Cytodataframe

Changes

- Add `matplotlib` as production dependency; remove `plotly` (d33bs via 49)
- Bump jupyterlab from 4.3.2 to 4.3.3 (dependabot via 52)
- Bump matplotlib from 3.9.3 to 3.9.4 (dependabot via 51)
- Bump jupytext from 1.16.4 to 1.16.5 (dependabot via 50)

Changes

- Enable adaptive image display adjustments and "bring your own image processor" capabilities (d33bs via 45)
- Add pre-commit CI lite for automated fixes (d33bs via 29)
- Bump coverage from 7.6.8 to 7.6.9 (dependabot via 47)
- Bump jupyterlab from 4.3.1 to 4.3.2 (dependabot via 46)
- Bump pytest from 8.3.3 to 8.3.4 (dependabot via 44)
- Bump pyarrow from 18.0.0 to 18.1.0 (dependabot via 43)
- Bump coverage from 7.6.7 to 7.6.8 (dependabot via 42)
- Bump tornado from 6.4.1 to 6.4.2 (dependabot via 41)
- Bump jupyterlab from 4.3.0 to 4.3.1 (dependabot via 36)
- Bump coverage from 7.6.4 to 7.6.7 (dependabot via 37)
- Bump dunamai from 1.22.0 to 1.23.0 (dependabot via 38)
- Read outlines or masks from `segmentation_file_regex` parameter (d33bs via 25)
- Bump pyarrow from 16.1.0 to 18.0.0 (dependabot via 23)

Changes

- Remove `show_report` capabilities and `cosmicqc` dependency (d33bs via 21)

Changes

- Add JUMP image data compatibility and example notebook (d33bs via 18)
- Bump ipython from 8.12.3 to 8.18.1 (dependabot via 17)
- Bump coverage from 7.6.0 to 7.6.4 (dependabot via 16)
- Remove unnecessary docs steps which cause bugs during docs build (d33bs via 14)

Note: we tag this version as v0.0.11 as it reflects the relevant version from `coSMicQC`, from which `CytoDataFrame` development originated.

Changes

- Bump pytest from 8.2.1 to 8.3.3 (dependabot via 13)
- Bump myst-nb from 1.1.1 to 1.1.2 (dependabot via 12)
- Bump plotly from 5.22.0 to 5.24.1 (dependabot via 11)
- Bump sqlalchemy from 1.4.54 to 2.0.36 (dependabot via 10)
- Bump html2image from 2.0.4.3 to 2.0.5 (dependabot via 9)
- Enable Dependabot updates to Poetry, fix tests and docs build (d33bs via 6)
- Migrate `CytoDataFrame` from `coSMicQC` as standalone package (d33bs via 4)