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Refactor docs #3

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ESKYoung
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Revised cookiecutter structure, and associated docs.

Main revisions are:

  • Removal of outdated Python 2 references;
  • Bugfix in tests for folder name checking;
  • Consolidation of all documentation into Sphinx Markdown format;
  • Consolidation of all AQA documentation; and
  • General refactoring.

Eric Young added 16 commits February 11, 2020 12:19
Refactor most of `docs/docs/index.md` to 120 character line width; some
URLs are longer than 120 line width, so have been left as is.

Also revised the `README.md` files across the project to have a 120
line width maximum.

Add a `docs/_static` folder for Sphinx builds, and refactor the line
widths of `index.rst` and `conf.py` to 120 characters.
`test_folders` is originally:

```python
set(abs_expected_dirs + ignored_dirs) - set(abs_dirs)
```

This is the folders in `set(abs_dirs)` not in
`set(abs_expected_dirs + ignored_dirs)`.

However, it does NOT check the reverse, i.e. folders in
`set(abs_expected_dirs + ignored_dirs)` not in `set(abs_dirs)`. In this
case, the test always passes.
List all items in alphabetical order with files first, followed by
folders.
The `.envrc` file replaces the existing `.env` file.

Also detail how to import these environmental files, and to set up and
import a `.secrets` file as well.
Comment out option from `Makefile`, and also remove now redundant
`data` rule.
Also set Python 3 as default throughout the cookiecutter project.
`autodoc` allows automatic documentation generation from docstrings.

`napoleon` allows docstrings to be in Google or NumPy format, as well
as reStructuredText format, which is the default.
`autosummary` creates stub pages for each and every function.

`recommonmark` allows Sphinx to parse Markdown as well as
reStructuredText. Also add `sphinx-markdown-tables` to parse Markdown
tables correctly.

Also exclude the `pull_request_template.md` from Sphinx build.
Combine the two files, and consolidate the documentation to refer to
the `Makefile`, and all possible `make` rules.

Move this combined Markdown file into a sub-folder for clarity.
Refactor `index.rst` to `index.md`, and use
`recommonmark.transform.AutoStructify` to enable reStructuredText
transformations in Sphinx.
Remove `{{ cookiecutter.repo_name }}/references` folder as well, and
edit folder organisation diagrams.

Edit `pull_request_template.md` to reflect these changes.
Also add all TOC references, as required.
Also fix all folder organisation charts to reflect changes.

Amend `README.md`s for consistency, and any associated tests.
Ensure information about AQA documents is clearly marked. Ensure links
in `pull_request_template.md` work correctly (relative to GitHub); add
tests to check this.
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