Fixes #546 by using level-3 headings in all Markdown source files for…

… subsections. We continue to use level-4 headings for objectives, key points, callout boxes, and challenges.
swcarpentry · Jun 18, 2014 · a6fd62d · a6fd62d
1 parent aba78cf
commit a6fd62d
Show file tree

Hide file tree

Showing 17 changed files with 43 additions and 81 deletions.
diff --git a/intermediate/git/00-intro.md b/intermediate/git/00-intro.md
@@ -5,8 +5,6 @@ title: Introducing Distributed Version Control, and Introducing Yourself to Git
 level: intermediate
 ---
 
-## Introducing Distributed Version Control
-
 Barbara Biologist and Candace Cosmologist have been hired by Universal Missions
 (a space services spinoff from Euphoric State University)
 to figure out where the company should send its next planetary lander.
@@ -70,7 +68,7 @@ the most important thing to learn is not the details of their more obscure comma
 but the fundamentals of how they work,
 and the workflow that they encourage.
 
-## Introducing Yourself to Git
+### Introducing Yourself to Git
 
 The first time you use Git on a new machine,
 you need to run commands to configure a few things.

diff --git a/intermediate/git/01-conversational-git.md b/intermediate/git/01-conversational-git.md
@@ -4,6 +4,18 @@ root: ../..
 title: Conversational Git
 level: intermediate
 ---
+<div class="objectives" markdown="1">
+
+#### Objectives
+
+* Participate in collaborative development by copying Git repositories
+  using the `git clone` command.
+* View historical changes in their Git repositories using `git log`.
+* Navigate the history of their Git repositories using `git reflog` and
+  `git checkout`.
+* Restore saved versions of files using `git checkout`.
+
+</div>
 
 When you travel to a country
 where you don't speak the native language,
@@ -29,17 +41,6 @@ Please keep in mind, though,
 that Git uses some of its verbs and nouns
 very differently from other revision control systems.
 
-## Objectives
-
-After this lesson, students should be able to:
-
-* Participate in collaborative development by copying Git repositories
-  using the `git clone` command.
-* View historical changes in their Git repositories using `git log`.
-* Navigate the history of their Git repositories using `git reflog` and
-  `git checkout`.
-* Restore saved versions of files using `git checkout`.
-
 ## Copying Repositories (git clone)
 
 The first concept we introduce
@@ -106,7 +107,7 @@ we will lose our local copy of the project's history,
 and any changes or commits
 we had not published yet.
 
-## Viewing History (git log)
+### Viewing History (git log)
 
 We are looking
 at the latest *revision*,
@@ -314,7 +315,7 @@ cbd6ff5 Added data file
  2 files changed, 60 insertions(+)
 ~~~
 
-## Time travel (git checkout)
+### Time travel (git checkout)
 
 Git can't really travel through time,
 but it does allow us to inspect its repositories

diff --git a/intermediate/git/02-relational-structure.md b/intermediate/git/02-relational-structure.md
@@ -5,7 +5,7 @@ title: Basic Relational Structure of Git Repositories
 level: intermediate
 ---
 
-##The Bones of Git
+## The Bones of Git
 
 In earlier lessons, we've explored some of the basic procedures for creating and navigating a git repository; in this lesson, we'll start learning about the formal structure of a git repo, so that we can understand some of git's more advanced uses when we come to them in later lessons.
 
@@ -98,7 +98,7 @@ A new revision has been created which records the changes you staged to new.txt
 
 Now that we understand this basic relational structure, we're ready to learn about a new tool for walking around our chain of commits: `git reset`.
 
-##`git reset`
+## `git reset`
 
 Let's suppose that in the course of our work, we make some kind of mistake, and we want to rewind the project to an earlier point - `git reset` might be the right tool for the job; think of it as git's big 'undo' button.  `git reset` has three options to choose from: `--hard`, `--mixed`, or `--soft`.  The simplest to understand is the most drastic: `git reset --hard HEAD` will empty the index, change everything in the working tree to match the version recorded at `HEAD`, and move the `HEAD` pointer to point at whatever revision we pointed at (which in the example of `git reset --hard HEAD` of course doesn't move `HEAD` at all, but it would if we did something like `git reset --hard HEAD~1`, or used an earlier revision hash instead of `HEAD`).  So continuing our example from the last section, if we did `git reset --hard HEAD~1`, our repo would look something like:
 

diff --git a/intermediate/git/index.md b/intermediate/git/index.md
@@ -18,8 +18,7 @@ can and should be stored in a version control system.
 
 Topics
 ------
-* [Introducing Distributed Version Control, and Introducing
-Yourself to Git](00-intro.html)
+* [Introducing Distributed Version Control, and Introducing Yourself to Git](00-intro.html)
 * [Conversational Git](01-conversational-git.html)
 * [The Git Development Workflow](02-developing.html)
 * [Collaborating with Git and GitHub](03-collaborating.html)
diff --git a/intermediate/make/04-macros.md b/intermediate/make/04-macros.md
@@ -89,7 +89,7 @@ now, when we want to move our Makefile from one machine to another, we only have
 However, while we no longer have to worry about consistency,
 we're still making changes to a file that's under version control that we *don't* want written back to the repository.
 
-> ### Parenthesizing Macros in Make
+> #### Parenthesizing Macros in Make
 >
 > We have to put curly brackets or parentheses around a macro's name when we use it&mdash;we can't just write `$MACRO`.
 > If we do, Make will interpret it as `$M` (a reference to the macro `M`) followed by "ACRO".

diff --git a/intermediate/shell/01-perm.md b/intermediate/shell/01-perm.md
@@ -4,20 +4,4 @@ root: ../..
 title: Permissions
 level: intermediate
 ---
-<div class="objectives" markdown="1">
-## Objectives
-*   FIXME
-</div>
-
-## Lesson
-
-<div class="keypoints" markdown="1">
-## Key Points
-*   FIXME
-</div>
-
-<div class="challenges" markdown="1">
-## Challenges
-
-1.  FIXME
-</div>
+FIXME
diff --git a/intermediate/shell/02-ssh.md b/intermediate/shell/02-ssh.md
@@ -5,12 +5,10 @@ title: Working Remotely
 level: intermediate
 ---
 <div class="objectives" markdown="1">
-## Objectives
+#### Objectives
 *   FIXME
 </div>
 
-## Lesson
-
 Let's take a closer look at what happens when we use a desktop or laptop
 computer. The first step is to log in so that the operating system knows
 who we are and what we're allowed to do. We do this by typing our
@@ -287,12 +285,8 @@ $ exit
 ~~~
 
 <div class="keypoints" markdown="1">
-## Key Points
-*   FIXME
-</div>
 
-<div class="challenges" markdown="1">
-## Challenges
+#### Key Points
+*   FIXME
 
-1.  FIXME
 </div>
diff --git a/intermediate/shell/03-var.md b/intermediate/shell/03-var.md
@@ -5,12 +5,10 @@ title: Variables
 level: intermediate
 ---
 <div class="objectives" markdown="1">
-## Objectives
+#### Objectives
 *   FIXME
 </div>
 
-## Lesson
-
 The shell is just a program, and like other programs, it has variables.
 Those variables control its execution, and by changing their values, you
 can change how the shell and other programs behave.
@@ -248,12 +246,8 @@ As you can see, aliases can save us a lot of typing, and hence a lot of
 typing mistakes.
 
 <div class="keypoints" markdown="1">
-## Key Points
-*   FIXME
-</div>
 
-<div class="challenges" markdown="1">
-## Challenges
+#### Key Points
+*   FIXME
 
-1.  FIXME
 </div>
diff --git a/intermediate/shell/04-job.md b/intermediate/shell/04-job.md
@@ -5,12 +5,10 @@ title: Job Control
 level: intermediate
 ---
 <div class="objectives" markdown="1">
-## Objectives
+#### Objectives
 *   FIXME
 </div>
 
-## Lesson
-
 Our next topic is how to control programs *once they're running*. This
 is called [job control](glossary.html#job-control), and while it's less
 important today than it was back in the Dark Ages, it is coming back
@@ -157,12 +155,6 @@ to run and control programs on remote computers elsewhere on the
 network. We'll look at how to do this [later in this chapter](#s:ssh).
 
 <div class="keypoints" markdown="1">
-## Key Points
+#### Key Points
 *   FIXME
 </div>
-
-<div class="challenges" markdown="1">
-## Challenges
-
-1.  FIXME
-</div>
diff --git a/novice/git/01-backup.md b/novice/git/01-backup.md
@@ -28,7 +28,7 @@ version control is much better for this than this:
   <p>"Piled Higher and Deeper" by Jorge Cham, http://www.phdcomics.com</p>
 </div>
 
-#### Setting Up
+### Setting Up
 
 The first time we use Git on a new machine,
 we need to configure a few things.
@@ -59,7 +59,7 @@ we're telling Git:
 The four commands above only need to be run once:
 the flag `--global` tells Git to use the settings for every project on this machine.
 
-#### Creating a Repository
+### Creating a Repository
 
 Once Git is configured,
 we can start using it.
@@ -119,7 +119,7 @@ nothing to commit (create/copy files and use "git add" to track)
 ~~~
 {:class="out"}
 
-#### Tracking Changes to Files
+### Tracking Changes to Files
 
 Let's create a file called `mars.txt` that contains some notes
 about the Red Planet's suitability as a base.
@@ -281,7 +281,7 @@ and the log message Git was given when the revision was created.
 > so that our filesystem doesn't become cluttered
 > (and so that we can't accidentally edit or delete an old version).
 
-#### Changing a File
+### Changing a File
 
 Now suppose Dracula adds more information to the file.
 (Again, we'll edit with `nano` and then `cat` the file to show its contents;
@@ -534,7 +534,7 @@ Date:   Thu Aug 22 09:51:46 2013 -0400
 ~~~
 {:class="out"}
 
-#### Exploring History
+### Exploring History
 
 If we want to see what we changed when,
 we use `git diff` again,
@@ -627,7 +627,7 @@ index df0654a..b36abfd 100644
 ~~~
 {:class="out"}
 
-#### Recovering Old Versions
+### Recovering Old Versions
 
 All right:
 we can save changes to files and see what we've changed---how
@@ -725,7 +725,7 @@ If the introduction and conclusion are stored in separate files,
 on the other hand,
 moving backward and forward in time becomes much easier.
 
-#### Ignoring Things
+### Ignoring Things
 
 What if we have files that we do not want Git to track for us,
 like backup files created by our editor

diff --git a/novice/git/04-open.md b/novice/git/04-open.md
@@ -79,7 +79,7 @@ However,
 people who want to work this way need to make some decisions
 about what exactly "open" means in practice.
 
-#### Licensing
+### Licensing
 
 The first question is licensing.
 Broadly speaking,
@@ -202,7 +202,7 @@ Greg Wilson: "Software Carpentry: Lessons Learned". arXiv:1307.5448, July 2013.
 ~~~
 </div>
 
-#### Hosting
+### Hosting
 
 The second big question for groups that want to open up their work
 is where to host their code and data.

diff --git a/novice/shell/00-intro.md b/novice/shell/00-intro.md
@@ -54,7 +54,7 @@ As a bonus,
 once she has put a processing pipeline together,
 she will be able to use it again whenever she collects more data.
 
-#### What and Why
+### What and Why
 
 At a high level, computers do four things:
 

diff --git a/novice/shell/01-filedir.md b/novice/shell/01-filedir.md
@@ -381,7 +381,7 @@ but we'll see some uses for it soon.
 > Orthogonal systems tend to be easier for people to learn
 > because there are fewer special cases and exceptions to keep track of.
 
-#### Nelle's Pipeline: Organizing Files
+### Nelle's Pipeline: Organizing Files
 
 Knowing just this much about files and directories,
 Nelle is ready to organize the files that the protein assay machine will create.

diff --git a/novice/shell/03-pipefilter.md b/novice/shell/03-pipefilter.md
@@ -300,7 +300,7 @@ so that you and other people can put those programs into pipes to multiply their
 > have told the shell to send the contents of `ammonia.pdb` to `wc`'s
 > standard input.
 
-#### Nelle's Pipeline: Checking Files
+### Nelle's Pipeline: Checking Files
 
 Nelle has run her samples through the assay machines
 and created 1520 files in the `north-pacific-gyre/2012-07-03` directory described earlier.

diff --git a/novice/shell/04-loop.md b/novice/shell/04-loop.md
@@ -264,7 +264,7 @@ mv unicorn.dat original-unicorn.dat
 > isn't foolproof, but it's a handy way to see what's going to happen when
 > you're still learning how loops work.
 
-#### Nelle's Pipeline: Processing Files
+### Nelle's Pipeline: Processing Files
 
 Nelle is now ready to process her data files.
 Since she's still learning how to use the shell,

diff --git a/novice/shell/05-script.md b/novice/shell/05-script.md
@@ -303,7 +303,7 @@ what they discover about their data and their workflow with one call to `history
 and a bit of editing to clean up the output
 and save it as a shell script.
 
-#### Nelle's Pipeline: Creating a Script
+### Nelle's Pipeline: Creating a Script
 
 An off-hand comment from her supervisor has made Nelle realize that
 she should have provided a couple of extra parameters to `goostats` when she processed her files.

diff --git a/novice/shell/06-find.md b/novice/shell/06-find.md
@@ -422,7 +422,7 @@ $ grep FE $(find . -name '*.pdb' -print)
 > modern programming languages, Python included, have borrowed a lot of
 > ideas from it, and imitation is also the sincerest form of praise.
 
-#### Conclusion
+### Conclusion
 
 The Unix shell is older than most of the people who use it. It has
 survived so long because it is one of the most productive programming