Moved CLI to automlst.cli repo

.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 && pipx install . -e",
+	"postCreateCommand": "pip3 install --user -r requirements.txt",
 	"customizations": {
 		"vscode": {
 			"extensions": [

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "automlst"
+name = "automlst.engine"
 dynamic = ["version"]
 
 dependencies = [
@@ -13,9 +13,6 @@ dependencies = [
 requires-python = ">=3.11"
 description = "A tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
-[project.scripts]
-automlst = "automlst.cli.program:run"
-
 [tool.setuptools_scm]
 
 [tool.pyright]

src/automlst/cli/info.py

@@ -1,43 +0,0 @@
-from argparse import ArgumentParser
-import asyncio
-from automlst.engine.remote.databases.bigsdb import BIGSdbIndex
-
-
-def setup_parser(parser: ArgumentParser):
-    parser.description = "Fetches the latest BIGSdb MLST database definitions."
-    parser.add_argument(
-        "--retrieve-bigsdbs", "-l",
-        action="store_true",
-        dest="list_dbs",
-        required=False,
-        default=False,
-        help="Lists all known BIGSdb MLST databases (fetched from known APIs and cached)."
-    )
-
-    parser.add_argument(
-        "--retrieve-bigsdb-schemas", "-lschemas",
-        nargs="+",
-        action="extend",
-        dest="list_bigsdb_schemas",
-        required=False,
-        default=[],
-        type=str,
-        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)
-
-async def run(args):
-    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()))
-
-        for bigsdb_schema_name in args.list_bigsdb_schemas:
-            schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
-            for schema_desc, schema_id in schemas.items():
-                print(f"{schema_desc}: {schema_id}")
-
-def run_asynchronously(args):
-    asyncio.run(run(args))
-

src/automlst/cli/meta.py

@@ -1,2 +0,0 @@
-def get_module_base_name(name):
-    return name.split(".")[-1]

src/automlst/cli/program.py

@@ -1,27 +0,0 @@
-import argparse
-import asyncio
-import datetime
-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
-
-root_parser = argparse.ArgumentParser()
-subparsers = root_parser.add_subparsers(required=True)
-
-info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
-st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
-
-
-def run():
-    args = root_parser.parse_args()
-    args.func(args)
-
-if __name__ == "__main__":
-    run()

src/automlst/cli/st.py

@@ -1,69 +0,0 @@
-
-from argparse import ArgumentParser
-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
-
-
-def setup_parser(parser: ArgumentParser):
-    parser.description = "Returns MLST exact profile matches."
-    parser.add_argument(
-        "fastas",
-        nargs="+",
-        action='extend',
-        default=[],
-        type=str,
-        help="The FASTA files to process. Multiple can be listed."
-    )
-
-    parser.add_argument(
-        "seqdefdb",
-        help="The BIGSdb seqdef database to use for typing."
-    )
-
-    parser.add_argument(
-        "schema",
-        type=int,
-        help="The BIGSdb seqdef database schema ID (integer) to use for typing."
-    )
-
-    parser.add_argument(
-        "out",
-        default=f'./{datetime.datetime.now().strftime(r"%Y%m%d%H%M%S")}',
-        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",
-        dest="stop_on_fail",
-        required=False,
-        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)
-
-async def run(args):
-    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)
-            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"Completed fetching MLSTs for {len(args.fastas)} sequences.")
-
-def run_asynchronously(args):
-    asyncio.run(run(args))
-