By building our own images with common dependencies already installed,
we can make actual test runs faster and less wasteful. That said, do
keep directives for installing dependencies here in case of some of them
having been updated since the last rebuild of the images.

That way the runner will not waste time on installing Ensembl
dependencies in containers used to launch trigger-dependent-build.sh

1. Apply lessons learned from experiments with ensembl-test regarding
   the use of variables in trigger:project;
2. Remove 'trigger' from the template altogether, that way we will be
   able to use it for downstream jobs on both GitLab-CI (which will use
   triggering) and Travis (which will call a script);
3. Add a job to trigger dependent builds on Travis, with hopefully all
   required environment variables assigned the values of their GitLab-CI
   counterparts.

Devel::Cover still does not work with threads, causing weird failures
(possibly segfaults) in registry.t - and IMHO we shouldn't use different
threadedness for different versions of Perl we test.

Activate Gitlab CI

Patch test databases

Source: master branches of all relevant Ensembl repositories as of 10:00
today. This brings all test databases at hand to schema version 100.

Enscoresw 3267

Ameya Chaubal authored 5 years ago and Marek Szuba committed 5 years ago

Includes recent Variation schema updates.

Registry: add support for versioned ncbi_taxonomy DBs + improve support for versioned metadata DBs

Registry::get_species_and_object_type(): filter out versioned ensembl_metadata and ncbi_taxonomy DBs

Again, for ensembl_metadata this should have been part of ENSCORESW-3119.

For ensembl_metadata this should have been part of ENSCORESW-3119 but
alas, I missed it.

Not sure if ncbi_taxonomy is actually processed by this function but
let's play it safe, will have to confirm.

See ENSCORESW-3253. If both a versioned and an unversioned database are
present, use the versioned one if the version number matches that of the
software.

Add next-value buffering to Bio::EnsEMBL::Utils::Iterator

Fix fetch_all_by_outward_search

This is useful when working with coderefs that defer to
`$sth->fetchrow_arrayref`, which throws an error if called again after
having returned undef (which signifies the end of the data stream)

```
DBD::mysql::st fetchrow_arrayref failed: fetch() without execute()
```

Enable VGNC xrefs for callithrix_jacchus and papio_anubis [master]

E100 version bump

Travis: reactivate warnings about different API and schema versions

Deprecate Bio::EnsEMBL::DBSQL::GenomeContainer::get_total_length()

As per the Ensembl coding guidelines, i.e.: added a deprecation warning
to the method, tagged it as deprecated in the POD block, and listed it
as scheduled for removal in Ensembl 102.

Issue: ENSINT-283

Add an inactive proof-of-concept GitLab-CI config file

Patch non-core test databases to schema version 99

Since the Operations meeting on 2019-08-27 the bumping of Ensembl API
and DB-schema version numbers has been an Ensembl-wide policy.
Therefore, have Travis take notice of possible discrepancies in this
respect.

Note that simply removing the before_script line creating the file
disabling these checks is in general NOT sufficient - it might have
been left behind by a previous build in the event of runner re-use. It
is safer to make sure it does not exist regardless of initial conditions
of the runner.