Change .rst to .md Fix/#340

[connor-reid-tiffany]

Reformatted all .rst files to markdown files in sourmash/docs except for index.rst. Fix for issue #340

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov-io]

Codecov Report

Merging #356 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #356   +/-   ##
=======================================
  Coverage   87.15%   87.15%           
=======================================
  Files          14       14           
  Lines        2087     2087           
  Branches       36       36           
=======================================
  Hits         1819     1819           
  Misses        267      267           
  Partials        1        1

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[standage]

Thanks for this pull request, Connor. Almost there! It looks like this task was a little bit more involved than anticipated!

Minor changes:

• I've highlighted a few places in where you've retained the code block indentation. This can and probably should be removed.
• More generally, some of the spacing between sections is inconsistent. Sometime there are two or three lines between sections, and sometimes there are none (this makes it hard to scan through the Markdown and easily identify breaks between sections). We don't have any hard and fast rules about spacing, as long as everything renders ok. But it would be helpful to be consistent! :)

Major change:

• Several places in the command-line.md document it appears that you've copied and pasted some automatically generated text instead of using what are called "directives" in the Sphinx documentation system. We'll want to fix this before merging.

Let us know if anything is unclear. Thanks!

[standage]

It looks like this block isn't formatted correctly.

[standage]

I think you probably want the .. contents:: directive here. You've manually pasted in some links that should be dynamically generated by the documentation build system

[standage]

I may have been mistaken here too. If the .. contents:: directive doesn't work in Markdown, we'll have to figure out how to add anchors to the different sections—or simply just delete the contents block!

[standage]

Not a huge deal, but since other changes are required, should remove the leading spaces here.

[standage]

And in the other code blocks in this file.

[standage]

Also a copy/paste mistake. Instead of typing this out fully, this should be auto-generated with the .. Usage:: directive. That way changes to the code are automatically reflected in the documentation.

[standage]

My bad, I was mistaken. This is not a directive.

[standage]

You can drop all the leading spaces in each code block. In RST the indentation indicates that this is a code block. Since Markdown uses tick marks, the leading spaces aren't needed.

[standage]

It's looking much better now indeed. But having nothing but a table of contents on the index page is a bit jarring, and having a separate welcome page is a bit awkward.

You've had to go down the rabbit hole a bit with this PR, and try a lot of things to get it all to work. It might be helpful at this point to come back out of the rabbit hole a bit and re-assess. If you revert doc/index.rst to what it was before you started, I think everything should work as intended. Then you can drop this new welcome page you created, revert the changes to doc/_templates/navigation.html, and then focus on whitespace cleanup, at which point I think this PR will be ready to go!

Oh, there's also a merge conflict as well, but this should be simple to address.

[luizirber]

@recursive-deletion If you run git diff master.. -- index.rst you can see the differences to the original file

[luizirber]

Looking good! A small nitpick is that some files were added/removed without git keeping track of it (doc/command-line.md and doc/command-line.rst, for example). Wanna tackle that next? =]

Already fixed