openvax / pyensembl / 25757708650

85%

master: 83%

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push

github

Committed by web-flow

Commit Message

Fix #298: route Ensembl Genomes divisions through the right server (#343)

Adds the missing pieces to actually install non-vertebrate species from
the Ensembl Genomes FTP server:

* New `Species.ensembl_genomes` boolean. When True, GTF + FASTA URLs are
  built against ftp.ensemblgenomes.ebi.ac.uk under /pub/release-N/{division}/...
  (was only available for plants, via the legacy `is_plant` switch).
* New `MAX_ENSEMBL_GENOMES_RELEASE = 58` constant. The Ensembl Genomes
  release stream is numbered separately from the main Ensembl releases;
  `MAX_PLANTS_ENSEMBL_RELEASE` is preserved as an alias for back-compat.
* URL template builders now branch on `species.ensembl_genomes` and
  `species.division` instead of `is_plant`. `is_plant` keyword is still
  accepted on `Species.register` and implies `division="plants"` and
  `ensembl_genomes=True`.
* `EnsemblRelease(server=...)` defaults are upgraded so omitting `server`
  with an Ensembl Genomes species picks ftp.ensemblgenomes.ebi.ac.uk
  automatically.

Adds 9 new species across the four Ensembl Genomes divisions, with URLs
verified against ftp.ensemblgenomes.ebi.ac.uk release 58:

  Plants:    wheat, maize, tomato
  Fungi:     fission_yeast (pombe), aspergillus_nidulans, candida_albicans
  Metazoa:   anopheles_gambiae
  Protists:  plasmodium_falciparum, toxoplasma_gondii

Existing yeast / drosophila / C. elegans entries stay on main Ensembl
(unchanged release ranges, `ensembl_genomes=False`) so their installs
don't break.

Bump version to 2.9.0.

Coverage Stats

56 of 61 new or added lines in 5 files covered. (91.8%)

1 existing line in 1 file now uncovered.

1551 of 1838 relevant lines covered (84.39%)

3.38 hits per line