From 9498fe7a453572784057a02f41105b55525660c5 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Wed, 22 Jan 2025 21:36:45 +0000
Subject: [PATCH] Updated module imports

---
 pyproject.toml                               | 8 ++++++--
 requirements.txt                             | 2 +-
 src/{autoBIGSst => autobigs}/cli/__init__.py | 0
 src/{autoBIGSst => autobigs}/cli/info.py     | 2 +-
 src/{autoBIGSst => autobigs}/cli/meta.py     | 0
 src/{autoBIGSst => autobigs}/cli/program.py  | 4 ++--
 src/{autoBIGSst => autobigs}/cli/st.py       | 6 +++---
 7 files changed, 13 insertions(+), 9 deletions(-)
 rename src/{autoBIGSst => autobigs}/cli/__init__.py (100%)
 rename src/{autoBIGSst => autobigs}/cli/info.py (96%)
 rename src/{autoBIGSst => autobigs}/cli/meta.py (100%)
 rename src/{autoBIGSst => autobigs}/cli/program.py (93%)
 rename src/{autoBIGSst => autobigs}/cli/st.py (91%)

diff --git a/pyproject.toml b/pyproject.toml
index b1dee75..0e2c5e2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,14 +7,18 @@ name = "autoBIGS.cli"
 dynamic = ["version"]
 readme = "README.md"
 
+[project.urls]
+Repository = "https://github.com/RealYHD/autoBIGS.cli"
+Issues = "https://github.com/RealYHD/autoBIGS.cli/issues"
+
 dependencies = [
-    "autoBIGS-engine"
+    "autoBIGS.engine"
 ]
 requires-python = ">=3.11"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
 [project.scripts]
-autoBIGS = "autoBIGS.cli.program:run"
+autoBIGS = "autobigs.cli.program:run"
 
 [tool.setuptools_scm]
 
diff --git a/requirements.txt b/requirements.txt
index 438352a..7b54436 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,4 @@ pytest-cov
 build
 twine
 setuptools_scm
-autobigsst.engine
+autoBIGS.engine
diff --git a/src/autoBIGSst/cli/__init__.py b/src/autobigs/cli/__init__.py
similarity index 100%
rename from src/autoBIGSst/cli/__init__.py
rename to src/autobigs/cli/__init__.py
diff --git a/src/autoBIGSst/cli/info.py b/src/autobigs/cli/info.py
similarity index 96%
rename from src/autoBIGSst/cli/info.py
rename to src/autobigs/cli/info.py
index fd3a167..68a559b 100644
--- a/src/autoBIGSst/cli/info.py
+++ b/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."
diff --git a/src/autoBIGSst/cli/meta.py b/src/autobigs/cli/meta.py
similarity index 100%
rename from src/autoBIGSst/cli/meta.py
rename to src/autobigs/cli/meta.py
diff --git a/src/autoBIGSst/cli/program.py b/src/autobigs/cli/program.py
similarity index 93%
rename from src/autoBIGSst/cli/program.py
rename to src/autobigs/cli/program.py
index 3eb0d26..8332c36 100644
--- a/src/autoBIGSst/cli/program.py
+++ b/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.meta import get_module_base_name
+from autobigs.cli import info, st
+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.'
diff --git a/src/autoBIGSst/cli/st.py b/src/autobigs/cli/st.py
similarity index 91%
rename from src/autoBIGSst/cli/st.py
rename to src/autobigs/cli/st.py
index 341f29b..86848c9 100644
--- a/src/autoBIGSst/cli/st.py
+++ b/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.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
 
 
 def setup_parser(parser: ArgumentParser):