fix taxonomy, JGI changed format of superkingdom/domain;#8

Author: Jon Palmer

CITATION.cff

@@ -1,4 +1,4 @@
-cff-version: version = "25.4.30"
+cff-version: version = "25.5.26"
 title: 'funannotate2: eukaryotic genome annotation'
 message: >-
   If you use this software, please cite it using the
@@ -17,5 +17,5 @@ keywords:
   - functional annotation
   - consensus gene models
 license: BSD-2-Clause
-version: version = "25.4.30"
-date-released: '2025-05-01'
+version: version = "25.5.26"
+date-released: '2025-05-26'

funannotate2/utilities.py

@@ -299,7 +299,7 @@ def lookup_taxonomy(name):
     This function retrieves a taxonomy dictionary for a specified organism by querying
     an external taxonomy service. If the species name is valid, it returns a dictionary
     containing taxonomic levels and names. If the name is invalid or an error occurs,
-    it returns False.
+    it returns False. EDIT: JGI changed superkingdom to domain, so map it.
 
     Parameters:
     - name (str): The name of the organism to fetch, e.g., 'Aspergillus nidulans'.
@@ -321,7 +321,7 @@ def lookup_taxonomy(name):
             # reformat result to simpler version
             data = {}
             for i in [
-                "superkingdom",
+                "domain",
                 "kingdom",
                 "phylum",
                 "class",
@@ -331,7 +331,10 @@ def lookup_taxonomy(name):
                 "species",
             ]:
                 if i in result:
-                    data[i] = result[i]["name"]
+                    if i == "domain":
+                        data["superkingdom"] = result[i]["name"]
+                    else:
+                        data[i] = result[i]["name"]
             return data
     except requests.exceptions.RequestException as e:
         print("ERROR in taxonomy lookup: {}".format(e))

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "funannotate2"
-version = "25.4.30"
+version = "25.5.26"
 description = "Funannotate2: eukarytoic genome annotation pipeline"
 readme = {file = "README.md", content-type = "text/markdown"}
 authors = [