set v3.0.1 and requirements

.flake8

@@ -6,4 +6,6 @@ ignore =
     ; E203,  # space before ':'
     ; W503,  # line break before binary operator
     ; W191,  # indentation contains tabs
-    ; E101,  # indentation contains mixed spaces and tabs
+    ; E101,  # indentation contains mixed spaces and tabs
+
+    ; be more restrictive after the refactor code

requirements.txt

@@ -1,4 +1,15 @@
-# To ensure app dependencies are ported from your virtual environment/host machine into your container, run 'pip freeze > requirements.txt' in the terminal to overwrite this file
-apsw
-wget
-sh
+apsw==3.46.1.0
+black==24.8.0
+click==8.1.7
+flake8==7.1.1
+mccabe==0.7.0
+mypy-extensions==1.0.0
+packaging==24.1
+pathspec==0.12.1
+platformdirs==4.3.6
+pycodestyle==2.12.1
+pyflakes==3.2.0
+sh==2.0.7
+tomli==2.0.2
+typing_extensions==4.12.2
+wget==3.2

setup.py

@@ -21,11 +21,12 @@
 
 setuptools.setup(
     name="LOKI",
-    version="3.0.0",
+    version="3.0.1",
     author="Ritchie Lab",
     author_email="[email protected]",
     url="https://ritchielab.org",
     scripts=["loki-build.py"],
     packages=["loki", "loki.loaders", "loki.loaders.test", "loki.util"],
     data_files=[("", ["CHANGELOG"])],
+    install_requires=["apsw==3.46.1.0", "wget==3.2", "sh==2.0.7"],
 )