Updated python version requirement to 3.12 due to use of f-strings

README.md

@@ -1,19 +1,25 @@
-# autoBIGS.CLI
+# autoBIGS.cli
 
-A command-line interface based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV.
+A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST.
 
-This program is simply a command-line interface for [autoBIGS.Engine](https://pypi.org/project/autoBIGS.engine).
+This program is simply a command-line interface for [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine).
 
 ## Features
 
-This CLI is capable of exactly what [autoBIGS.Engine](https://pypi.org/project/autoBIGS.engine) is capable of:
+This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine) is capable of:
-- Import multiple FASTA files
+- Import multiple whole genome FASTA files
 - Fetch the available BIGSdb databases that is currently live and available
 - Fetch the available BIGSdb database schemas for a given MLST database
 - Retrieve exact/non-exact MLST allele variant IDs based off a sequence
 - Retrieve MLST sequence type IDs based off a sequence
 - Output all results to a single CSV
 
+## Planned Features for CLI
+- Specifications of multi-threading capacity
+- Session authentication for updated database schemas (as required by both PubMLST and Institut Pasteur)
+
+Please refer to [autoBIGS.engine](https://pypi.org/project/autoBIGS.engine) for more planned features.
+
 ## Usage
 
 This CLI can be installed with `pip`. Please ensure [pip is installed](https://pip.pypa.io/en/stable/installation/). Then:

pyproject.toml

@@ -10,11 +10,16 @@ readme = "README.md"
 dependencies = [
     "autoBIGS-engine"
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
+[project.urls]
+Repository = "https://github.com/RealYHD/autoBIGS.cli"
+Issues = "https://github.com/RealYHD/autoBIGS.cli/issues"
+
+
 [project.scripts]
-autoBIGS = "autoBIGS.cli.program:run"
+autoBIGS = "autobigs.cli.program:run"
 
 [tool.setuptools_scm]
 

requirements.txt

@@ -4,4 +4,4 @@ pytest-cov
 build
 twine
 setuptools_scm
-autobigsst.engine
+autoBIGS.engine

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.data.remote.databases.bigsdb import BIGSdbIndex
 
 def setup_parser(parser: ArgumentParser):
     parser.description = "Fetches the latest BIGSdb MLST database definitions."

src/autobigs/cli/program.py

@@ -3,8 +3,8 @@ from importlib import metadata
 from os import path
 import os
 
-from autoBIGS.cli import info, st
+from autobigs.cli import info, st
-from autoBIGS.cli.meta import get_module_base_name
+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.'

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.csv import write_mlst_profiles_as_csv
-from autoBIGS.engine.data.local.fasta import read_multiple_fastas
+from autobigs.engine.data.local.fasta import read_multiple_fastas
-from autoBIGS.engine.data.remote.databases.bigsdb import BIGSdbIndex
+from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
 
 
 def setup_parser(parser: ArgumentParser):