Class 7: Emacs and org-mode (DRAFT)

First, how do you find out which version of linux you are using? Most linux systems have a file that describes the version of linux. It's usually a "release" file in the /etc directory. "etc" is a directory tree that contains most of the system wide settings. On Redhat and CentOS Linux systems, there is a /etc/redhad-release file:

ls -l /etc/*release
# -rw-r--r-- 1 root root 27 Apr 25  2010 /etc/redhat-release

cat /etc/redhat-release 
CentOS release 5.5 (Final)

cat /etc/issue
CentOS release 5.5 (Final)
Kernel \r on an \m

Ubuntu and any other system that follows the Linux Standard Base (LSB) guidelines for Linux have one or both of two files named /etc/lsb-release and /etc/issue that document the version of the system:

cat /etc/issue
Ubuntu 11.04

cat /etc/lsb-release 
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=11.04
DISTRIB_CODENAME=natty
DISTRIB_DESCRIPTION="Ubuntu 11.04"

There are many different ways to look at the software on a Ubuntu computer, but this is the way that I go about it.

First, what is installed?

researchtools@ubuntu:~$ dpkg --get-selections | wc -l
1789

dpkg --get-selections | head
adduser                                         install
apel                                            install
apparmor                                        install
apparmor-utils                                  install
apport                                          install
apport-symptoms                                 install
apt                                             install
apt-transport-https                             install
apt-utils                                       install
apt-xapian-index                                install

dpkg --get-selections | grep emacs
emacs                                           install
emacs-jabber                                    install
emacs23                                         install
emacs23-bin-common                              install
emacs23-common                                  install
emacsen-common                                  install
python-ropemacs                                 install

If you want to read through them all, use a pager (e.g. more, less or most):

dpkg --get-selections | less

If you know a package that is installed, you can use listfiles option to dpkg. A common task is to list the programs available in a package.

dpkg --listfiles gmt | grep bin | head
/usr/bin
/usr/bin/GMT
/usr/lib/gmt/bin
/usr/lib/gmt/bin/gmt_shell_functions.sh
/usr/lib/gmt/bin/gmtget
/usr/lib/gmt/bin/gmtlogo
/usr/lib/gmt/bin/isogmt
/usr/lib/gmt/bin/psbbox.sh
/usr/lib/gmt/bin/blockmean
/usr/lib/gmt/bin/blockmedian

If you would like to know which package a file belongs to, you can ask the system. We can combine that with the command type that tells you where in your path a program is located. For example, the sudo command that gives you access to administrator capabilities (aka "root"). The "hashed" means that the shell has an internal table of commands to speed up searching.

type sudo
sudo is hashed (/usr/bin/sudo)

dpkg --search /usr/bin/sudo
sudo: /usr/bin/sudo

There are also an interactive text based program to examine packages without a full graphical interface:

http://wiki.debian.org/Aptitude

I missed one emacs package that we need for today in the Virtual Machine. Without a package called htmlize, org-mode output will not have code colored. It is a part of the emacs goodies package. texlive is used to produce PDF documents.

sudo apt-get install emacs-goodies-el
sudo apt-get install texlive
sudo apt-get install texlive-latex-extra

I will give an introduction to using emacs for basic files here. This really needs a video of the section to show what I'm doing.

• opening a directory
• searching with C-s

The format for org-mode is very similar to Mediawiki. However, the characters used to mark up the text are slightly different. There are large numbers of markup languages, but we will ignore the others right now.

Start by opening a new org mode file. Org-mode starts by default if the file name ends in ".org". "File" -> "Visit New File" and pick type in "example.org".

An alternative approach is to use the keyboard shortcut:

C-x C-f example.org

At the bottom of the window, you will see:

--:--- example.org All L1 (Org)------------

You are staring at a blank page, but there are helpers under the "Org" and "Tbl" (meaning table) menus that just appeared at the top of the Window. Select Org -> New Heading. You will see a "*" appear. Headings are made up of 1 or more "*" characters followed by the text.

* Introduction

Sub-headings have two like this:

** This is a sub heading

You can type paragraphs in any heading or sub-heading.

Lists start with "-". A list looks like this:

- first item
- another item
- yet another

The list will look like this:

• first item
• another item
• yet another

But how do we see what the results are??? We have to "publish" or "export" the document. There are many formats, but we will start with HTML.

"Org" -> "Export/Publish"

You will now see lots of options for the output. Start off by trying "export as HTML and open in browser".

Press the letter "b"

You now should see Firefox open up and show the file "example.html".

You can also export to a pdf:

"Org" -> "Export/Publish" -> press "d"

Tables are built with the vertical "|" character. Entries with all "—" characters create horizontal rulers.

| Column header  | something else           |
|----------------+--------------------------|
| hello          | world                    |
| a second entry | what do you want to say? |

Would look like this:

Column header	something else
hello	world
a second entry	what do you want to say?

You can also create example blocks and source code blocks. Inside of an example, it will not show the normal formatting. Try this:

#+BEGIN_EXAMPLE 
* This is a heading
#+END_EXAMPLE