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/obitaxon.go

@@ -0,0 +1,139 @@
+package obilua
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	lua "github.com/yuin/gopher-lua"
+)
+
+const luaTaxonTypeName = "Taxon"
+
+func registerTaxonType(luaState *lua.LState) {
+	taxonType := luaState.NewTypeMetatable(luaTaxonTypeName)
+	luaState.SetGlobal(luaTaxonTypeName, taxonType)
+	luaState.SetField(taxonType, "new", luaState.NewFunction(newTaxon))
+	luaState.SetField(taxonType, "nil", taxonomy2Lua(luaState, nil))
+
+	luaState.SetField(taxonType, "__index",
+		luaState.SetFuncs(luaState.NewTable(),
+			taxonMethods))
+}
+
+func taxon2Lua(interpreter *lua.LState,
+	taxon *obitax.Taxon) lua.LValue {
+	ud := interpreter.NewUserData()
+	ud.Value = taxon
+	interpreter.SetMetatable(ud, interpreter.GetTypeMetatable(luaTaxonTypeName))
+
+	return ud
+}
+
+func newTaxon(luaState *lua.LState) int {
+	taxonomy := checkTaxonomy(luaState)
+	taxid := luaState.CheckString(2)
+	parent := luaState.CheckString(3)
+	sname := luaState.CheckString(4)
+	rank := luaState.CheckString(5)
+
+	isroot := false
+
+	if luaState.GetTop() > 5 {
+		isroot = luaState.CheckBool(6)
+	}
+
+	taxon, err := taxonomy.AddTaxon(taxid, parent, rank, isroot, false)
+
+	if err != nil {
+		luaState.RaiseError("(%v,%v,%v) : Error on taxon creation: %v", taxid, parent, sname, err)
+		return 0
+	}
+
+	taxon.SetName(sname, "scientific name")
+
+	luaState.Push(taxon2Lua(luaState, taxon))
+	return 1
+}
+
+var taxonMethods = map[string]lua.LGFunction{
+	"string":          taxonAsString,
+	"scientific_name": taxonGetSetScientificName,
+	"parent":          taxonGetParent,
+	"taxon_at_rank":   taxGetTaxonAtRank,
+	"species":         taxonGetSpecies,
+	"genus":           taxonGetGenus,
+	"family":          taxonGetFamily,
+}
+
+func checkTaxon(L *lua.LState, i int) *obitax.Taxon {
+	ud := L.CheckUserData(i)
+	if v, ok := ud.Value.(*obitax.Taxon); ok {
+		return v
+	}
+	L.ArgError(i, "obitax.Taxon expected")
+	return nil
+}
+
+func taxonAsString(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+	luaState.Push(lua.LString(taxon.String()))
+	return 1
+}
+
+func taxonGetSetScientificName(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	if luaState.GetTop() > 1 {
+		sname := luaState.CheckString(2)
+		taxon.SetName(sname, "scientific name")
+		return 0
+	}
+
+	luaState.Push(lua.LString(taxon.ScientificName()))
+	return 1
+}
+
+func taxonGetParent(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	parent := taxon.Parent()
+	luaState.Push(taxon2Lua(luaState, parent))
+
+	return 1
+}
+
+func taxonGetSpecies(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	species := taxon.Species()
+	luaState.Push(taxon2Lua(luaState, species))
+
+	return 1
+}
+
+func taxonGetGenus(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	genus := taxon.Genus()
+	luaState.Push(taxon2Lua(luaState, genus))
+
+	return 1
+}
+
+func taxonGetFamily(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+
+	family := taxon.Family()
+	luaState.Push(taxon2Lua(luaState, family))
+
+	return 1
+}
+
+func taxGetTaxonAtRank(luaState *lua.LState) int {
+	taxon := checkTaxon(luaState, 1)
+	rank := luaState.CheckString(2)
+
+	taxonAt := taxon.TaxonAtRank(rank)
+
+	luaState.Push(taxon2Lua(luaState, taxonAt))
+
+	return 1
+}