Merge pull request #57 from AlexandrovLab/docker-updates

v1.4.2: Add automated Docker build and publish pipeline

Author: mdbarnesUCSD

.travis.yml

@@ -1,10 +1,22 @@
 dist: focal
 language: python
 
+on:
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'CHANGELOG.md'
+      - 'README.md'
+      - 'LICENSE'
+
 python:
   - "3.9"
   - "3.12"
 
+services:
+  - docker
+
 install:
   - pip install -q matplotlib
   - pip install .[tests]
@@ -14,3 +26,30 @@ script:
   - python3 sigProfilerPlotting/examples/plot_example.py
   # run unit tests
   - pytest -s -rw tests
+
+after_success:
+  - |
+    if [ "$TRAVIS_BRANCH" == "master" ] && [ "$TRAVIS_PULL_REQUEST" == "false" ] && [ "$TRAVIS_PYTHON_VERSION" == "3.12" ]; then
+      echo "Starting Docker deployment to Docker Hub..."
+      
+      # Dynamically get the version from setup.py for the tag
+      VERSION_TAG=$(grep "VERSION = " setup.py | cut -d'"' -f2)
+      echo "Building version: $VERSION_TAG for commit: $TRAVIS_COMMIT"
+      
+      # Log in securely using environment variables from Travis CI settings
+      echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
+      
+      # Build the image, passing the commit SHA and tagging with the version and "latest"
+      docker build \
+        --build-arg COMMIT_SHA=$TRAVIS_COMMIT \
+        -t mdbarnesucsd/sigprofilerplotting:$VERSION_TAG \
+        -t mdbarnesucsd/sigprofilerplotting:latest .
+        
+      # Push both tags to your personal Docker Hub account
+      docker push mdbarnesucsd/sigprofilerplotting:$VERSION_TAG
+      docker push mdbarnesucsd/sigprofilerplotting:latest
+      
+      echo "Docker deployment successful"
+    else
+      echo "Skipping Docker deployment"
+    fi

CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.4.2] - 2025-10-13
+
+### Added
+- Implemented a CI/CD pipeline with Travis CI to automate the building and publishing of Docker images to Docker Hub.
+- Added a `pyproject.toml` file to standardize the package build system.
+
 ## [1.4.1] - 2025-03-10
 
 ### Fixed

Dockerfile

@@ -4,23 +4,25 @@ FROM ubuntu:22.04
 # Avoid prompts from apt
 ARG DEBIAN_FRONTEND=noninteractive
 
-# Install Python and other dependencies, and apply updates
+# Install Python, git, and other dependencies, and apply updates
 RUN apt-get update && apt-get upgrade -y && \
-    apt-get install -y python3-pip python3-dev && \
+    apt-get install -y python3-pip python3-dev git && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
+# Argument to specify the commit, defaults to the 'master' branch
+ARG COMMIT_SHA=master
 
 # Set the working directory in the container
 WORKDIR /usr/src/app
 
-# Install SigProfilerMatrixGenerator using pip
-RUN pip3 install SigProfilerPlotting==1.3.21
+# Install the package directly from the specific commit on GitHub
+RUN pip3 install 'git+https://github.com/AlexandrovLab/SigProfilerPlotting.git@'${COMMIT_SHA}
 
-# Create a non-root user named 'spm_user'
+# Create a non-root user
 RUN useradd -m -s /bin/bash spm_user
 
-# Change the ownership of the /usr/src/app directory and its contents to the new non-root user
+# Change the ownership of the working directory
 RUN chown -R spm_user:spm_user /usr/src/app
 
-# Switch to the non-root user for subsequent commands and when running the container
+# Switch to the non-root user for security
 USER spm_user

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=61", "wheel", "build"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -14,7 +14,7 @@ def readme():
         return f.read()
 
 
-VERSION = "1.4.1"
+VERSION = "1.4.2"
 
 
 def write_version_py(filename="sigProfilerPlotting/version.py"):
@@ -23,7 +23,7 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-update = 'v1.4.1: Update plotSV to use pandas >= 2.0.0.'
+update = 'v1.4.2: Add automated Docker build and publish pipeline'
     
     """
     fh = open(filename, "w")

sigProfilerPlotting/version.py

@@ -1,7 +1,7 @@
 
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
-short_version = '1.4.1'
-version = '1.4.1'
-update = 'v1.4.1: Update plotSV to use pandas >= 2.0.0.'
+short_version = '1.4.2'
+version = '1.4.2'
+update = 'v1.4.2: Add automated Docker build and publish pipeline'