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CHANGELOG

v1.11.0 (2025-01-02)

Features

Co-authored-by: Joshua Siraj joshua.siraj@ryerson.ca

Refactoring

  • Improve logging, logic, and type annotations (#151, ef4d0e7)

  • New Features - Enhanced logging flexibility with new parameters for specifying logger names. - Improved progress reporting in the folder crawling process with descriptive progress bars.

  • Bug Fixes - Updated error handling for invalid file actions and DICOM tag checks for clearer user feedback.

  • Documentation - Improved docstring clarity and formatting across multiple functions.

  • Refactor - Streamlined configuration files for testing and linting processes. - Restructured class and function definitions for better readability and maintainability.

  • Style - Consistent formatting applied to function signatures and docstrings.

  • Modules/datagraph.py (#153, 41a7c88)

v1.10.1 (2024-12-03)

Bug Fixes

  • Update .gitignore to exclude SQLite and database files (95a2179)

Chores

v1.10.0 (2024-12-03)

Chores

Features

  • Begin indexing database, update find-dicoms cli, add cli documentation (#148, 48598e7)

Release Notes

  • New Features - Enhanced find_dicoms function to support limiting results and filtering by search input.

  • Documentation - Updated installation instructions and expanded "Getting Started" section in the README. - Improved navigation structure in documentation, adding new entries for CLI reference.

  • Bug Fixes - Streamlined error handling and logging for various functions, ensuring clearer outputs and improved functionality.

  • Chores - Updated dependencies and configuration files for better management and performance.

v1.9.4 (2024-11-29)

Bug Fixes

  • Configure Git credentials for GitHub Actions and update documentation deployment step (adf4e04)

  • Update GitHub Actions workflow for concurrency and permissions; (45cddb4)

Chores

v1.9.3 (2024-11-29)

Bug Fixes

  • Improve logging maintainability and temporarily remove json logging configuration (#146, afdcc98)

Refactor logging code for improved maintainability by temporarily removing JSON logging functionality.

Update the .gitignore to exclude .dcm and .sqlite files.

Introduce an environment variable for debug logging and set the default log level based on this variable.

Summary by CodeRabbit

  • New Features - Introduced a new LoggingManager class for structured logging management. - Added support for JSON logging configuration (currently commented out). - Added a new environment variable for logging level configuration in development. - New entries in .gitignore to ignore .dcm and .sqlite files. - Enhanced CI/CD pipeline with new jobs for building and publishing documentation.

  • Improvements - Enhanced logging control by utilizing environment variables for log levels. - Updated logging directory structure and default log filename for better organization. - Improved management of logging levels based on verbosity settings.

  • Bug Fixes - Improved handling of logging level discrepancies with user-specified settings.

  • Documentation - Updated docstrings and comments for clarity on new logging setup and features.

Chores

v1.9.2 (2024-11-22)

Bug Fixes

  • Pipeline entry no longer needs to manually configure loglevel (66f8119)

Chores

  • deps: Update med-imagetools to version 1.9.1 and update sha256 checksum (ab77c58)

  • sem-ver: 1.9.2 (22d8fb7)

Refactoring

  • logging: Simplify logger configuration and enhance environment variable handling (c1f624b)

v1.9.1 (2024-11-22)

Bug Fixes

  • Downstream bug where datagraph.py was missing from wheel due to data* being ignored in .gitignore (2dbb245)

Chores

Documentation

v1.9.0 (2024-11-22)

Chores

Features

  • Dicom-finder cli tool, and improve documentation (#142, 2981baa)

  • docs: add mkdocs-include-markdown plugin for Markdown file inclusion

  • docs: add tag helpers documentation for DICOM utilities

  • docs: add documentation for finding DICOM files

  • Update src/imgtools/cli/dicomfind.py

  • feat: add regex filtering and improved logging for dicom_finder function

  • chore: exclude CLI files from coverage reporting

v1.8.2 (2024-11-21)

Bug Fixes

  • Update README with new CLI point and reorganize, and formatting (96c6ab6)

Chores

v1.8.1 (2024-11-21)

Bug Fixes

Chores

v1.8.0 (2024-11-21)

Chores

Features

  • Add dicomsorting cli entry (d435f93)

v1.7.0 (2024-11-19)

Chores

Features

  • Implement logging and some standards for ruff config (#134, 7c31019)

  • feat(logging): add structlog integration with custom processors and example logger

  • chore: remove star imports

  • feat(lint): update ruff configuration to include new linting rules and extend exclusions

  • refactor: update pixi.lock and pixi.toml for ruff command structure and remove unused betapipeline entry

  • refactor(logging): standardize string quotes and improve logger configuration handling

  • feat(logging): integrate structured logging and enhance debug information in AutoPipeline and StructureSet

  • fix: #134 (comment)

  • fix: #134 (comment)

  • fix: #134 (comment)

  • refactor(logging): streamline logging configuration and ensure log directory creation

  • chore: add log files to .gitignore to prevent tracking of generated logs

  • fix: Update src/imgtools/logging/init.py

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

  • fix: #134 (comment)

  • chore: update .gitignore to include log files in imgtools directory

  • feat(datagraph): integrate logging for edge table processing and visualization

  • feat(ops): add timing for graph formation and update DataGraph initialization

  • chore: rename workflow from Test to CI-CD and restrict push triggers to main branch

  • feat(crawl): integrate logging for folder crawling and data saving processes

  • fix(structureset): enhance logging for ROI point retrieval errors

  • fix(autopipeline): update logger level to use environment variable for flexibility

  • fix(logging): streamline error handling for log directory creation

  • fix: #134 (comment)

  • refactor(logging): enhance logging configuration and streamline JSON setup

  • chore(pixi.lock): add license_family field for clarity

  • refactor(logging): enhance LoggingManager with valid log levels and improve JSON logging setup

  • refactor(logging): enhance documentation and improve LoggingManager configuration options

  • refactor(logging): validate log level assignment before setting self.level

  • feat(logging): add mypy and type-checking support; refactor logging manager and improve error handling

  • refactor(logging): remove unused Optional import from typing

v1.6.0 (2024-11-15)

Chores

Features

  • feat: started port to pixi

  • feat: updated test suite for pixi and started refactor of cicd

  • build: added coverage to gha

  • fix: explicitly direct location of package code and update pixi in pipeline

  • fix: added linux to pixi

  • chore: update GitHub Actions workflow for improved deployment process

  • chore: clean up GitHub Actions workflow by removing commented-out jobs and updating dependencies

  • chore: update GitHub Actions workflow to deploy from both main and devel branches, and refresh dependencies in pixi.lock

  • chore(sem-ver): 1.6.0-rc.1

  • fix: update version_toml path in pyproject.toml for semantic release

  • chore(sem-ver): 1.6.0-rc.2

  • chore: remove requirements.txt file and poetry.lock

  • chore: update authors and maintainers in pyproject.toml, and add version in init.py

  • chore: remove setup.py file as part of project restructuring

  • chore: update pixi.lock and add ruff configuration for linting

  • chore: fix some recommendations from coderabbit

Co-authored-by: semantic-release

v1.5.8 (2024-10-25)

Bug Fixes

  • datagraph: Iteration through edge_types wasnt updated for seg (#131, e7cca2a)

  • fix(datagraph): update edge_types to 8 and handle new edge type for SEG->CT/MR mapping in final dataframe processing

  • fix(pyproject): update attrs version constraint to allow all 23.x versions and above

Chores

v1.5.7 (2024-10-23)

Bug Fixes

  • Ci-cd - add id in release for pypi step (7abd175)

Chores

v1.5.6 (2024-10-23)

Bug Fixes

  • Update ci to release to pypi (a92a41f)

Chores

v1.5.5 (2024-10-23)

Bug Fixes

  • Remove deprecated pydicom.dicomdir.DicomDir variable type option (#130, 56ef37e)

  • fix: remove deprecated pydicom.dicomdir.DicomDir variable type option

  • style: removed Union since dicom_data can only be a FileDataset

  • refactor: remove Union import for linting

  • Update ci to use semver bot (98e3bd0)

Chores

  • #126 update docstring for StructureSetToSegmentation (reopen) (#128, 272078c)

  • chore: bump artifact action version

  • refactor: update StructureSetToSegmentation docstring and remove unused dev group in pyproject.toml

  • chore: fix download action in workflow to use correct artifact version

  • chore: correct instantiation reference and update parameter description in StructureSetToSegmentation docstring

  • chore: enhance StructureSetToSegmentation docstring to support None as a roi_names option for loading all ROIs

v1.5.4 (2024-06-12)

Bug Fixes

Chores

v1.5.3 (2024-06-10)

Bug Fixes

Chores

v1.5.2 (2024-05-29)

Bug Fixes

  • Upload latest version to pypi (1debad3)

Chores

v1.5.1 (2024-05-29)

Bug Fixes

Chores

v1.5.0 (2024-05-29)

Chores

Features

v1.1.0 (2024-05-29)

Bug Fixes

  • Add codecov badge (f43d042)

  • Explicit module to track for code coverage (f15d45d)

Chores

Features

  • feat: semantic release

  • fix: if statement issue

v1.0.3 (2022-10-14)