API reference

Everything ligase exports — 90 names, generated from the package’s own docstrings against version 0.4.0. Anything not listed here is an implementation detail and may change without notice, including ligase._core, the compiled module.

Group	Names
Loading data	13	A loader reads what it can from the file and takes the rest as declarations
Declaring and running steps	10	A step is an ordinary annotated Python function
Steps you do not have to write	6	ligase.steps is curated rather than convenient: a step is in it only once it declares its tool’s version capture, its citation, the dimensions of its output and how that output canonicalises (D42)
Checking without running	2	Both of these read headers only
Data types	16	Every type is a Dataset carrying the dimensions inferred from its file
Standardising molecules	3	The one part of Ligase that needs a chemistry toolkit, and the only module that imports one
Resistance interpretation	8	Turning variant calls into HIV-1 drug-resistance calls
Provenance and auditing	16	What a run recorded about itself: the versions every tool actually ran at, every parameter as it was hashed, and the references by accession and checksum — and, the other way round, what a number you published rests on
Errors	14	Every failure mode has its own type, so a caller can tell a reference mismatch from a naming mismatch without reading the message
Version	2

How this page stays true

The reference is generated by web/scripts/generate_api.py on every docs build, which imports the package and reads its docstrings. Three things fail the build rather than producing a page that is quietly wrong:

a name in __all__ that no group lists — a public API nobody documented
a name a group lists that __all__ does not export — a page describing something callers cannot reach
any exported name, or any method or property on one, with no docstring

The grouping is by what a reader is trying to do rather than by module, and is declared in that script rather than inferred.