Ci switch

.github/workflows/ci.yml

@@ -0,0 +1,94 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
+  packages: write
+
+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: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y poppler-utils
+
+    - name: Upgrade pip, setuptools, and packaging
+      run: |
+        python -m pip install --upgrade pip setuptools packaging
+
+    - name: Cache src directory
+      uses: actions/cache@v4
+      with:
+        path: ./src/
+        key: ${{ runner.os }}-src-grch37
+        restore-keys: |
+          ${{ runner.os }}-src-
+
+    - name: Download GRCh37.tar.gz if not present
+      run: |
+        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
+
+    - name: Install package with tests
+      run: |
+        pip install .[tests]
+
+    - name: Install genome
+      run: |
+        python install_genome.py ${{ github.workspace }}/src/
+
+    - name: Run unit tests
+      run: |
+        pytest tests
+
+    - name: Run integration test
+      run: |
+        python3 test.py
+
+    - name: Build and push Docker image
+      if: github.ref == 'refs/heads/main' && github.event_name == 'push' && matrix.python-version == '3.12'
+      run: |
+        echo "Starting Docker deployment to GHCR for sigprofilersuite..."
+
+        VERSION_TAG=$(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: $IMAGE_NAME"
+
+        echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io \
+          --username "${{ github.actor }}" \
+          --password-stdin
+
+        docker build \
+          --build-arg COMMIT_SHA=${{ 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"

CHANGELOG.md

@@ -6,6 +6,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+## [1.1.2] - 2026-01-23
+### Fixed
+- Fixed Python 3.12 compatibility issues with pandas DataFrame/Series indexing and method calls:
+  - Updated `to_csv()` calls to use keyword arguments (`sep="\t"`) instead of positional arguments
+  - Changed DataFrame/Series index access from `[0]` to `.iloc[0]` throughout the codebase
+  - Fixed dtype assignment when converting columns to strings with "%" suffix
+
+### Changed
+- Switched CI/CD from Travis CI to GitHub Actions. Updated README badge to reflect the new CI/CD platform.
+
 ## [1.1.1] - 2026-01-06
 ### Added
 - Added missing COSMIC v3.5 signature files: exome versions for all supported genome builds, mm39 genome build signatures, and rn7 genome build signatures.

README.md

@@ -1,6 +1,6 @@
 [![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://osf.io/mz79v/wiki/home/) 
 [![License](https://img.shields.io/badge/License-BSD\%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
-[![Build Status](https://api.travis-ci.com/AlexandrovLab/SigProfilerAssignment.svg?branch=main)](https://app.travis-ci.com/AlexandrovLab/SigProfilerAssignment)
+[![CI](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml/badge.svg)](https://github.com/SigProfilerSuite/SigProfilerAssignment/actions/workflows/ci.yml)
 
 <img src="SigProfilerAssignment/figures/SigProfilerAssignment.png" alt="drawing" width="1000"/>
 

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py

@@ -254,11 +254,11 @@ def plot_7_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py

@@ -251,11 +251,11 @@ def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py

@@ -245,13 +245,13 @@ def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cos_dist = statistics["Cosine Distance"][0]
-    cor_dist = statistics["Correlation Distance"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cos_dist = statistics["Cosine Distance"].iloc[0]
+    cor_dist = statistics["Correlation Distance"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py

@@ -251,11 +251,11 @@ def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py

@@ -260,11 +260,11 @@ def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py

@@ -278,11 +278,11 @@ def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,

SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SV32.py

@@ -255,11 +255,11 @@ def plot_7_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict):
 # 	c_draw 		- (Canvas) The canvas to draw the graph decomposition on.
 # 	statistics 	- (Pandas Dataframe) Dataframe w/ calculations
 def draw_statistics(c_draw, statistics, sig_version, custom_text):
-    cos_sim = statistics["Cosine Similarity"][0]
-    cor_coeff = statistics["Correlation Coefficient"][0]
-    l1_norm_percent = statistics["L1 Norm %"][0]
-    l2_norm_percent = statistics["L2 Norm %"][0]
-    kl_divergence = statistics["KL Divergence"][0]
+    cos_sim = statistics["Cosine Similarity"].iloc[0]
+    cor_coeff = statistics["Correlation Coefficient"].iloc[0]
+    l1_norm_percent = statistics["L1 Norm %"].iloc[0]
+    l2_norm_percent = statistics["L2 Norm %"].iloc[0]
+    kl_divergence = statistics["KL Divergence"].iloc[0]
 
     c_draw.drawString(
         WIDTH_GAP + 15,