Merge pull request #184 from AlexandrovLab/docker-ghcr

v1.0.2: Add automated Docker build and publish pipeline

Author: mdbarnesUCSD

.travis.yml

@@ -1,14 +1,16 @@
 dist: focal
 language: python
 
+branches:
+  only:
+    - main
+
 python:
+  - '3.9'
   - '3.12'
 
-cache:
-  directories:
-    - $TRAVIS_BUILD_DIR/src/
-  branch:
-    - master
+services:
+  - docker
 
 addons:
   apt:
@@ -22,9 +24,41 @@ before_install:
 install:
   - pip install .[tests]
 
+cache:
+  directories:
+    - $TRAVIS_BUILD_DIR/src/
+
 before_script:
   - python3 install_genome.py $TRAVIS_BUILD_DIR/src/
 
 script: 
   - pytest tests
   - python3 test.py
+
+after_success:
+  - |
+    if [ "$TRAVIS_BRANCH" == "main" ] && [ "$TRAVIS_PULL_REQUEST" == "false" ] && [ "$TRAVIS_PYTHON_VERSION" == "3.12" ]; then
+      echo "Starting Docker deployment to GHCR for alexandrovlab..."
+
+      VERSION_TAG=$(grep "VERSION = " setup.py | cut -d'"' -f2)
+
+      # Get the repository name and convert it to lowercase
+      REPO_NAME=$(basename $TRAVIS_REPO_SLUG | tr '[:upper:]' '[:lower:]')
+      IMAGE_NAME="ghcr.io/alexandrovlab/$REPO_NAME"
+
+      echo "Building version: $VERSION_TAG for image: $IMAGE_NAME"
+
+      echo "$GHCR_PASSWORD" | docker login ghcr.io -u "$GHCR_USERNAME" --password-stdin
+
+      docker build \
+        --build-arg COMMIT_SHA=$TRAVIS_COMMIT \
+        -t $IMAGE_NAME:$VERSION_TAG \
+        -t $IMAGE_NAME:latest .
+
+      docker push $IMAGE_NAME:$VERSION_TAG
+      docker push $IMAGE_NAME:latest
+
+      echo "Docker deployment to GHCR successful"
+    else
+      echo "Skipping Docker deployment"
+    fi

CHANGELOG.md

@@ -6,6 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.0.2] - 2025-10-28
+
+### Added
+- Implemented a CI/CD pipeline with Travis CI to automate the building and publishing of Docker images to Docker Hub.
+
 ## [1.0.1] - 2025-10-20
 
 ### Fixed

Dockerfile

@@ -4,28 +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 git && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
+# Argument to specify the commit, defaults to the 'main' branch
+ARG COMMIT_SHA=main
+
 # Set the working directory in the container
 WORKDIR /usr/src/app
 
-# Clone the specific branch of the repository
-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
+# Install the package directly from the specific commit on GitHub
+RUN pip3 install 'git+https://github.com/AlexandrovLab/SigProfilerAssignment.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
-USER spm_user
+# Switch to the non-root user for security
+USER spm_user

setup.py

@@ -6,7 +6,7 @@
 if os.path.exists("dist"):
     shutil.rmtree("dist")
 
-VERSION = "1.0.1"
+VERSION = "1.0.2"
 
 
 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 = 'v1.0.1:  Refine CPU parameter logic to pass directly instead of via devopts'
+Update = 'v1.0.2: Add automated Docker build and publish pipeline'
 
     """
     fh = open(filename, "w")