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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[1.1.3] - 2026-01-23

Fixed

  • Fixed Python 3.12 compatibility issues with pandas StringArray in set_index() calls:
    • Replaced set_index() with direct index assignment using pd.Index() to avoid StringArray unhashable type errors
    • Fixed index restoration from devopts dictionary in both denovo_refit_option and decompose_fit_option paths
    • Fixed index assignment in make_final_solution() for process matrices, exposure matrices, and signature statistics

[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.
  • Updated COSMIC v3.5 signature files to match official COSMIC download (includes all signatures: CN26, ID24/ID25, SV11/SV12).

Fixed

  • Fixed missing COSMIC v3.5 signature files that were not included in the initial v3.5 release.

[1.1.0] - 2026-01-05

Added

  • Support for COSMIC v3.5 mutational signatures as the default reference signature version.
  • Added COSMIC v3.5 signature files for all supported genome builds (GRCh37, GRCh38, mm9, mm10, rn6).

Changed

  • Updated default cosmic_version parameter from 3.4 to 3.5 across all functions and CLI.
  • Updated Tobacco_signatures subgroup to include new signatures SBS100 and SBS109.
  • Updated README.md to reflect COSMIC v3.5 as the default version and include 3.5 in valid version options.

[1.0.4] - 2026-01-05

Added

  • Support for decompose_fit in higher mutation contexts (288 and 1536) without collapsing to 96 when collapse_to_SBS96=False.
  • Support for custom signature names in signature decomposition workflows.

Changed

  • Improved context type handling in decomposition plots to correctly pass the mutation context type.

Fixed

  • Fixed variable reusage error in nested for loop that could cause incorrect behavior.
  • Fixed missing rn7 and mm39 reference signatures in package distribution (now included in MANIFEST.in).
  • Updated README.md to include correct exclude_signature_subgroups parameter documentation.

[1.0.3] - 2025-10-31

Added

  • Added add_background_signatures parameter (default: True) to control whether background signatures SBS1 and SBS5 are automatically added during signature assignment.
  • Parameter available in spa_analyze(), signature_decomposition(), and all Analyzer functions (decompose_fit(), denovo_fit(), cosmic_fit()).
  • CLI parameter --add_background_signatures added to match Python API functionality.
  • When set to False, background signatures are not forced but may still be detected naturally if present in samples.

Changed

  • Background signature assignment logic now respects the add_background_signatures parameter instead of always forcing SBS1/SBS5 inclusion.

[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

  • Refactored the handling of the cpu parameter. The logic has been updated to pass the CPU count directly via the function's parameters, instead of through an internal devopts dictionary, to reduce complexity and improve code clarity.

Added

  • Added the cpu parameter to the metadata output log.

[1.0.0] - 2025-10-07

Added

  • Parallel execution of SPA runs for improved performance on multi-core systems.
  • cpu parameter to control the number of processor cores used during assignment. Defaults to -1 to use all available cores.

Documentation

  • Updated README to document the new cpu parameter.

[0.2.6] - 2025-09-17

Added

  • Support for assigning mutational signatures using the rn7 and mm39 genome builds.

Security

  • Updated dependency requirement to pypdf>=6.0.0 (previous versions contained a security vulnerability).

[0.2.5] - 2025-08-07

Added

  • Support for generating decomposition plots for custom signature sets.

Changed

  • Refactored the test script to be more readable and maintainable.

Fixed

  • Removed redundant plotting of COSMIC signatures in the decomposition plots.

[0.2.4] - 2025-08-07

Added

  • Added rn7 and mm39 reference signatures.

[0.2.3] - 2025-05-07

Changed

  • Modified rounding exposure values to handle low mutation counts.

[0.2.2] - 2025-05-02

Changed

  • Replaced PDF-to-PNG conversion backend from PyMuPDF to pdf2image for compatibility with Conda and improved portability.
  • Added new CLI parameter: --sample_reconstruction_plots with options 'none' (default), 'pdf', 'png', and 'both'.
  • Updated spa_analyze and CLI dispatch logic to support format-based sample reconstruction plot output.
  • Default behavior now skips sample reconstruction plots unless explicitly requested.
  • Removed fitz dependency; added system requirement note for poppler in setup.py and README.

Added

  • Added a pyproject.toml file to the repository for better project management and configuration.

[0.2.1] - 2025-04-29

Fixed

  • CLI from returning non-zero exit code when --help flag is passed.

Changed

  • Update CI/CD pipelines installation of reference genome to include timeout to prevent long waits during installation.

[0.2.0] - 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

[0.1.9] - 2024-11-12

Changed

  • Replaced PdfMerger with PdfWriter due to deprecation in pypdf >= 5.0.0.

Fixed

  • Addressed deprecation issues with PdfMerger, ensuring compatibility with recent pypdf versions.

[0.1.8] - 2024-08-20

Added

  • Added a Dockerfile to the repository for containerization. Documentation on how to use the Dockerfile needs to be added to the README.

Changed

  • Removed unnecessary imports from setup.py to clean up the codebase.

[0.1.7] - 2024-06-21

Added

  • Added CLI boolean handling to improve command-line interface usability.
  • Added new pytests for CLI to ensure correct handling of booleans.
  • Updated the README to reflect the new pytest additions.
  • Updated CI/CD pipelines to accommodate pytest changes.

Changed

  • Improved input_type value check mechanism to use .lower() before checking against values 'vcf' or 'matrix'.
  • Updated dependency from PyPDF2 to pypdf to increase compatibility and resolve installation issues on bioconda.