Changes to be committed:

modified:   go.mod
	modified:   go.sum
	modified:   pkg/obilua/obilib.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obilua/obiseqslice.go
	new file:   pkg/obilua/obitaxon.go
	new file:   pkg/obilua/obitaxonomy.go
	modified:   pkg/obioptions/version.go

pkg/obilua/obitaxonomy.go

@@ -0,0 +1,110 @@
+package obilua
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	lua "github.com/yuin/gopher-lua"
+)
+
+func RegisterObiTaxonomy(luaState *lua.LState) {
+	registerTaxonomyType(luaState)
+	registerTaxonType(luaState)
+}
+
+const luaTaxonomyTypeName = "Taxonomy"
+
+func registerTaxonomyType(luaState *lua.LState) {
+	taxonomyType := luaState.NewTypeMetatable(luaTaxonomyTypeName)
+	luaState.SetGlobal(luaTaxonomyTypeName, taxonomyType)
+	luaState.SetField(taxonomyType, "new", luaState.NewFunction(newTaxonomy))
+	luaState.SetField(taxonomyType, "default", luaState.NewFunction(defaultTaxonomy))
+	luaState.SetField(taxonomyType, "has_default", luaState.NewFunction(hasDefaultTaxonomy))
+	luaState.SetField(taxonomyType, "nil", taxon2Lua(luaState, nil))
+	luaState.SetField(taxonomyType, "__index",
+		luaState.SetFuncs(luaState.NewTable(),
+			taxonomyMethods))
+}
+
+func taxonomy2Lua(interpreter *lua.LState,
+	taxonomy *obitax.Taxonomy) lua.LValue {
+	ud := interpreter.NewUserData()
+	ud.Value = taxonomy
+	interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaTaxonomyTypeName))
+
+	return ud
+}
+
+func newTaxonomy(luaState *lua.LState) int {
+	name := luaState.CheckString(1)
+	code := luaState.CheckString(2)
+
+	charset := obiutils.AsciiAlphaNumSet
+	if luaState.GetTop() > 2 {
+		charset = obiutils.AsciiSetFromString(luaState.CheckString(3))
+	}
+
+	taxonomy := obitax.NewTaxonomy(name, code, charset)
+
+	luaState.Push(taxonomy2Lua(luaState, taxonomy))
+	return 1
+}
+
+func defaultTaxonomy(luaState *lua.LState) int {
+	taxonomy := obitax.DefaultTaxonomy()
+
+	if taxonomy == nil {
+		luaState.RaiseError("No default taxonomy")
+		return 0
+	}
+
+	luaState.Push(taxonomy2Lua(luaState, taxonomy))
+	return 1
+}
+
+func hasDefaultTaxonomy(luaState *lua.LState) int {
+	taxonomy := obitax.DefaultTaxonomy()
+
+	luaState.Push(lua.LBool(taxonomy != nil))
+	return 1
+}
+
+var taxonomyMethods = map[string]lua.LGFunction{
+	"name":  taxonomyGetName,
+	"code":  taxonomyGetCode,
+	"taxon": taxonomyGetTaxon,
+}
+
+func checkTaxonomy(L *lua.LState) *obitax.Taxonomy {
+	ud := L.CheckUserData(1)
+	if v, ok := ud.Value.(*obitax.Taxonomy); ok {
+		return v
+	}
+	L.ArgError(1, "obitax.Taxonomy expected")
+	return nil
+}
+
+func taxonomyGetName(luaState *lua.LState) int {
+	taxo := checkTaxonomy(luaState)
+	luaState.Push(lua.LString(taxo.Name()))
+	return 1
+}
+
+func taxonomyGetCode(luaState *lua.LState) int {
+	taxo := checkTaxonomy(luaState)
+	luaState.Push(lua.LString(taxo.Code()))
+	return 1
+}
+
+func taxonomyGetTaxon(luaState *lua.LState) int {
+	taxo := checkTaxonomy(luaState)
+	taxid := luaState.CheckString(2)
+	taxon, err := taxo.Taxon(taxid)
+
+	if err != nil {
+		luaState.RaiseError("%s : Error on taxon taxon: %v", taxid, err)
+		return 0
+	}
+
+	luaState.Push(taxon2Lua(luaState, taxon))
+	return 1
+}