Upgrade v0.1.8: Add Dockerfile and remove uncessary dependencies

Author: mdbarnesUCSD

CHANGELOG.md

@@ -1,4 +1,3 @@
-
 # Changelog
 
 All notable changes to this project will be documented in this file.
@@ -7,6 +6,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [0.1.8] - 2024-08-20
+
+### Added
+- Added a Dockerfile to the repository for containerization. Documentation on how to use the Dockerfile needs to be added to the README.
+
+### Changed
+- Removed unnecessary imports from `setup.py` to clean up the codebase.
+
 ## [0.1.7] - 2024-06-21
 
 ### Added
@@ -18,5 +25,3 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Changed
 - Improved input_type value check mechanism to use .lower() before checking against values 'vcf' or 'matrix'.
 - Updated dependency from PyPDF2 to pypdf to increase compatibility and resolve installation issues on bioconda.
-
-

Dockerfile

@@ -13,11 +13,14 @@ RUN apt-get update && apt-get upgrade -y && \
 WORKDIR /usr/src/app
 
 # Clone the specific branch of the repository
-RUN git clone --branch container https://github.com/AlexandrovLab/SigProfilerAssignment.git .
+RUN git clone https://github.com/AlexandrovLab/SigProfilerAssignment.git .
 
 # Install the dependencies from the requirements.txt in the cloned repository
 RUN pip3 install --no-cache-dir -r requirements.txt
 
+# Install the SigProfilerAssignment package from PyPI
+RUN pip3 install SigProfilerAssignment==0.1.8
+
 # Create a non-root user named 'spm_user'
 RUN useradd -m -s /bin/bash spm_user
 

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "0.1.7"
+VERSION = "0.1.8"
 
 
 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 = 'v0.1.7: Update CLI, add pytest, and update pypdf dependency.'
+Update = 'v0.1.8: Add Dockerfile and remove uncessary dependencies'
 
     
     """