Good catch - I'll review.

@gvwilson Did you get a chance to review this or does it still need review?

I haven't had a chance to review - could you please?

@gvwilson not sure how to test this. When I run
make preview
it only updates the README.html...

You can look at the README.md file in your favourite markdown aware viewer, or just browse the files as of my commit right here on GitHub using GitHub's rendering, e.g.:
https://github.com/peterjc/python-novice-inflammation/blob/a4009e55195018f3a1e5b04e2fcc7f3b278170de/01-numpy.md

@peterjc you missed one:

$ ack '&#' -G .*md
01-numpy.md
39:numpy.loadtxt(fname='inflammation-01.csv', delimiter=',')

@abostroem you can force make to update everything by doing make preview -B

@gvwilson any idea why this is like this in the first place?

@aaren Apologies for losing the thread - why what is like what?

@gvwilson I think the question was how did these over-escaped HTML entities get into the markdown source?

@aaren Good catch on the HTML escaped quotes, give my a moment and I'll fix that in another commit...

@gvwilson yes, why are these html things (', etc.) in the markdown at all? Is there a systemic reason?

Rebased and the quote fixed.

I haven't down a grep across all the lessons (I only have a handful cloned locally), but it looks like something went wrong on this lesson only?

Here is the full (?) list of html entities still in the markdown:

$ ack '&' -G '.*md$'
05-defensive.md
71:<ipython-input-19-33d87ea29ae4> in <module&gt;()

04-cond.md
412:    That means that on a 40&times;60 data set, we are performing the same calculation 2400 times.

01-numpy.md
39:numpy.loadtxt(fname=&#39;inflammation-01.csv&#39;, delimiter=&#39;,&#39;)
238:if we have an M&times;N array in Python,
468:The expression `(40,)` tells us we have an N&times;1 vector,

@peterjc can you fix the defensive programming one as well?

As for the others (&times), I'm not sure what to do with these. If we had mathjax we could replace with latex, but I don't think that we do so either leave them as is or replace with x.

I thought I did all the less-than and greater-than signs, thanks again @aaren.

I'm not sure what is best for the times signs - they should look nice in the HTML output at least.

It's almost certainly a side effect of an automatic translator (probably
the IPython Notebook to Markdown translation). There's no reason to
keep the escapes. I'm happy to replace them all with "natural" characters.

@aaren and @peterjc does the current form render correctly and this just fixes the code to be all html or does the current version (pre-PR) render incorrectly?

Please let me know when you are ready to merge

@abostroem the pre-PR version renders incorrectly. Look at 01-numpy.html in your browser. This PR modifies the markdown input to not use html escaped characters and then updates the html to reflect that.

I deliberately committed in the changes to *.html as generated by make preview as per my understanding of the instructions.

(Personally I don't understand why generated *.html files are under source code control, but that's a different issue.)

I deliberately committed in the changes to |*.html| as generated by
|make preview| as per my understanding of the instructions.

Thanks.

(Personally I don't understand why generated |*.html| files are under
source code control, but that's a different issue.)

From https://github.com/swcarpentry/lesson-template/blob/gh-pages/DESIGN.md:

Using Pandoc instead of Jekyll means that we have to compile our
Markdown into HTML on our own machines and commit it to the |gh-pages|
branch of the lesson's GitHub repository.

It's considered bad practice to put computer-generated files under
version control, but the HTML pages put into the lesson's root
directory by Pandoc /must/ be committed to version control in order
for the lesson to be displayed properly on GitHub.

It's also considered bad practice to put generated files in the same
directory as source files. We do it because some authors may use
auxiliary source files such as R Markdown and IPython Notebook files
which are executable, and contain paths to things like images and data
files. If we put our source files in a sub-directory, those paths
won't work (or conversely, if we put our generated files in a
different directory, the paths won't work there).

Dr. Greg Wilson | gvwilson@software-carpentry.org
Software Carpentry | http://software-carpentry.org

This looks good to me. I'll leave it to @abostroem to merge.