Updated local repository publishing requirement for CI

Jenkinsfile

@@ -40,7 +40,6 @@ pipeline {
                     when {
                         branch '**/main'
                     }
-
                     environment {
                         CREDS = credentials('username-password-rs-git')
                     }

pyproject.toml

@@ -8,7 +8,7 @@ dynamic = ["version"]
 readme = "README.md"
 license = {text = "GPL-3.0-or-later"}
 dependencies = [
-    "autoBIGS-engine==0.13.*"
+    "autoBIGS-engine==0.14.*"
 ]
 requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."

src/autobigs/cli/info.py

@@ -53,18 +53,19 @@ async def run(args: Namespace):
                     writer.writerows(sorted_seqdef_dbs)
                     print("\nDatabase output written to {0}".format(args.csv_output))
 
-        csv_scheme_rows = []
+        if args.list_bigsdb_schemes:
-        for bigsdb_scheme_name in args.list_bigsdb_schemes:
+            csv_scheme_rows = []
-            schemes = await bigsdb_index.get_schemes_for_seqdefdb(bigsdb_scheme_name)
+            for bigsdb_scheme_name in args.list_bigsdb_schemes:
-            csv_scheme_rows.extend([(name, id, bigsdb_scheme_name) for name, id in sorted(schemes.items())])
+                schemes = await bigsdb_index.get_schemes_for_seqdefdb(bigsdb_scheme_name)
-            print("The following are the known schemes for \"{0}\", and their associated IDs:".format(bigsdb_scheme_name))
+                csv_scheme_rows.extend([(name, id, bigsdb_scheme_name) for name, id in sorted(schemes.items())])
-            print("\n".join(["{0}: {1}".format(name, id) for name, id, database in csv_scheme_rows]))
+                print("The following are the known schemes for \"{0}\", and their associated IDs:".format(bigsdb_scheme_name))
-        if args.csv_output:
+                print("\n".join(["{0}: {1}".format(name, id) for name, id, database in csv_scheme_rows]))
-            with open(args.csv_output, "w") as csv_out_handle:
+            if args.csv_output:
-                writer = csv.writer(csv_out_handle)
+                with open(args.csv_output, "w") as csv_out_handle:
-                writer.writerow(("Name", "ID", "Database Name"))
+                    writer = csv.writer(csv_out_handle)
-                writer.writerows(csv_scheme_rows)
+                    writer.writerow(("Name", "ID", "Database Name"))
-            print("\nscheme list output written to {0}".format(args.csv_output))
+                    writer.writerows(csv_scheme_rows)
+                print("\nscheme list output written to {0}".format(args.csv_output))
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))

src/autobigs/cli/st.py

@@ -79,7 +79,7 @@ async def run(args: Namespace):
             if not isinstance(mlst_profiler, BIGSdbMLSTProfiler):
                 raise TypeError("MLST profiler type invalid")
             mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, args.stop_on_fail)
-            failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
+            failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out, await bigsdb_index.get_scheme_loci(args.seqdefdb, selected_scheme_id))
             if len(failed) > 0:
                 print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")
             print(f"Completed fetching from {args.seqdefdb} for {scheme_name_lookup[selected_scheme_id]}s for {len(fastas)} sequences.")