Continuation of refactoring package name

src/autoBIGSst/cli/info.py

@@ -1,6 +1,6 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
-from autoBIGSst.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autoBIGS.engine.data.remote.databases.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
     parser.description = "Fetches the latest BIGSdb MLST database definitions."

src/autoBIGSst/cli/program.py

@@ -3,8 +3,8 @@ from importlib import metadata
 from os import path
 import os
 
-from autoBIGSst.cli import info, st
-from autoBIGSst.cli.meta import get_module_base_name
+from autoBIGS.cli import info, st
+from autoBIGS.cli.meta import get_module_base_name
 import importlib
 
 root_parser = argparse.ArgumentParser(epilog='Use "%(prog)s info -h" to learn how to get available MLST databases, and their available schemas.'
@@ -20,17 +20,17 @@ root_parser.add_argument(
     action="store_true",
     default=False,
     required=False,
-    help="Displays the autoBIGSst.CLI version, and the autoBIGSst.Engine version."
+    help="Displays the autoBIGS.CLI version, and the autoBIGS.Engine version."
 )
 
 
 def run():
     args = root_parser.parse_args()
     if args.version:
-        print(f'autoBIGSst.CLI is running version {
-              metadata.version("autoBIGSst-cli")}.')
-        print(f'autoBIGSst.Engine is running version {
-              metadata.version("autoBIGSst-engine")}.')
+        print(f'autoBIGS.CLI is running version {
+              metadata.version("autoBIGS-cli")}.')
+        print(f'autoBIGS.Engine is running version {
+              metadata.version("autoBIGS-engine")}.')
     if hasattr(args, "run"):
         args.run(args)
 

src/autoBIGSst/cli/st.py

@@ -2,9 +2,9 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
 import datetime
-from autoBIGSst.engine.data.local.csv import write_mlst_profiles_as_csv
-from autoBIGSst.engine.data.local.fasta import read_multiple_fastas
-from autoBIGSst.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autoBIGS.engine.data.local.csv import write_mlst_profiles_as_csv
+from autoBIGS.engine.data.local.fasta import read_multiple_fastas
+from autoBIGS.engine.data.remote.databases.bigsdb import BIGSdbIndex
 
 
 def setup_parser(parser: ArgumentParser):