Jeroen F.J. Laros authored 9 years ago and Vermaat committed 9 years ago

Existing `transcript_to_protein` is factored out into a separate
`mutalyzer.ncbi` module.

Add Ter as a valid AA in the HGVS grammar

Previously, the `PSubst` rule did not register `MutationType`, so it
was a bit awkward how to check for a `p.` substitution. We can now:

    >>> grammar.parse('NP_00011.1:p.Asp23Tyr').RawVar.MutationType
    'subst'

Refactor unit tests using py.test

Especially lxml takes very long to install. By specifying the `-O0`
compiler flag this is reduced by more than half.

The actual unit tests are slightly slower with the non-optimized
C modules, but we have a netto win.

Travis CI updates

Release 2.0.13

Fix query bug in update transcript-protein links

Test database migrations

Push to release branch requires passing status checks

Release 2.0.12

Fix transcript protein link query

Bi-directional cachinig of transcript-protein links

Previously transcript-protein links were assumed to always be
indexed by transcript, and cached entries were allowed to have
a `null` protein (meaning caching the knowledget that there is
no link for this transcript).

Now we can cache links in both directions. Both transcript and
protein are allowed to be `null` (but not at the same time),
and the protein column has a new unique constraint.

Fix off-by-one in slicing chromosome by gene name