openvax / pyensembl

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LAST BUILD ON BRANCH v2.8.0

branch: v2.8.0

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Build # 25752455864

Build Type

push

github

Committed by web-flow

Commit Message

Add Species.division and prettier 'pyensembl available' output (#342)

Species now carries a division field ("vertebrates" by default, plus
"plants", "fungi", "metazoa", "protists", "bacteria") and exposes
matching predicates (is_plant, is_fungus, is_animal, is_vertebrate,
is_invertebrate, is_protist, is_bacterium). The legacy is_plant
keyword on Species.register is preserved and translates to
division="plants" so external callers keep working.

Existing species are tagged taxonomically: arabidopsis/rice → plants,
yeast → fungi, drosophila/C. elegans → metazoa. URL routing still goes
through is_plant, so no behavior change for installs in this release.

pyensembl available now renders as a single aligned table with division
section headers (Vertebrates / Invertebrates / Plants / Fungi), an
en-dashed release range, single-release entries shown as the bare
number, and a dimmed latin-name column. ANSI styling is auto-enabled
when stdout is a TTY and suppressed when piped.

Unblocks #298 (adding more plants / fungi / metazoa species) by
giving registrations a real taxonomic field to plug into.

Bump version to 2.8.0.

Coverage Stats

72 of 83 new or added lines in 3 files covered. (86.75%)

1524 of 1810 relevant lines covered (84.2%)

3.37 hits per line