Med-imagetools

Bug Fixes

- Update .gitignore to exclude SQLite and database files
([`95a2179`](https://github.com/bhklab/med-imagetools/commit/95a217913798b2f1f4aa2555f1f8fddc65b5b44d))

Features

- Begin indexing database, update find-dicoms cli, add cli documentation
([148](https://github.com/bhklab/med-imagetools/pull/148),
[`48598e7`](https://github.com/bhklab/med-imagetools/commit/48598e7206c14bcd856e8a64b41cb88369647454))

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.

Bug Fixes

- Configure Git credentials for GitHub Actions and update documentation deployment step
([`adf4e04`](https://github.com/bhklab/med-imagetools/commit/adf4e0431533d7434780951edd6ec82737cac21e))

- Update GitHub Actions workflow for concurrency and permissions;
([`45cddb4`](https://github.com/bhklab/med-imagetools/commit/45cddb4fd65be0df14a7f9d2a28261c5cc36159b))

Bug Fixes

- Improve logging maintainability and temporarily remove json logging configuration
([146](https://github.com/bhklab/med-imagetools/pull/146),
[`afdcc98`](https://github.com/bhklab/med-imagetools/commit/afdcc98a6f3fbd9e26da579fa39b37de7dbfd600))

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.

Bug Fixes

- Pipeline entry no longer needs to manually configure loglevel
([`66f8119`](https://github.com/bhklab/med-imagetools/commit/66f8119e6e2e1356c1e3b154e7ad2143cb77ea52))

Chores

- **deps**: Update med-imagetools to version 1.9.1 and update sha256 checksum
([`ab77c58`](https://github.com/bhklab/med-imagetools/commit/ab77c5887e5bb8ae1fa477d2780b94dcdf3297a6))

Refactoring

- **logging**: Simplify logger configuration and enhance environment variable handling
([`c1f624b`](https://github.com/bhklab/med-imagetools/commit/c1f624b7dc14d85176d97bf22918fb2f49dc4a8b))

Bug Fixes

- Downstream bug where datagraph.py was missing from wheel due to data* being ignored in .gitignore
([`2dbb245`](https://github.com/bhklab/med-imagetools/commit/2dbb2455e1edcbf663effd8d40b6bff88dc92082))

Documentation

- Fix broken images
([`a7d0e3a`](https://github.com/bhklab/med-imagetools/commit/a7d0e3a70959e9a754efcade9f9f3aa75206c9ad))