Updated CLI to output more useful information.

src/automlst/cli/info.py

@@ -1,6 +1,6 @@
-from argparse import ArgumentParser
+from argparse import ArgumentParser, Namespace
 import asyncio
-from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+from automlst.engine.data.remote.databases.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
     parser.description = "Fetches the latest BIGSdb MLST database definitions."
@@ -24,9 +24,10 @@ def setup_parser(parser: ArgumentParser):
         help="Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given."
     )
 
-    parser.set_defaults(func=run_asynchronously)
+    parser.set_defaults(run=run_asynchronously)
+    return parser
 
-async def run(args):
+async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         if args.list_dbs:
             known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
@@ -37,6 +38,9 @@ async def run(args):
             for schema_desc, schema_id in schemas.items():
                 print(f"{schema_desc}: {schema_id}")
 
-def run_asynchronously(args):
+        if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
+            print("Nothing to do. Try specifying \"-l\".")
+
+def run_asynchronously(args: Namespace):
     asyncio.run(run(args))
 

src/automlst/cli/program.py

@@ -1,27 +1,39 @@
 import argparse
-import asyncio
-import datetime
+from importlib import metadata
 from os import path
 import os
 
 from automlst.cli import info, st
 from automlst.cli.meta import get_module_base_name
-from automlst.engine.data.genomics import NamedString
-from automlst.engine.local.abif import read_abif
-from automlst.engine.local.csv import write_mlst_profiles_as_csv
-from automlst.engine.local.fasta import read_fasta
-from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+import importlib
 
-root_parser = argparse.ArgumentParser()
-subparsers = root_parser.add_subparsers(required=True)
+root_parser = argparse.ArgumentParser(epilog='Use "%(prog)s info -h" to learn how to get available MLST databases, and their available schemas.'
+                                      + ' Once that is done, use "%(prog)s st -h" to learn how to retrieve MLST profiles.'
+                                      )
+subparsers = root_parser.add_subparsers(required=False)
 
 info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
 st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
 
+root_parser.add_argument(
+    "--version",
+    action="store_true",
+    default=False,
+    required=False,
+    help="Displays the autoMLST.CLI version, and the autoMLST.Engine version."
+)
+
 
 def run():
     args = root_parser.parse_args()
-    args.func(args)
+    if args.version:
+        print(f'autoMLST.CLI is running version {
+              metadata.version("automlst-cli")}.')
+        print(f'autoMLST.Engine is running version {
+              metadata.version("automlst-engine")}.')
+    if hasattr(args, "run"):
+        args.run(args)
+
 
 if __name__ == "__main__":
-    run()
+    run()

src/automlst/cli/st.py

@@ -1,10 +1,10 @@
 
-from argparse import ArgumentParser
+from argparse import ArgumentParser, Namespace
 import asyncio
 import datetime
-from automlst.engine.local.csv import write_mlst_profiles_as_csv
-from automlst.engine.local.fasta import read_multiple_fastas
-from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
+from automlst.engine.data.local.csv import write_mlst_profiles_as_csv
+from automlst.engine.data.local.fasta import read_multiple_fastas
+from automlst.engine.data.remote.databases.bigsdb import BIGSdbIndex
 
 
 def setup_parser(parser: ArgumentParser):
@@ -52,9 +52,10 @@ def setup_parser(parser: ArgumentParser):
         default=False,
         help="Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches)."
     )
-    parser.set_defaults(func=run_asynchronously)
+    parser.set_defaults(run=run_asynchronously)
+    return parser
 
-async def run(args):
+async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
         gen_strings = read_multiple_fastas(args.fastas)
         async with await bigsdb_index.build_profiler_from_seqdefdb(args.seqdefdb, args.schema) as mlst_profiler: