Med-imagetools

Features

- Dicom-finder cli tool, and improve documentation
([142](https://github.com/bhklab/med-imagetools/pull/142),
[`2981baa`](https://github.com/bhklab/med-imagetools/commit/2981baac719da97d6ec6c3c444c046389d44baf3))

* 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

Bug Fixes

- Update README with new CLI point and reorganize, and formatting
([`96c6ab6`](https://github.com/bhklab/med-imagetools/commit/96c6ab60488f97ee3830c7d4be8f96f1ebad0cac))

Bug Fixes

- Common prefix for tree
([`a940969`](https://github.com/bhklab/med-imagetools/commit/a94096910b3b95629e96e809ec21a705505fe841))

Features

- Add dicomsorting cli entry
([`d435f93`](https://github.com/bhklab/med-imagetools/commit/d435f93f0f2fda67094e4aeaa8a1828a570c534d))

Features

- Implement logging and some standards for ruff config
([134](https://github.com/bhklab/med-imagetools/pull/134),
[`7c31019`](https://github.com/bhklab/med-imagetools/commit/7c310196f87e4e3ba8503d12c45f799c831954e1))

* 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: https://github.com/bhklab/med-imagetools/pull/134#discussion_r1846958744

* fix: https://github.com/bhklab/med-imagetools/pull/134#discussion_r1846958749

* fix: https://github.com/bhklab/med-imagetools/pull/134#discussion_r1846958747

* 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: https://github.com/bhklab/med-imagetools/pull/134#discussion_r1847024952

* 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: https://github.com/bhklab/med-imagetools/pull/134#discussion_r1847278305

* 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

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Features

- Transfer project management to Pixi ([133](https://github.com/bhklab/med-imagetools/pull/133),
[`a268211`](https://github.com/bhklab/med-imagetools/commit/a26821164b55579aa42e87c28386db6c9398f2d6))

* 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 <semantic-release>