Switching to kramdown

README.md

@@ -204,26 +204,29 @@ you will need to install Jekyll 1.0.3 or later in order to preview things locall
 If you have Ruby installed on your computer,
 this *should* be as simple as:
 
+    gem install github-pages
+
+or if that doesn't work:
+
     gem install jekyll
-    gem install redcarpet
+    gem install kramdown
 
-We try to use the same MarkDown interpreters as GitHub does for
-consistency.  On OS X, we suggest you use a recent Ruby to get access
-to these.  If you don't have Homebrew or MacPorts installed, here's a
-quick recipe to get started using HomeBrew.
+(We use Kramdown for translating Markdown instead of the default
+Redcarpet because Kramdown will handle Markdown inside HTML blocks).
+On OS X, we suggest you use a recent Ruby to get access to these.  If
+you don't have Homebrew or MacPorts installed, here's a quick recipe
+to get started using HomeBrew.
 
 ```
 ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
 brew install ruby
-gem install jekyll
-gem install redcarpet 
 ```
 
-If you don't have `make` in your machine, you can build the preview with:
+and then `gem install` as above.  If you don't have `make` in your
+machine, you can build the preview with:
 
     jekyll -t build -d _site
 
-
 Layout and Variables
 --------------------
 

_config.yml

@@ -1,4 +1,7 @@
-markdown        : redcarpet
+markdown        : kramdown
+kramdown        :
+  entity_output : as_input # — is output as —
+  smart_quotes  : [39, 39, 34, 34] # decimal for left/right single/double quotes
 pygments        : true
 contact         : "info@software-carpentry.org"
 github_url      : "https://github.com/swcarpentry"

bash/novice/00-intro.md

@@ -4,11 +4,14 @@ root: ../..
 title: Introducing the Shell
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Explain how the shell relates to the keyboard, the screen, the operating system, and users' programs.
 *   Explain when and why command-line interfaces should be used instead of graphical interfaces.
 </div>
 
+## Lesson
+
 Nelle Nemo, a marine biologist,
 has just returned from a six-month survey of the
 [North Pacific Gyre](http://en.wikipedia.org/wiki/North_Pacific_Gyre),
@@ -123,7 +126,8 @@ the command line is often the easiest way to interact with remote machines.
 As clusters and cloud computing become more popular for scientific data crunching,
 being able to drive them is becoming a necessary skill.
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   A shell is a program whose primary purpose is to read commands and run other programs.
 *   The shell's main advantages are its high action-to-keystroke ratio,
     its support for automating repetitive tasks,

bash/novice/01-filedir.md

@@ -4,7 +4,8 @@ root: ../..
 title: Files and Directories
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Explain the similarities and differences between a file and a directory.
 *   Translate an absolute path into a relative path and vice versa.
 *   Construct absolute and relative paths that identify specific files and directories.
@@ -13,6 +14,8 @@ level: novice
 *   Demonstrate the use of tab completion, and explain its advantages.
 </div>
 
+## Lesson
+
 The part of the operating system responsible for managing files and directories
 is called the [file system](../../gloss.html#filesystem).
 It organizes our data into files,
@@ -349,7 +352,8 @@ and so on.
 This is called [tab completion](../../gloss.html#tab-completion),
 and we will see it in many other tools as we go on.
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   The file system is responsible for managing information on disk.
 *   Information is stored in files, which are stored in directories (folders).
 *   Directories can also store other directories, which forms a directory tree.
@@ -371,8 +375,8 @@ and we will see it in many other tools as we go on.
 *   Most commands take options (flags) which begin with a '-'.
 </div>
 
-<div class="challenges">
-### Challenges
+<div class="challenges" markdown="1">
+## Challenges
 
 <img src="./img/filesystem-challenge.png" alt="Filesystem for Challenge Questions" />
 

bash/novice/02-create.md

@@ -4,13 +4,16 @@ root: ../..
 title: Creating Things
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Create a directory hierarchy that matches a given diagram.
 *   Create files in that hierarchy using an editor or by copying and renaming existing files.
 *   Display the contents of a directory using the command line.
 *   Delete specified files and/or directories.
 </div>
 
+## Lesson
+
 We now know how to explore files and directories,
 but how do we create them in the first place?
 Let's go back to Vlad's home directory,
@@ -252,7 +255,8 @@ but it does find the copy in `thesis` that we didn't delete:
 > `/home/vlad/data`. This only works if it is the first character in the
 > path: `here/there/~/elsewhere` is *not* `/home/vlad/elsewhere`.
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   Unix documentation uses '^A' to mean "control-A".
 *   The shell does not have a trash bin: once something is deleted, it's really gone.
 *   `mkdir path` creates a new directory.
@@ -264,8 +268,8 @@ but it does find the copy in `thesis` that we didn't delete:
 *   `rmdir path` removes (deletes) an empty directory.
 </div>
 
-<div class="challenges">
-### Challenges
+<div class="challenges" markdown="1">
+## Challenges
 
 1.  What is the output of the closing `ls` command in the sequence shown below?
 

bash/novice/03-pipefilter.md

@@ -1,17 +1,20 @@
----
+-- markdown="1"-
 layout: lesson
 root: ../..
 title: Pipes and Filters
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Redirect a command's output to a file.
 *   Process a file instead of keyboard input using redirection.
 *   Construct command pipelines with two or more stages.
 *   Explain what usually happens if a program or pipeline isn't given any input to process.
 *   Explain Unix's "small pieces, loosely joined" philosophy.
 </div>
 
+## Lesson
+
 Now that we know a few basic commands,
 we can finally look at the shell's most powerful feature:
 the ease with which it lets us combine existing programs in new ways.
@@ -304,7 +307,8 @@ the '\*' matches any number of characters;
 the expression `[AB]` matches either an 'A' or a 'B',
 so this matches all the valid data files she has.
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   `command > file` redirects a command's output to a file.
 *   `first | second` is a pipeline: the output of the first command is used as the input to the second.
 *   The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).
@@ -315,8 +319,8 @@ so this matches all the valid data files she has.
 *   `wc` counts lines, words, and characters in its inputs.
 </div>
 
-<div class="challenges">
-### Challenges
+<div class="challenges" markdown="1">
+## Challenges
 
 1.  If we run `sort` on each of the files shown on the left in the table
     below, *without* the `-n` flag, the output is as shown on the right:

bash/novice/04-loop.md

@@ -4,7 +4,8 @@ root: ../..
 title: Loops
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Write a loop that applies one or more commands separately to each file in a set of files.
 *   Trace the values taken on by a loop variable during execution of the loop.
 *   Explain the difference between a variable's name and its value.
@@ -13,6 +14,8 @@ level: novice
 *   Re-run recently executed commands without retyping them.
 </div>
 
+## Lesson
+
 Wildcards and tab completion are two ways to reduce typing (and typing mistakes).
 Another is to tell the shell to do something over and over again.
 Suppose we have several hundred genome data files named `basilisk.dat`, `unicorn.dat`, and so on.
@@ -312,7 +315,8 @@ so she decides to get some coffee and catch up on her reading.
 > then she can re-run `goostats` on `NENE01729B.txt` simply by typing
 > `!458`.
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   Use a `for` loop to repeat commands once for every thing in a list.
 *   Every `for` loop needs a variable to refer to the current "thing".
 *   Use `$name` to expand a variable (i.e., get its value).
@@ -322,8 +326,8 @@ so she decides to get some coffee and catch up on her reading.
 *   Use `history` to display recent commands, and `!number` to repeat a command by number.
 </div>
 
-<div class="challenges">
-### Challenges
+<div class="challenges" markdown="1">
+## Challenges
 
 1.  Suppose that `ls` initially displays:
 

bash/novice/05-script.md

@@ -4,13 +4,16 @@ root: ../..
 title: Shell Scripts
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Write a shell script that runs a command or series of commands for a fixed set of files.
 *   Run a shell script from the command line.
 *   Write a shell script that operates on a set of files defined by the user on the command line.
 *   Create pipelines that include user-written shell scripts.
 </div>
 
+## Lesson
+
 We are finally ready to see what makes the shell such a powerful programming environment.
 We are going to take the commands we repeat frequently and save them in files
 so that we can re-run all those operations again later by typing a single command.
@@ -248,16 +251,17 @@ she could modify her script to check for command-line parameters,
 and use `*[AB].txt` if none were provided.
 Of course, this introduces another tradeoff between flexibility and complexity.
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   Save commands in files (usually called shell scripts) for re-use.
 *   Use `bash filename` to run saved commands.
 *   `$*` refers to all of a shell script's command-line parameters.
 *   `$1`, `$2`, etc., refer to specified command-line parameters.
 *   Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.
 </div>
 
-<div class="challenges">
-### Challenges
+<div class="challenges" markdown="1">
+## Challenges
 
 1.  Leah has several hundred data files, each of which is formatted like this:
 

bash/novice/06-find.md

@@ -4,13 +4,16 @@ root: ../..
 title: Finding Things
 level: novice
 ---
-<div class="objectives">
+<div class="objectives" markdown="1">
+## Objectives
 *   Use `grep` to select lines from text files that match simple patterns.
 *   Use `find` to find files whose names match simple patterns.
 *   Use the output of one command as the command-line parameters to another command.
 *   Explain what is meant by "text" and "binary" files, and why many common tools don't handle the latter well.
 </div>
 
+## Lesson
+
 You can guess someone's age by how they talk about search:
 young people use "Google" as a verb,
 while crusty old Unix programmers use "grep".
@@ -318,7 +321,8 @@ North Whitehead wrote in 1911, "Civilization advances by extending the
 number of important operations which we can perform without thinking
 about them."
 
-<div class="keypoints">
+<div class="keypoints" markdown="1">
+## Key Points
 *   Everything is stored as bytes, but the bytes in binary files do not represent characters.
 *   Use nested loops to run commands for every combination of two lists of things.
 *   Use `\` to break one logical line into several physical lines.
@@ -329,8 +333,8 @@ about them."
 *   `man command` displays the manual page for a given command.
 </div>
 
-<div class="challenges">
-### Challenges
+<div class="challenges" markdown="1">
+## Challenges
 
 1.  Write a short explanatory comment for the following shell script: