24521187249
90%

Ran 16 Apr 2026 04:22PM UTC

Jobs 3

Files 34

Run time 1min

Badge

Embed ▾

Committed 16 Apr 2026 04:15PM UTC coverage: 88.402%. Remained the same

Build # 24521187249

Build Type

push

github

Committed by

iskandr

Commit Message

Documentation sweep for newcomer readability

Fixes from a full audit of README + docs for an outside expert:

Must-fix:
- Ensembl release mismatch: README said 110, index.md said 93.
  Standardized on 112 (current GRCh38 default).  self_proteome.md
  examples no longer hardcode a release (use pyensembl's default).
- WT predictions (wt.Affinity.score etc.) documented in ranking.md
  as working but they return NaN.  Added a prominent "Not yet
  implemented" callout with a link to #123.

Should-fix:
- Installation section: added Python ≥ 3.9 requirement, pirlygenes
  install, and MHC predictor setup guidance (mhcflurry via pip,
  DTU tools via license) to both README and docs/index.md.
- Output columns: added a table to quickstart.md showing what the
  returned DataFrame contains (peptide, allele, kind, affinity,
  percentile_rank, score, prediction_method_name) so newcomers
  know what they're getting back.

mkdocs --strict clean.

Coverage Stats

3689 of 4173 relevant lines covered (88.4%)

2.65 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.12 - 24521187249.1	16 Apr 2026 04:23PM UTC	34	88.4	GitHub Action Run
2	python-3.11 - 24521187249.2	16 Apr 2026 04:22PM UTC	34	88.4	GitHub Action Run
3	python-3.10 - 24521187249.3	16 Apr 2026 04:22PM UTC	34	88.4	GitHub Action Run

openvax / topiary / 24521187249
90%

README BADGES
x

Markdown

Textile

RDoc

HTML

Rst

Jobs

Source Files on build 24521187249

openvax / topiary / 24521187249 90%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

Jobs

Source Files on build 24521187249

openvax / topiary / 24521187249
90%

README BADGES
x