Add support for BNGL models (cont.) - #508

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dweindl wants to merge 12 commits into

PEtab-dev:mainfrom

dweindl:bngl-corpus-fetch-on-demand

Commits on Aug 12, 2026

Add support for BNGL models as a PEtab model language

wshlavacek
authored and
dweindl
committed
19a719f
Harden the BNGL block reader: block aliases + seed-species $ clamp

wshlavacek
authored and
dweindl
committed
3cad3d6
Harden the BNGL block reader: join line continuations

wshlavacek
authored and
dweindl
committed
c59773f
Harden the BNGL block reader: strip line labels (index + named)

wshlavacek
authored and
dweindl
committed
9c32839
Add a corpus regression gate: parse_bngl vs a cached BNG2.pl golden

wshlavacek
authored and
dweindl
committed
5407d3e
Match BNG2.pl: drop the `molecules`/`rules` block aliases (keep `species`)

wshlavacek
authored and
dweindl
committed
82bce38
Make None defaults Optional and pin utf-8 in to_file

wshlavacek
authored and
dweindl
committed
571cdac
Remove vendored BNGL corpus fixtures; fetch on demand instead
dweindl
committed
2617a1a
Fetch the BNGL test corpus on demand instead of vendoring it
dweindl
committed
4115063
doc
dweindl
committed
0956c55
ruff
dweindl
committed
170f219

Commits on Aug 13, 2026

Merge branch 'main' into bngl-corpus-fetch-on-demand
dweindl
authored
686023d