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py3 only is fine. this is necessary for the IAB build.

Currently biab html and biab ipynb assume that the branch should be master when generating links. It'd be nice to have a command line parameter for this that defaults to master, but can be overwritten for testing. This is useful when working on big PRs that involved a lot of work in a non-master branch (for example https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/pull/140).

Related to #5.

• if there is markdown in a heading (i.e., md line starting with #) the heading will be cut off at the start of the markdown. if heading starts with markdown, the build will fail with a non-informative error message
• if there is more than on top-level heading (i.e., single #) in a single document, all content beginning with the second top-level heading will dropped from the output
• if a header is missing a link tag the build fails with the following traceback: AttributeError: 'IDFinder' object has no attribute '_ID'.

Ideally, they'd be something like:

IAB: <chapter name>

The notebook and static HTML builds have inconsistent numbering of sections across the TOCs (e.g., click into one of the number sections in the static HTML, and you'll see that the TOC in the section you clicked into has letters instead of numbers. Examples below. We want to have these numbered at all times (e.g., 1.2.3.4, 2.1.3.5, ...).

in IAB, I hard code image links as:

https://raw.githubusercontent.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/master/book/fundamentals/images/upgma-tree-final.png

It'd be nice to auto-generate the part of those links that never change (which could also support branch-awareness by replacing master with a branch name): https://raw.githubusercontent.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/master/book/

• it's pretty ugly and dense right now, so some general CSS improvements would be nice.
• number (instead of bullet) lists and sublists
• we should be able to specify the TOC depth in different sections. For example, we don't want to list all of the glossary terms in the top-level table of contents. This can probably be specified in the index.yaml files.