Migrating to 2.0

tacular 2.0 is a breaking API cleanup. The data is the same as 1.2. Renamed names have no aliases, so an import or attribute error tells you exactly what to change. The tables below list every removed or renamed public name.

Renamed

1.x	2.0
tacular.Proteases	tacular.Protease
info.dict_composition[k] = v (mutating in place)	read-only now (TypeError): info.update(dict_composition=dict(info.dict_composition) | {k: v})
tacular.PROTEASE_LITERALS	tacular.ProteaseLiteral
tacular.PROTEASES_DICT	tacular.PROTEASE_DICT
tacular.XlModInfo / tacular.XlModLookup	tacular.XlmodInfo / tacular.XlmodLookup
info.mass(monoisotopic) (ontology entries, monosaccharides)	info.get_mass(monoisotopic=...)
ELEMENT_LOOKUP.mass(key, monoisotopic)	ELEMENT_LOOKUP.get_mass(key, monoisotopic=...)
AA_LOOKUP.mass(key, monoisotopic)	AA_LOOKUP.get_mass(key, monoisotopic=...)
AA_LOOKUP.one_letter(c) / three_letter(c) / name(n) (raised KeyError)	AA_LOOKUP[c] (raises), or query_one_letter / query_three_letter / query_name (return None)
MONOSACCHARIDE_LOOKUP.proforma(name)	MONOSACCHARIDE_LOOKUP[name] or MONOSACCHARIDE_LOOKUP.query_name(name)
RefMolInfo.chemical_formula (field and to_dict key)	RefMolInfo.formula
NeutralDeltaInfo.to_dict()["dict_composition"]	NeutralDeltaInfo.to_dict()["composition"]
ElementLookup.NEUTRON_MASS	tacular.constants.NEUTRON_MASS
ELEMENT_LOOKUP.element_data	ELEMENT_LOOKUP.items() / keys() / values()

Removed or made private

1.x	Use instead
AA_LOOKUP.one_letter_to_info / three_letter_to_info / name_to_info	AA_LOOKUP.query_* or AA_LOOKUP.items()
MONOSACCHARIDE_LOOKUP.proforma_to_monosaccharide	MONOSACCHARIDE_LOOKUP.items()
PROTEASE_LOOKUP.name_to_info / id_to_info	PROTEASE_LOOKUP.query_name / query_id / items()
OntologyLookup.strip_id / convert_key / str(lookup)	lookup.query_id(key) (accepts every prefix form); repr(lookup)
tacular.obo_entity.filter_infos	a list comprehension over lookup.values()
tacular.update.OBO_SOURCES / ONTOLOGIES	tacular status / tacular.update.update(ontologies)
XlmodInfo.id_tag override	inherited OboEntity.id_tag (same result)

Changed behaviour

1.x	2.0
KeyError, ValueError or TypeError from lookup[key]	TacularKeyError, which is a KeyError and a ValueError, so existing except KeyError / except ValueError still work. A bad ELEMENT_LOOKUP tuple key no longer raises TypeError.
ValueError for a missing mass or composition, choice() with no match, an unknown ontology in update	TacularError (a ValueError)
get_mass(True), to_dict(4), choice(False, False), query_mass(m, 0.1)	keyword-only: get_mass(monoisotopic=True), to_dict(float_precision=4), choice(require_monoisotopic_mass=False, ...), query_mass(m, tolerance=0.1)
AminoAcidInfo, FragmentIonInfo, NeutralDeltaInfo, ProteaseInfo, RefMolInfo had an instance __dict__ (for cached_property)	frozen, slotted dataclasses (no __dict__); use dataclasses.replace to derive a new one
ElementInfo.to_dict() / AminoAcidInfo.to_dict()	also include is_monoisotopic / is_mass_ambiguous and is_ambiguous
NeutralDeltaInfo.to_dict()["amino_acids"] in set order	sorted, so jsons/neutral_losses.json is deterministic
OntologyLookup(data, name, version, prefixes, id_prefix) positional	OntologyLookup(data, name, *, version=, accession_prefixes=, id_prefix=)
Only long accession prefixes (UNIMOD:21)	short prefixes too (U:, M:, R:, X:, G:), and on names (U:Phospho)
ElementInfo.neutron_count on an element entry, serialize(0)	raise TacularError (a ValueError, as before)
UNIMOD_LOOKUP.keys() (every ontology lookup) returned lowercased names ("phospho")	returns the raw accession ids ("21"), the same keys items() uses; for names use [info.name for info in lookup.values()]
info.update(**changes) on ontology entries ignored unknown keywords and rebuilt the entry from a fixed field list	dataclasses.replace: an unknown keyword raises TypeError and subclass fields are kept
ELEMENT_LOOKUP["013C"] parsed as carbon-13	raises TacularKeyError (no leading zeros)
tacular.update.update() let parser ValueError s escape	raises TacularError chained from the parser’s error
tacular update reused a cached download forever	always downloads the current release; tacular clear also removes obo/

New

• tacular.constants: PROTON_MASS, ELECTRON_MASS, NEUTRON_MASS (CODATA 2018), HYDROGEN_MASS and C13_C12_MASS_DIFF (AME2016, matching the bundled isotope table).

• items() on every lookup; query_name on MONOSACCHARIDE_LOOKUP.

• tacular.ElementKey: the type of every key ELEMENT_LOOKUP accepts.

• tacular.tolerance: ppm_error, da_to_ppm, ppm_to_da, tolerance_window and within_tolerance; query_mass takes tolerance_unit="da"|"ppm" (the keyword every tacular-omics package uses).

• tacular.types: ToleranceUnit and Polarity, the shared vocabulary the other packages import instead of defining their own.