Merge pull request #166 from AlexandrovLab/cli-fix

CLI fix

Author: mdbarnesUCSD

.travis.yml

@@ -12,7 +12,7 @@ cache:
 
 before_install:
   - pip install --upgrade pip setuptools packaging
-  - if ! [ -f ./src/GRCh37.tar.gz ]; then wget ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/; fi
+  - if ! [ -f ./src/GRCh37.tar.gz ]; then wget --connect-timeout=10 --tries=20 ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/GRCh37.tar.gz -P ./src/; fi
 
 install:
   - pip install .[tests]

CHANGELOG.md

@@ -6,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [0.2.1] - 2025-04-29
+
+### Fixed
+- CLI from returning non-zero exit code when --help flag is passed.
+
+### Changed
+- Update CI/CD pipelines installation of reference genome to include timeout to prevent long waits during installation.
+
 ## [0.2.0] - 2025-02-11
 
 ### Changed

SigProfilerAssignment/SigProfilerAssignment_CLI.py

@@ -13,7 +13,7 @@ def main_function():
 
     if len(sys.argv) < 2 or sys.argv[1].lower() not in commands:
         print_usage(commands)
-        sys.exit(1)
+        return
 
     command = sys.argv[1].lower()
     args = sys.argv[2:]

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.2.0"
+VERSION = "0.2.1"
 
 
 def write_version_py(filename="SigProfilerAssignment/version.py"):
@@ -15,7 +15,7 @@ def write_version_py(filename="SigProfilerAssignment/version.py"):
 # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-Update = 'v0.2.0: Require Pandas and Numpy >= 2.0.0 and Python >= 3.9'
+Update = 'v0.2.1: Fix bug in CLI returning non-zero exit code'
 
     
     """