Emacs

Running Python and R inside Emacs

Posted on by John

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  orgmode.org. 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

    #+begin_src
    #+end_src

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
    sqrt(42)
    #+end_src

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

    #+results:
    : 6.48074069840786

Now suppose we do the same with Python:

    #+begin_src python
    from math import sqrt
    sqrt(42)
    #+end_src

This time we get disappointing results:

    #+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)
    2**10
    #+end_src

This produces the lines

    #+results:
    : 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 The version of org-mode that shipped with Emacs 23.3 was quite out of date.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-do-load-languages
        '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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Advantages of everything-is-text

Posted on by John

In a typical Windows program, some output text can be copied as text but some is only an image. For example, the text in the body of a document is text, but the words on the menus are not. The text in a dialog box may or may not be.

In Emacs, text is just text, no matter where you see it. This means that Emacs is less visually interesting because there is less variety. But this also has several advantages that may not be immediately obvious. I’ll give a couple examples.

The Emacs directory editor dired lists files in a text buffer. The output is essentially the output of ls. (On Windows, Emacs emulates ls.) That means you can do anything to the output you could do to text: copy, paste, search, etc. No text is off-limits. And in editable mode, you can rename files just by editing their names. You could, for example, rename many files at once using regular expressions.

Dired also lets you navigate the file system with the same commands you use to edit files. In particular, you can keep your hands on the keyboard. (It’s possible to use the Windows file explorer without a mouse, but it’s limited and awkward.)

Another advantage of everything simply being text is that you can run a shell inside Emacs. Why not? A shell is just text output. In an ordinary shell, editing commands are mostly limited to the current line. Not all text is created equal. But when you’re running a shell inside an editor, all text is equal: current line, previous lines, and text on either side of the command prompt. And if you want a transcript of a shell session, just save the buffer displaying the session.

If you’re shopping for a text editor and spend an hour trying each one out, Emacs may not look very promising. It has odd terminology, weird key strokes, etc. But if you try Emacs long enough, and particularly if you have someone to help you get started, you start to appreciate the advantages of subtle features such as everything simply being a text buffer.

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A surprise with Emacs and Office 2007

Posted on by John

I had a little surprise when I tried to open an Excel file from Emacs. I was using dired, a sort of file explorer inside Emacs. I expected one of two things to happen. Maybe Emacs would know to launch the file using Excel. Or maybe it would open the binary file as a bunch of gibberish. Instead I got something like this:

screenshot

This was disorienting at first. Then I thought about how Office 2007 documents are zipped XML files. But how does dired know that my .xlsx file is a zip file? I suppose since Emacs is a Unix application at heart, it’s acting like a Unix application even though I was using it on Windows. It’s determining the file type by inspected the file itself and ignoring the file extension.

(Office 2007 documents are not entirely XML. The data and styling directives are XML, but embedded files are just files. The spreadsheet in this example contains a large photo. That photo is a JPEG file that gets zipped up with all the XML files that make up the spreadsheet.)

So I learned that Emacs knows how to navigate inside zip files, and that a convenient way to poke around inside an Office 2007 file is to browse into it from Emacs.

Here’s another post that discusses Emacs and Office 2007, contrasting their interface designs: Clutter-discoverability trade-off

Mental context switches are evil

Posted on by John

This week I’ve run across two examples of technical strategies to reduce mental context switches.

The first example is Pete Kruckenberg’s story of why his team chose to develop a web application using node.js even though he had extensive experience in Perl/Apache. One of his arguments is that since the client-side code has to be written in JavaScript, it saves mental energy to use JavaScript for the server-side code as well. Even for someone who knows JavaScript and Perl well, it takes mental energy to oscillate between the two languages.

There’s much more to node.js than its use of JavaScript. It requires a very different approach to developing web applications. Kruckenberg and his colleagues had to weigh multiple factors in deciding their development framework. But it may not be too much of a simplification to say they chose a big, one-time mental context switch—the node.js style of development—in order to avoid countless daily context switches between JavaScript and Perl.

The second example is Ryan Barrett’s blog post Why I run shells inside Emacs.

Mental context switches are evil. Some people handle them better than others, but not me. I handle them worse. I feel it, almost physically, when context switches whittle down my precious flow piece by piece.

Barrett explains that he first tried configuring Emacs and his shell to be similar, but the very similarity made the context switch more irritating.

Even something as small as switching between Emacs and the shell can hurt, especially when I do it thousands of times a day. … What’s worse, only some parts are different, so my muscle memory is constantly seduced into a false sense of familiarity, only to have the rug yanked out from under it seconds later.

Both examples highlight the cost of context switches. Neither Kruckenberg nor Barrett mentioned the cost of learning two contexts. Instead both focused on the cost switching between two contexts. Novices might understandably want to avoid having to learn two similar tools, but these stories were from men who had learned two tools and wanted to avoid oscillating between them.

My favorite line from Barrett is “context switches whittle down my precious flow piece by piece.” I’ve felt little distractions erode my ability to concentrate but hadn’t expressed that feeling in words.

It’s no exaggeration to call flow “precious.” Productivity can easily vary by an order of magnitude depending on whether you’re in the zone. It may sound fussy to try to eliminate minor distractions, but if these distractions make it harder to get into the zone, they’re worth eliminating.

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Bumblebee software

Posted on by John

Some say that aerodynamics can’t explain how a bumblebee flies. Perhaps that was once the case, but as far as I know there are no difficulties now. The bumblebee story persists as an urban legend. And it makes a nice metaphor for things that work better in practice than in theory.

Here’s the passage that brought the bumblebee story to mind.

Almost every software engineering principle that has become generally accepted as useful and valuable, Emacs flouts. The code is 24 years old, huge, and written by hundreds of different people. By rights, the whole thing should blow up. But it works—and works rather well.

This comes from Jim Blandy’s chapter in Beautiful Architecture. Blandy explains that Emacs’ architecture has allowed it to thrive despite some apparent disadvantages. Emacs is mostly written in its own programming language, Emacs Lisp.

Emacs Lisp has no object system, it’s module system is just a naming convention, all the fundamental text editing operations use implicit global arguments, and even local variables aren’t quite local.

In short, Emacs expects developers to be self-disciplined and does not enforce a great deal of external discipline. However, because the software is so light on bureaucracy, it is easy to customize and to contribute to.

TeX is another bumblebee project. Like Emacs, it has thrived for decades without following currently fashionable software techniques. Knuth implies in this presentation that TeX would have been a dismal failure if it had used technologies that are trendy now.

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Personal organization software

Posted on by John

I’ve tried various strategies and pieces of software for personal organization and haven’t been happy with most of them. I’ll briefly describe my criteria and what I’ve found.

My needs are fairly simple. I don’t need or want something that could scale to running a multinational corporation.

I’d like something with a portable, transparent data format. I don’t want the data stored in a hidden file or in a proprietary format. I’d like to be able to read the data without the software that was used to write it.

I’d like to be as structured or unstructured as I choose and not have to conform to a rigid database schema. I’d like to be able to do ad hoc queries as well as strongly typed queries.

I’d like something that exports to paper easily.

Here’s what I found: org-mode. It’s an Emacs mode for editing text files. It provides sophisticated functionality, but all the sophistication is in the software, not the data format. It’s more convenient to work with org-mode files in Emacs, but the raw file format is just a light-weight mark-down, easy for a person or a computer to parse.

When I went back to using Emacs a year ago after a 15-year hiatus, I heard good things about org-mode but didn’t understand what people liked about it. I heard it described as a to-do list manager and was not impressed. I’m not interested in the features I was first introduced to: tracking the status of to-do items and making agendas. I still don’t use those features. It took me a while to realize that org-mode was what I had been looking for. It was similar in spirit to something I’d thought about writing.

Emacs is an acquired taste. But someone who doesn’t use Emacs could get some good ideas from looking at org-mode. I imagine some people have borrowed its ideas and implemented them for other editors. If not, someone should.

The org-mode site has links to numerous introductions and tutorials. I like the FLOSS Weekly interview with org-mode’s creator Carsten Dominik. In it he explains his motivation for writing org-mode and gives a high-level overview of its features.

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Emacs calculator

Posted on by John

Emacs has quite a sophisticated scientific calculator. Like many other things in Emacs, it is both powerful and idiosyncratic.

The calc module ships with Emacs as of version 22. The calc manual has full documentation, but it takes some work to understand. This post may make it easier to read the manual.

The manual says you can start calc with the command M-#. That did not work for me, but the command M-x calc did.

Calc has two modes: RPN (reverse Polish notation) and algebraic. RPN is the default mode and uses very terse commands, often one or two letters. Most people will find the algebraic mode syntax more familiar. Commands in algebraic mode begin with a quote and use longer, more descriptive names.

For example, suppose you want to find the cosine of 5. You can do this in RPN mode by typing 5 and pressing return, then typing shift-C. To do the same calculation in algebraic mode, type 'cos(5) and return.

I’ll step through to gamma function documentation as an example of how to interpret the manual. It says

The f g (calc-gamma) [gamma] command computes the Euler gamma function. …

This means that in RPN mode, you enter the argument of the gamma function, say 5, and then type fg. (Not f g as you might expect.) You could also enter 5 and then type M-x calc-gamma. In algebraic mode, the syntax would be 'gamma(5). So the pattern in the manual is

RPN keystrokes (lisp function) [algebraic syntax].

The calc module has an amazing range of functionality — symbolic calculation, matrix operations, graphics, etc. — though I don’t imagine I’d use much of it. In my mind, the benefit of calc is being able to do a quick calculation without leaving Emacs. Although one could do sophisticated calculations in calc, I doubt I would for two reasons. First, if I have to look up how to do something in calc, I lose the benefit of not interrupting my workflow. Second, I don’t want to start a computation in calc and then discover I need something that isn’t there and then have to switch to another tool such as SciPy, Mathematica, or R.

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Emacs command to add HTML tags

Posted on by John

A while back I asked Jason Fruit how to add HTML tags to text in Emacs, something like the format painter in Microsoft applications. He said he didn’t know of anything and wrote the following macro for me.

(defun tag-word-or-region (tag)
    "Surround current word or region with a given tag."
    (interactive "sEnter tag (without <>): ")
    (let (pos1 pos2 bds start-tag end-tag)
    (setq start-tag (concat "<" tag ">"))
    (setq end-tag (concat "</" tag ">"))
    (if (and transient-mark-mode mark-active)
        (progn
            (goto-char (region-end))
            (insert end-tag)
            (goto-char (region-beginning))
            (insert start-tag))
        (progn
            (setq bds (bounds-of-thing-at-point 'symbol))
            (goto-char (cdr bds))
            (insert end-tag)
            (goto-char (car bds))
            (insert start-tag)))))

I added the following line to my .emacs file to bind Jason’s macro to the key sequence C-x t.

    (global-set-key "C-xt" 'tag-word-or-region)

To add a tag to a single word, place the cursor before or in the word and execute the command. To tag a block of text, select the text first then execute the command.

More Emacs posts

Miscellaneous Emacs adventures

Posted on by John

I recently found out there’s an Emacs command M-x woman that’s a pun on “w/o man”, i.e. a way to read online help without using the usual man command.

* * *

I tried to edit a 1.2 GB text file with Emacs the other day. I got an error saying that Emacs has a 500 MB file size limit on 32-bit systems. This was on a 32-bit Windows XP machine, so the warning was reasonable. I appreciated that it promptly said it could not open the file.

I tried again on my 64-bit Windows 7 machine and got the same message; I believe I’m running a 32-bit version of Emacs on my 64-bit PC.

I also tried opening the file with Emacs on a 64-bit Red Hat Enterprise Linux box with 16 GB of memory. This time I did not get a file size message. Instead, Emacs crashed.

The file opened quickly on Windows, even my 32-bit XP box, using Notepad++.

* * *

When I set up Emacs on Windows, I created an “Open with Emacs” context menu following the instructions here. That has worked well except for two problems.

  1. Every file is opened in a new instance of Emacs.
  2. It stopped working on one of my computers for reasons unknown.

I’ve been meaning to solve the first problem, and when the second happened I decided it was time. According to the Emacs documentation,

The recommended way to associate files is to associate them with
emacsclientw.exe. In order for this to work when Emacs is not yet started, you will also need to set the environment variable ALTERNATE_EDITOR to runemacs.exe. To open files in a running instance of Emacs, you will need to add the following to your init file: (server-start)

I had to tinker with that a little to make it work. I know I had to add the path to my Emacs bin directory to my PATH environment variable but I don’t remember what else I did.

The key thing to note is that you should associate files with emacsclientw.exe rather than with runemacs.exe. I used the instructions in this article to remove the association with the latter. Thanks to Mark for pointing out the article.

(The Windows “Open with” feature remains a mystery. The article above explains how to remove a program from the “Open with” list, and the directions worked for removing runemacs.exe. But they did not work for removing other programs. I’m also unclear how you add something to the “Open with” list. If you right-click on a file and select “Open with -> Choose program …” the program you select may appear in the “Open with” list next time. Or not. This did add emacsclientw.exe to the list.)

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