Updated CLI to follow APIs specified by the 0.12.0 engine

.devcontainer/devcontainer.json

@@ -12,7 +12,7 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt",
+	"postCreateCommand": "pip3 install --user -r requirements.txt && pip install -e .",
 	"customizations": {
 		"vscode": {
 			"extensions": [

.gitignore

@@ -212,3 +212,4 @@ pyrightconfig.json
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
+out.csv

Jenkinsfile

@@ -33,10 +33,10 @@ pipeline {
             parallel {
                 stage ("git.reslate.systems") {
                     environment {
-                        TOKEN = credentials('git.reslate.systems')
+                        CREDS = credentials('username-password-rs-git')
                     }
                     steps {
-                        sh returnStatus: true, script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh script: 'python -m twine upload --repository-url https://git.reslate.systems/api/packages/ydeng/pypi -u ${CREDS_USR} -p ${CREDS_PSW} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
                 stage ("pypi.org") {
@@ -47,7 +47,7 @@ pipeline {
                         TOKEN = credentials('pypi.org')
                     }
                     steps {
-                        sh returnStatus: true, script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
+                        sh script: 'python -m twine upload -u __token__ -p ${TOKEN} --non-interactive --disable-progress-bar --verbose dist/*'
                     }
                 }
             }

pyproject.toml

@@ -6,9 +6,9 @@ build-backend = "setuptools.build_meta"
 name = "autoBIGS.cli"
 dynamic = ["version"]
 readme = "README.md"
-
+license = {file = "LICENSE"}
 dependencies = [
-    "autoBIGS-engine"
+    "autoBIGS-engine==0.12.*"
 ]
 requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."

src/autobigs/cli/info.py

@@ -1,6 +1,6 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
-from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
     parser.description = "Fetches the latest BIGSdb MLST database definitions."
@@ -31,15 +31,17 @@ 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)
-            print("\n".join(known_seqdef_dbs.keys()))
+            print("The following are all known BIGS database names (sorted alphabetically):")
+            print("\n".join(sorted(known_seqdef_dbs.keys())))
 
         for bigsdb_schema_name in args.list_bigsdb_schemas:
             schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
+            print("The following are the known schemas for \"{0}\", and their associated IDs:".format(bigsdb_schema_name))
             for schema_desc, schema_id in schemas.items():
                 print(f"{schema_desc}: {schema_id}")
 
         if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
-            print("Nothing to do. Try specifying \"-l\".")
+            print("Nothing to do. Try specifying \"-l\" for a list of known databases, or \"-h\" for more information.")
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))

src/autobigs/cli/program.py

@@ -33,6 +33,8 @@ def run():
               metadata.version("autoBIGS-engine")}.')
     if hasattr(args, "run"):
         args.run(args)
+    elif not args.version:
+        root_parser.print_usage()
 
 
 if __name__ == "__main__":

src/autobigs/cli/st.py

@@ -2,9 +2,9 @@
 from argparse import ArgumentParser, Namespace
 import asyncio
 import datetime
-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
+from autobigs.engine.writing import write_mlst_profiles_as_csv
+from autobigs.engine.reading import read_multiple_fastas
+from autobigs.engine.analysis.bigsdb import BIGSdbIndex
 
 
 def setup_parser(parser: ArgumentParser):
@@ -35,15 +35,6 @@ def setup_parser(parser: ArgumentParser):
         help="The output CSV name (.csv will be appended)."
     )
 
-    parser.add_argument(
-        "--exact", "-ex",
-        action="store_true",
-        dest="exact",
-        required=False,
-        default=False,
-        help="Should run exact matching rather than returning all similar ones"
-    )
-
     parser.add_argument(
         "--stop-on-fail", "-sof",
         action="store_true",
@@ -58,11 +49,11 @@ def setup_parser(parser: ArgumentParser):
 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:
-            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings, exact=args.exact)
+        async with await bigsdb_index.build_profiler_from_seqdefdb(False, args.seqdefdb, args.schema) as mlst_profiler:
+            mlst_profiles = mlst_profiler.profile_multiple_strings(gen_strings)
             failed = await write_mlst_profiles_as_csv(mlst_profiles, args.out)
             if len(failed) > 0:
-                print(f"A total of {len(failed)} IDs failed:\n{"\n".join(failed)}")
+                print(f"A total of {len(failed)} IDs failed (no profile found):\n{"\n".join(failed)}")
             print(f"Completed fetching MLSTs for {len(args.fastas)} sequences.")
 
 def run_asynchronously(args):