the system clipboard or to  /dev/kill to add it to the Emacs kill ring.

And now for a little silliness. Here’s an excerpt from Tron featuring Eshell.

It goes by very fast, but here’s the frame that shows Eshell:

eshell screen shot

For much more on Eshell, see A Complete Guide to Mastering Eshell.

Mixing R, Python, and Perl in 14 lines of code

This is a continuation of my previous post, Running Python and R inside Emacs. That post shows how to execute independent code blocks in Emacs org-mode. This post illustrates calling one code block from another, each written in a different language.

The example below computes sin2(x) + cos2(x) by computing the sine function in R, the cosine function in Python, and summing their squares in Perl. As you’d hope, it returns 1. (Actually, it returns 0.99999999999985 on my machine.)

To execute the code, go to the #+call line and type C-c C-c.

#+name: sin_r(x=1)
#+begin_src R

#+name: cos_p(x=0)
#+begin_src python
import math
return math.cos(x)

#+name: sum_sq(a = 0, b = 0)
#+begin_src perl
$a*$a + $b*$b;

#+call: sum_sq(sin_r(1), cos_p(1))

Apparently each function argument has to have a default value. If that’s documented, I missed it. I gave the sine and cosine functions default values that would cause the call to sum_sq to return more than 1 if the defaults were used.

Running Python and R inside Emacs

Emacs org-mode lets you manage blocks of source code inside a text file. You can execute these blocks and have the output display in your text file. Or you could export the file, say to HTML or PDF, and show the code and/or the results of executing the code.

Here I’ll show some of the most basic possibilities. For much more information, see And for the use of org-mode in research, see A Multi-Language Computing Environment for Literate Programming and Reproducible Research.

Source code blocks go between lines of the form


On the #+begin_src line, specify the programming language. Here I’ll demonstrate Python and R, but org-mode currently supports C++, Java, Perl, etc. for a total of 35 languages.

Suppose we want to compute √42 using R.

#+begin_src R

If we put the cursor somewhere in the code block and type C-c C-c, org-mode will add these lines:

: 6.48074069840786

Now suppose we do the same with Python:

#+begin_src python
from math import sqrt

This time we get disappointing results:

: None

What happened? The org-mode manual explains:

… code should be written as if it were the body of such a function. In particular, note that Python does not automatically return a value from a function unless a return statement is present, and so a ‘return’ statement will usually be required in Python.

If we change sqrt(42) to return sqrt(42) then we get the same result that we got when using R.

By default, evaluating a block of code returns a single result. If you want to see the output as if you were interactively using Python from the REPL, you can add :results output :session following the language name.

#+begin_src python :results output :session
print "There are %d hours in a week." % (7*24)

This produces the lines

: There are 168 hours in a week.
: 1024

Without the :session tag, the second line would not appear because there was no print statement.

I had to do a couple things before I could get the examples above to work. First, I had to upgrade org-mode. The version of org-mode that shipped with Emacs 23.3 was quite out of date. Second, the only language you can run by default is Emacs Lisp. You have to turn on support for other languages in your .emacs file. Here’s the code to turn on support for Python and R.

    'org-babel-load-languages '((python . t) (R . t)))

Update: My next post shows how to call code in written in one language from code written in another language.

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