Replace the in-house stubbing by the facilities offered
by pyfakefs for running tests. We don't use `io.open`
anymore, because pyfakefs does not stub it correctly.
We rely on a patched version of pyfakefs, as a few bug
remain in the official repo.
The update is done transparently, and displays a warning message explaining the change.
All the update machinery has been moved to the new update module.
First this brings a change to the paper API: the terminology of bibdata
and bibentry is clarified: now bibentry is a dictionary of the form
{citekey: bibdata} where bibdata corresponds to the actual dictionary of
bibliographic fields and values {author: ..., year: ...}.
Now bibentry is an attribute of the paper object that is generated from
citekey and bibdata.
This commit fixes all tests in particular an issue with citekey in
bibentry not updated.
Also removes prints in tests and deprecated assertEquals.
Usecase tests now fail if the command ask for unexpected inputs.
Removes queries for user input in attach and add commands (for deletion
of a copied document file). The input was not coherent with tests and is
annoying.
* only bibtex format is supported
* all tests except test_repo.py and edit test pass
* edit and update commands were not updated
* removed --format argument from export, only bibtex is supported.
