I have moved less pertinent material to appendixes. The idea is that
a print edition should contain only the most important material,
and online appendixes allow the reader to access supplemental material.
The PDF was not setting the Preface as a unnumbered chapter.
I think there is more work to get it's subsections unnumbered.
Added empty Particl filter chapter. Had to renumber the chapters
to make it fit in.
Too many to mention. Read through several chapters and made changes
as I went. I've had people (correctly) question me on several points,
and pointing out typos.
I think I prefer just letting nbconvert generating static files,
but if I want to switch to using Bokeh or other javascript based
rendering I'll need the HTML conversion facility.
I finally learned that the raw cells let you put latex directly
into the output. So now I have the appendix being created without
the [1] %%latex showing up in the output. Also wrote code to parse
the .tex file to make the Preface a chapter without numbering, so it
is now a proper preface, and not "chapter 0".
I have not touched the Windows generation tools, so PDF generation
in Windows is now broken. I don't think I care.
Some sections jumped from level 2 to level 4, for example.
Also played around with generating book to HTML. I like it, but
it needs some work. The Calico table of content generator cannot
deal with different headers with the same name, for example.
I want to go to HTML so I can use Bokeh to have interactive plots.
But that means no more PDF, because Bokeh will not export to
PDF.
I moved book_format.py to the root directory so that all of the
notebooks do not need to modify the system path to import it. It
modifies the path on import so that all of the code in ./code can
then be accessed.
Altered links to nbviewer to account for no longer using subdirectories.
