Update docs; remove need for conda (library) in dev install - #847

@sroet : Can you verify that this fixes for you? Since the change is in a secondary script in the repo, not the conda_ops_dev_install.sh script itself, you can run the normal procedure, except do:

bash conda_ops_dev_install.sh openpathsampling docs_deploy

That will check out the openpathsampling/docs_deploy branch, where these changes are, and run the install based on the information in that repo (using the updated script to get requirements, which shouldn't require that conda is installed.)

Also, could you review the changes here, since most of them are to address lack of clarity in the docs that you identified in #846?

fails for 3.5 because of yaml versions

Just curious: what do you mean by this?

(Also, currently having some weird flaky test fail in test_pyemma notebook; I'll try to track that down before merging. I can't imagine it has anything to do with this PR, but there also don't seem to be any version changes in requirements).

On python=3.5 this still fails to install matplotlib, due to

Traceback (most recent call last):
  File "devtools/install_recipe_requirements.py", line 42, in <module>
    required_packages = recipe_to_requirements(recipe_yaml)
  File "devtools/install_recipe_requirements.py", line 34, in recipe_to_requirements
    reqs = yaml.load(recipe_yaml, Loader=yaml.FullLoader)['requirements']
AttributeError: module 'yaml' has no attribute 'FullLoader'

which is probably due to the fact that pyyaml=3.13 for py3.5 and 5.1.1 for py3.6.

Ah, yeah, the script to find reqs will now require newer versions of pyyaml, and I guess they never released those for Python 3.5. The explicit Loader silences an annoying warning in pyyaml. Story behind that here.

We're definitely getting flakey errors in the test_pyemma notebook. Something to do with storage, it appears. But I can't find any version differences that make the problem evident.

Anyway, @sroet says that this fixes his problems, and it's mainly docs anyway, so I'm going to ahead and merge this.