* Update GitHub links

* Clean the about page

* Update dependencies

While working on this, I came to the conclusion it's not a good idea to
split accession and version. It introduces a lot of complexity for
little benefit.

In general, Mutalyzer always sees 'accession.version' as the identifier
of the reference and because we always want exact identifiers, there is
little need for accession numbers without version.

The most obvious use case I see for a split is that we can easily query
available references with a certain accession, not taking version into
account, as a way to inform the user when a specific reference
identifier was not found. But I guess we better have this use case as
the exception, and make our life easier for the rest.

So I guess I'm aborting this for now. Addition of the `version` column
has already landed in the master branch, but this is easy to roll
back. The original column has not yet been touched in master.

This corrects #396 in which we were a bit too quick actually dropping
the column. As per our migration policy, we should first update the code
to work without the column, then drop the column at least one release
later.

The NCBI is phasing out the use of sequence GIs, so we have no other
choice than to drop support for them.

https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/

Fixes #349

Follow-up to #387, fixes #389

Follow-up to #387, fixes #388

Previously, the original source for a reference file was implicit:

1. If accession number starts with `LRG_`, it came from the LRG FTP
   archive.
2. If a download URL is known, it was downloaded from there.
3. If slice data is known, it was sliced from the NCBI.
4. If a GI number is known, it was downloaded from the NCBI.
5. Otherwise, it was uploaded.

In preparation for the removal of GI numbers (#349), this had to be
revisited. We now store the source explicitely in a new `source` field
on the `Reference` model. If additional information is needed to
re-fetch the file from this source (e.g., download URL), this is stored
in a new `source_data` field (always serialized as a string). This
scheme should be both more explicit and more generic.

Note that we explicitely only support LRG references as transcripts,
so using c. positioning to convert to/from chromosomal positioning.

Supporting LRG references as genomic referenes, so using g. positioning
can be future work but converting them to/from LRG transcripts is of
course already done by the name checker.

Converting between genomic LRG positioning and chromosomal positioning
directly is not something that can be easily supported in the current
setup of the position converter.

Instead of querying the existing mappings for overlap and either
updating or inserting depending on the result, we now delete
overlapping mappings first and then only insert.

This is roughly twice as fast. But of course still a horrible
setup compared to some kind of UPSERT functionality which is
unfortunately missing in current PostgreSQL.

This is now created on use, by #111.

Fixes #112

This data is now in Redis, by #94.

Fixes #95

This speeds up lookup of transcript mappings by genomic position
a lot. By filtering on bin index, such a query now uses the index
on the bin column, where previously this would involve a
sequential table scan.

http://interval-binning.readthedocs.org/

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.

Not sure how this came to be, but NCBI36 was incorrectly named GRCh36.
Changing this, however, breaks the sort order in assembly lists. So we
now sort on the UCSC alias (hg18).

Fixes #8

Don't fix what ain't broken. Unfortunately, string handling in Mutalyzer
really is broken. So we fix it.

Internally, all strings should be represented by unicode strings as much as
possible. The main exception are large reference sequence strings. These can
often better be BioPython sequence objects, since that is how we usually get
them in the first place.

These changes will hopefully make Mutalyzer more reliable in working with
incoming data. As a bonus, they're a first (small) step towards Python 3
compatibility [1].

Our strategy is as follows:

1. We use `from __future__ import unicode_literals` at the top of every file.
2. All incoming strings are decoded to unicode (if necessary) as soon as
   possible.
3. Outgoing strings are encoded to UTF8 (if necessary) as late as possible.
4. BioPython sequence objects can be based on byte strings as well as unicode
   strings.
5. In the database, everything is UTF8.
6. We worry about uploaded and downloaded reference files and batch jobs in a
   later commit.

Point 1 will ensure that all string literals in our source code will be
unicode strings [2].

As for point 4, sometimes this may even change under our eyes (e.g., calling
`.reverse_complement()` will change it to a byte string). We don't care as
long as they're BioPython objects, only when we get the sequence out we must
have it as unicode string. Their contents are always in the ASCII range
anyway.

Although `Bio.Seq.reverse_complement` works fine on Python byte strings (and
we used to rely on that), it crashes on a Python unicode string. So we take
care to only use it on BioPython sequence objects and wrote our own reverse
complement function for unicode strings (`mutalyzer.util.reverse_complement`).

As for point 5, SQLAlchemy already does a very good job at presenting decoding
from and encoding to UTF8 for us.

The Spyne documentation has the following to say about their `String` and
`Unicode` types [3]:

> There are two string types in Spyne: `spyne.model.primitive.Unicode` and
> `spyne.model.primitive.String` whose native types are `unicode` and `str`
> respectively.
>
> Unlike the Python `str`, the Spyne `String` is not for arbitrary byte
> streams. You should not use it unless you are absolutely, positively sure
> that you need to deal with text data with an unknown encoding. In all other
> cases, you should just use the `Unicode` type. They actually look the same
> from outside, this distinction is made just to properly deal with the quirks
> surrounding Python-2's `unicode` type.
>
> Remember that you have the `ByteArray` and `File` types at your disposal
> when you need to deal with arbitrary byte streams.
>
> The `String` type will be just an alias for `Unicode` once Spyne gets ported
> to Python 3. It might even be deprecated and removed in the future, so make
> sure you are using either `Unicode` or `ByteArray` in your interface
> definitions.

So let's not ignore that and never use `String` anymore in our webservice
interface.

For the command line interface it's a bit more complicated, since there seems
to be no reliable way to get the encoding of command line arguments. We use
`sys.stdin.encoding` as a best guess.

For us to interpret a sequence of bytes as text, it's key to be aware of their
encoding. Once decoded, a text string can be safely used without having to
worry about bytes. Without unicode we're nothing, and nothing will help
us. Maybe we're lying, then you better not stay. But we could be safer, just
for one day. Oh-oh-oh-ohh, oh-oh-oh-ohh, just for one day.

[1] https://docs.python.org/2.7/howto/pyporting.html
[2] http://python-future.org/unicode_literals.html
[3] http://spyne.io/docs/2.10/manual/03_types.html#strings

Also, the value for nuclear chromosomes is now `nucleus` instead of
`chromosome` for better alignment with the other value `mitochondrion`.

Note that I did not bother to make an Alembic migration for this, since
we don't have any installations besides my own yet anyway.

Genome assembly definitions for GRCh36, GRCh37, and GRCm38 are included
as JSON files in `extras/assemblies`.

This includes changing a lot of routes and parameter names to be more
consistent. We try to remain backwards compatible as much as possible
by providing redirects from old routes and parameter names.

This introduces a proper notion of genome assemblies. Transcript
mappings for alle genome assemblies are in the same database, which
is better for maintenance. Updating transcript mappings is also
simplified a lot, especially from NCBI mapview files where we now
require a preprocessing sort on the input file.

Overall, this port touches a lot of Mutalyzer code, so beware.

This involves making the SQLAlchemy session reconfigurable at run-time,
which is done automatically on updating the Mutalyzer configuration using
configuration update callbacks.

Port the entire batch job infrastructure, including scheduler, to use
the SQLAlchemy ORM instead of the old Db module.