Refactor the renee python package and move the GUI here

CHANGELOG.md

@@ -1,11 +1,22 @@
 ## RENEE development version
 
-- Minor documentation improvements. (#132, #135, @kelly-sovacool)
+### New features
+
 - Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
-- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
-- Add GUI instructions to the documentation website. (#38, @samarth8392)
+- Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
+- Add `renee gui` subcommand to launch the graphical user interface. (#94, @kelly-sovacool)
+  - Previously, `renee_gui` (with an underscore) was a command in the `ccbrpipeliner` module.
+
+### Bug fixes
+
 - Ensure `renee build` creates necessary `config` directory during initialization. (#139, @kelly-sovacool)
+
+### Documentation updates
+
+- Minor documentation improvements. (#132, #135, @kelly-sovacool)
+- Add GUI instructions to the documentation website. (#38, @samarth8392)
 - The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
+- Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
 
 ## RENEE 2.5.12
 

bin/redirect

@@ -67,4 +67,4 @@ elif [[ $ISFRCE == true ]];then
 	export PATH="/mnt/projects/CCBR-Pipelines/bin:$PATH"
 fi
 
-${TOOLDIR}/src/renee/__main__.py "$@" || true
+${TOOLDIR}/main.py "$@" || true

main.py

@@ -0,0 +1,16 @@
+#!/usr/bin/env python
+import os
+import re
+import sys
+from src.renee.__main__ import main
+
+# add script directory to the path to allow the CLI to work out-of-the-box
+# without the need to install it via pip first
+SCRIPT_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src", "renee")
+sys.path.append(SCRIPT_DIR)
+
+if (
+    __name__ == "__main__"
+):  # this block is adapted from the executable file created by `pip install`
+    sys.argv[0] = re.sub(r"(-script\.pyw|\.exe)?$", "", sys.argv[0])
+    sys.exit(main())

pyproject.toml

@@ -33,12 +33,13 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.11"
 dependencies = [
+    "argparse",
     "Click >= 8.1.3",
+    "PySimpleGui < 5",
     "snakemake >= 7, < 8",
     "snaketool-utils >= 0.0.5",
-    "argparse"
 ]
 
 [project.optional-dependencies]