Migrate from Travis CI to GitHub Actions and update org references

.github/workflows/ci.yml

@@ -0,0 +1,69 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.12']
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Upgrade pip, setuptools, and packaging
+      run: |
+        python -m pip install --upgrade pip setuptools packaging
+
+    - name: Install package with tests
+      run: |
+        pip install matplotlib
+        pip install .[tests]
+
+    - name: Run plot example
+      run: |
+        python3 sigProfilerPlotting/examples/plot_example.py
+
+    - name: Run unit tests
+      run: |
+        pytest -s -rw tests
+
+    - name: Build and push Docker image
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.python-version == '3.12'
+      env:
+        GHCR_USERNAME: ${{ secrets.GHCR_USERNAME }}
+        GHCR_PASSWORD: ${{ secrets.GHCR_PASSWORD }}
+      run: |
+        echo "Starting Docker deployment to GHCR for sigprofilersuite..."
+
+        VERSION_TAG=$(grep "VERSION = " setup.py | cut -d'"' -f2)
+
+        # Get the repository name and convert it to lowercase
+        REPO_NAME=$(basename ${{ github.repository }} | tr '[:upper:]' '[:lower:]')
+        IMAGE_NAME="ghcr.io/sigprofilersuite/$REPO_NAME"
+
+        echo "Building version: $VERSION_TAG for image: $IMAGE_NAME"
+
+        echo "$GHCR_PASSWORD" | docker login ghcr.io -u "$GHCR_USERNAME" --password-stdin
+
+        docker build \
+          --build-arg COMMIT_SHA=${{ github.sha }} \
+          -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"

Dockerfile

@@ -16,7 +16,7 @@ ARG COMMIT_SHA=master
 WORKDIR /usr/src/app
 
 # Install the package directly from the specific commit on GitHub
-RUN pip3 install 'git+https://github.com/AlexandrovLab/SigProfilerPlotting.git@'${COMMIT_SHA}
+RUN pip3 install 'git+https://github.com/sigprofilersuite/SigProfilerPlotting.git@'${COMMIT_SHA}
 
 # Create a non-root user
 RUN useradd -m -s /bin/bash spm_user

README.md

@@ -1,4 +1,4 @@
-[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/2aj6t/wiki/home/) [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause) [![Build Status](https://app.travis-ci.com/AlexandrovLab/SigProfilerPlotting.svg?branch=master)](https://app.travis-ci.com/AlexandrovLab/SigProfilerPlotting)
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/2aj6t/wiki/home/) [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause) [![CI](https://github.com/sigprofilersuite/SigProfilerPlotting/actions/workflows/ci.yml/badge.svg)](https://github.com/sigprofilersuite/SigProfilerPlotting/actions/workflows/ci.yml)
 
 # SigProfilerPlotting
 SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.