openvax / pyensembl
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master: 83%

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LAST BUILD ON BRANCH v2.9.0
branch: v2.9.0
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coverage: 84.385% (+0.2%) from 84.199%
25757722028

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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.

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

Relevant lines Covered
1838 RELEVANT LINES 1551 COVERED LINES
3.38 HITS PER LINE
Source Files on v2.9.0

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
25757722028 v2.9.0 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 URL... push web-flow github
84.39
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