feat: add script to allow the CLI to work without pip install

parallels CCBR/CHAMPAGNE#180

README.md

@@ -33,6 +33,7 @@ CCBR template for creating Nextflow pipelines <!-- TODO: replace this line with
    .github/ISSUE_TEMPLATE/bug_report.yml
    .github/ISSUE_TEMPLATE/config.yml
    .github/workflows/build.yml
+   bin/tool_name
    CHANGELOG.md
    CITATION.cff
    README.md

bin/tool_name

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+# script that allows the CLI to work out-of-the-box
+# without the need to install it via pip first
+
+TOOLDIR=$(realpath $(dirname $(dirname ${BASH_SOURCE})))
+
+${TOOLDIR}/main.py "$@"

main.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+# this script gets called by bin/tool_name
+import os
+import re
+import sys
+
+# 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")
+sys.path.append(SCRIPT_DIR)
+from src.__main__ import main
+
+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())