SigProfilerExtractor 1.2.5__tar.gz → 1.4.0__tar.gz

sigprofilerextractor-1.4.0/.github/workflows/ci.yml

@@ -0,0 +1,103 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: Test (${{ matrix.python-version }}, pandas ${{ matrix.pandas-version }})
+    runs-on: ubuntu-latest
+    continue-on-error: ${{ matrix.experimental }}
+    permissions:
+      contents: read
+      packages: write
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - python-version: '3.10'
+            pandas-version: '2.2.3'
+            experimental: false
+          - python-version: '3.12'
+            pandas-version: '2.2.3'
+            experimental: false
+          - python-version: '3.12'
+            pandas-version: '3.0.2'
+            experimental: false
+          - python-version: '3.14'
+            pandas-version: '3.0.2'
+            experimental: true
+    
+    steps:
+    - uses: actions/checkout@v6
+    
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    
+    - name: Upgrade pip, setuptools, and packaging
+      run: |
+        python -m pip install --upgrade pip setuptools packaging
+
+    - name: Pin pandas ${{ matrix.pandas-version }}
+      run: |
+        python -m pip install --upgrade "pandas==${{ matrix.pandas-version }}"
+    
+    - name: Cache src directory
+      uses: actions/cache@v5
+      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
+      run: |
+        pip install .
+    
+    - name: Install genome
+      run: |
+        python install_genome.py ${{ github.workspace }}/src/
+    
+    - name: Run tests
+      run: |
+        python3 test.py
+
+    - name: Build and push Docker image
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.python-version == '3.12' && matrix.pandas-version == '3.0.2'
+      run: |
+        echo "Starting Docker deployment to GHCR for sigprofilersuite..."
+        
+        python -m pip install --upgrade setuptools_scm
+        VERSION_TAG=$(python -m setuptools_scm)
+        VERSION_TAG=${VERSION_TAG//+/-}
+        
+        # Get the repository name and convert it to lowercase
+        REPO_NAME=$(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 -u "${{ github.actor }}" --password-stdin
+        
+        docker build \
+          --build-arg COMMIT_SHA=${{ 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"

sigprofilerextractor-1.4.0/.github/workflows/create-version-tag.yml

@@ -0,0 +1,53 @@
+name: Create version tag
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: "Version without leading v, for example x.y.z"
+        required: true
+        type: string
+      target_branch:
+        description: "Branch to tag"
+        required: true
+        default: "master"
+        type: string
+
+permissions:
+  contents: write
+
+jobs:
+  tag:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Validate version
+        run: |
+          if ! [[ "${{ inputs.version }}" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+            echo "Version must look like x.y.z"
+            exit 1
+          fi
+
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.target_branch }}
+          fetch-depth: 0
+
+      - name: Create and push tag
+        run: |
+          tag="v${{ inputs.version }}"
+
+          if git rev-parse "$tag" >/dev/null 2>&1; then
+            echo "Tag $tag already exists locally"
+            exit 1
+          fi
+
+          if git ls-remote --tags origin "$tag" | grep -q "$tag"; then
+            echo "Tag $tag already exists on origin"
+            exit 1
+          fi
+
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+
+          git tag -a "$tag" -m "SigProfilerExtractor $tag"
+          git push origin "$tag"

sigprofilerextractor-1.4.0/.github/workflows/docs.yml

@@ -0,0 +1,54 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: github-pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Configure Pages
+        uses: actions/configure-pages@v5
+
+      - name: Install docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install mkdocs mkdocs-material pymdown-extensions
+
+      - name: Build site
+        run: |
+          mkdocs build --clean
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4
+

sigprofilerextractor-1.4.0/.github/workflows/release.yml

@@ -0,0 +1,92 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.12"
+
+    - name: Install build tooling
+      run: |
+        python -m pip install --upgrade pip build twine
+
+    - name: Build distributions
+      run: |
+        python -m build
+
+    - name: Check distributions
+      run: |
+        python -m twine check dist/*
+
+    - name: Verify package version
+      run: |
+        python -m pip install dist/*.whl
+        python -c "import SigProfilerExtractor; print(SigProfilerExtractor.__version__)"
+
+    - name: Upload distributions
+      uses: actions/upload-artifact@v7
+      with:
+        name: python-package-distributions
+        path: dist/
+        if-no-files-found: error
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/SigProfilerExtractor
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish package distributions to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    if: github.event_name == 'release' && github.event.action == 'published'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/SigProfilerExtractor
+    permissions:
+      id-token: write
+    steps:
+    - name: Download distributions
+      uses: actions/download-artifact@v5
+      with:
+        name: python-package-distributions
+        path: dist/
+
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

sigprofilerextractor-1.4.0/.github/workflows/static.yml

@@ -0,0 +1,43 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["master"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload entire repository
+          path: '.'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

sigprofilerextractor-1.4.0/.gitignore

@@ -0,0 +1,142 @@
+.DS_Store
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+SigProfilerExtractor/_version.py
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# test script output
+test_csv_output/
+test_matobj_output/
+test_segCNV_output/
+test_text_output/
+test_vcf_output/
+test_matrix_*_output/
+SigProfilerExtractor/data/VCFInput/logs/
+SigProfilerExtractor/data/VCFInput/input/
+SigProfilerExtractor/data/VCFInput/output/

sigprofilerextractor-1.4.0/CHANGELOG.md

@@ -0,0 +1,80 @@
+
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [1.2.7] - 2026-01-22
+
+### Fixed
+- Fixed NumPy 2.0 compatibility issue by removing the `nimfa` dependency, which was incompatible with NumPy 2.0 due to use of deprecated `np.mat()` function.
+- Fixed pandas 3.12 compatibility issues:
+  - Updated `to_csv()` calls to use `sep` as keyword argument instead of positional argument
+  - Fixed `set_index()` calls to work with pandas 3.12's stricter type checking by converting StringArray to list
+  - Fixed `iloc` assignment for string conversion operations
+  - Fixed Series indexing to use `.iloc[0]` for positional access instead of `[0]` for label-based access
+- Fixed compatibility issues in SigProfilerAssignment and SigProfilerPlotting packages for pandas 3.12
+
+### Changed
+- Removed `nimfa` dependency and implemented NNDSVD initialization directly in the codebase.
+- Updated `sigProfilerPlotting` dependency to >=1.4.3 for pandas 3.12 compatibility.
+- Removed TMB debug file output.
+- Migrated CI/CD pipeline from Travis CI to GitHub Actions for improved reliability and modern workflow management.
+
+### Added
+- Added `SigProfilerExtractor/nndsvd.py` with standalone NNDSVD implementation supporting all variants (nndsvd, nndsvda, nndsvdar, nndsvd_min).
+
+## [1.2.6] - 2026-01-06
+
+### Changed
+- Updated default COSMIC version from 3.4 to 3.5. Added support for COSMIC v3.5 signatures in the `cosmic_version` parameter.
+- Updated SigProfilerAssignment dependency requirement from >=1.0.1 to >=1.1.0 to support COSMIC v3.5 signatures.
+
+## [1.2.5] - 2025-10-28
+
+### Added
+- Implemented a CI/CD pipeline with Travis CI to automate the building and publishing of Docker images to Docker Hub.
+- Added a Dockerfile to the repository for containerization. Documentation on how to use the Dockerfile needs to be added to the README.
+
+## [1.2.4] - 2025-10-20
+
+### Added
+- Added the `assignment_cpu` parameter to independently control the number of CPU cores used for the signature assignment step. This change enables full support for the parallel processing enhancements in **SigProfilerAssignment v1.0.0**, allowing for significant performance improvements and more granular resource control.
+
+## [1.2.3] - 2025-09-19
+
+### Added
+- Added support for rn7 and mm39 genomes in SigProfilerExtractor.
+
+## [1.2.2] - 2025-08-11
+
+### Added
+- Added mutation count and stability to 4608 plots in All_Solutions
+- Add a stop parameter to the CLI to stop after de novo extraction.
+
+## [1.2.1] - 2025-05-14
+
+### Fixed
+- Fixed an issue where the CLI was returning a non-zero exit code when the `--help` flag was passed.
+
+ ### Added
+- Added `pyproject.toml` for modern Python packaging support.
+
+## [1.2.0] - 2025-02-11
+
+### Changed
+- Updated dependencies: Now requires **Pandas >= 2.0.0**, **NumPy >= 2.0.0**, and **Python >= 3.9**.
+- Dropped support for **Python 3.8**
+- **Intel-based MacBooks are no longer supported** due to upstream changes in **PyTorch**, which has dropped support for macOS x86_64. Users with Intel-based MacBooks will need to migrate to Apple Silicon (M1/M2) or use a Linux-based development environment.
+
+## [1.1.25] - 2024-12-09
+
+### Added
+- Introduced a Command-Line Interface (CLI) for SigProfilerExtractor, enabling users to interact with the tool via terminal commands.
+
+### Updated
+- Improved the formatting of the parameter table for sigProfilerExtractor function for better readability and consistency.
+- The CI/CD badge link has been fixed.

sigprofilerextractor-1.4.0/Dockerfile

@@ -0,0 +1,26 @@
+# CUDA-enabled base image for GPU support
+FROM nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu22.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG COMMIT_SHA=master
+
+# Install Python + minimal deps
+RUN apt-get update && apt-get install -y \
+    python3-pip python3-dev git && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /usr/src/app
+
+# Install GPU-enabled PyTorch wheels
+RUN pip3 install --no-cache-dir \
+    torch torchvision torchaudio \
+    --extra-index-url https://download.pytorch.org/whl/cu118
+
+# Install SigProfilerExtractor from specific commit
+RUN pip3 install --no-cache-dir \
+    'git+https://github.com/SigProfilerSuite/SigProfilerExtractor.git@'${COMMIT_SHA}
+
+# Create a non-root user
+RUN useradd -m -s /bin/bash spm_user
+RUN chown -R spm_user:spm_user /usr/src/app
+USER spm_user

{sigprofilerextractor-1.2.5 → sigprofilerextractor-1.4.0}/MANIFEST.in

@@ -4,5 +4,4 @@ include SigProfilerExtractor/data/CNVInput/*
 include SigProfilerExtractor/data/CSVInput/*
 include SigProfilerExtractor/data/MatObjInput/*
 include SigProfilerExtractor/data/ReferenceFiles/*
-include SigProfilerExtractor/controllers/*
-
+include SigProfilerExtractor/controllers/*