Added Github Atom to env.rst

Also small PEP8 fixes by flake8.


**Unrelated to pull request:** We should also add/discuss some rules about new lines between headings. 
The style guide is pretty descriptive, but it doesn't touch this subject, which results into many files with varying number of new lines between headings. 

My suggestions are:
* Chapter and page title remain unchanged
* Section and sub section should have 2 new lines for extra readibility
The tool is simply named Atom. Perhaps you meant to say 

```rst
GitHub's `Atom <https://atom.io/>`_ ...
```

If that isn't what you meant, please change this to just be `Atom`.