add the --raw-taxid option

Release-notes.md

@@ -16,6 +16,12 @@
 - A new option **--csv** is added to every obitools to indicate that the input
   format is CSV
 
+- The new version of obitools are now printing the taxids in a fancy way
+  including the scientific name and the taxonomic rank (`"taxon:9606 [Homo
+  sapiens]@species"`). But if you need the old fashion raw taxid, a new option
+  **--raw-taxid** has been added to get obitools printing the taxids without any
+  decorations (`"9606"`).
+
 
 ## March 1st, 2025. Release 4.4.0
 

pkg/obidefault/taxonomy.go

@@ -4,6 +4,15 @@ var __taxonomy__ = ""
 var __alternative_name__ = false
 var __fail_on_taxonomy__ = false
 var __update_taxid__ = false
+var __raw_taxid__ = false
+
+func UseRawTaxids() bool {
+	return __raw_taxid__
+}
+
+func UseRawTaxidsPtr() *bool {
+	return &__raw_taxid__
+}
 
 func SelectedTaxonomy() string {
 	return __taxonomy__

pkg/obioptions/options.go

@@ -186,6 +186,10 @@ func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bo
 	options.BoolVar(obidefault.UpdateTaxidPtr(), "update-taxid", obidefault.UpdateTaxid(),
 		options.Description("Make obitools automatically updating the taxid that are declared merged to a newest one."),
 	)
+
+	options.BoolVar(obidefault.UseRawTaxidsPtr(), "raw-taxid", obidefault.UseRawTaxids(),
+		options.Description("When set, taxids are printed in files with any supplementary information (taxon name and rank)"),
+	)
 }
 
 // CLIIsDebugMode returns whether the CLI is in debug mode.

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "706b44c"
+var _Commit = "78df7db"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obitax/taxonnode.go

@@ -5,6 +5,7 @@ import (
 	"regexp"
 	"strings"
 
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -37,6 +38,10 @@ type TaxNode struct {
 // Returns:
 //   - A formatted string representing the TaxNode in the form "taxonomyCode:id [scientificName]@rank".
 func (node *TaxNode) String(taxonomyCode string) string {
+	if obidefault.UseRawTaxids() {
+		return *node.id
+	}
+
 	if node.HasScientificName() {
 		return fmt.Sprintf("%s:%v [%s]@%s",
 			taxonomyCode,