Cosmicqc

Changes

- Remove `cytodataframe.show_report` references (d33bs via 153)
- Enhance `find_outliers` and `identify_outliers` performance by avoiding duplication and filtering columns (d33bs via 140)
- Bump poethepoet from 0.30.0 to 0.31.1 (dependabot via 151)
- Bump coverage from 7.6.8 to 7.6.9 (dependabot via 150)
- Bump jupyterlab from 4.3.1 to 4.3.2 (dependabot via 149)
- Add pre-commit CI lite for automated fixes (d33bs via 132)
- Bump coverage from 7.6.4 to 7.6.8 (dependabot via 147)
- Bump pytest from 8.3.3 to 8.3.4 (dependabot via 148)
- Bump selenium from 4.26.1 to 4.27.1 (dependabot via 145)
- Bump sqlalchemy from 1.4.54 to 2.0.36 (dependabot via 144)
- Bump aiohttp from 3.10.5 to 3.10.11 (dependabot via 143)
- Bump cryptography from 43.0.0 to 43.0.1 (dependabot via 142)
- Bump tornado from 6.4.1 to 6.4.2 (dependabot via 141)
- Bump umap-learn from 0.5.6 to 0.5.7 (dependabot via 135)
- Bump cytotable from 0.0.10 to 0.0.12 (dependabot via 136)
- Bump jupyterlab from 4.2.5 to 4.3.1 (dependabot via 137)
- Bump dunamai from 1.22.0 to 1.23.0 (dependabot via 138)
- Bump sphinx-wagtail-theme from 6.3.0 to 6.4.0 (dependabot via 139)
- Documentation updates (`CONTIBUTING.md` link, redirector, and local build guidance) (d33bs via 133)
- Bump myst-nb from 1.1.1 to 1.1.2 (dependabot via 131)
- Bump pytest from 8.2.1 to 8.3.3 (dependabot via 130)
- Bump poethepoet from 0.27.0 to 0.30.0 (dependabot via 129)
- Bump coverage from 7.6.0 to 7.6.4 (dependabot via 128)
- Bump selenium from 4.25.0 to 4.26.1 (dependabot via 127)

Changes

- Bump `cytodataframe` versions within lockfile (d33bs via 126)

Changes

- Enable updated versions of CytoDataFrame to be used (d33bs via 125)
- Update ruff formatting to `py310` (d33bs via 123)
- Add `CytoDataFrame` dependency; remove migrated code (d33bs via 121)
- Bump hvplot from 0.10.0 to 0.11.1 (dependabot via 119)
- Bump jupyterlab-code-formatter from 2.2.1 to 3.0.2 (dependabot via 118)
- Bump black from 24.4.2 to 24.10.0 (dependabot via 117)
- Bump plotly from 5.22.0 to 5.24.1 (dependabot via 116)
- Bump pyyaml from 6.0.1 to 6.0.2 (dependabot via 115)
- Bump html2image from 2.0.4.3 to 2.0.5 (dependabot via 114)
- Bump jupytext from 1.16.2 to 1.16.4 (dependabot via 113)
- Bump s3fs from 2024.9.0 to 2024.10.0 (dependabot via 112)
- Bump fire from 0.6.0 to 0.7.0 (dependabot via 111)
- Bump selenium from 4.24.0 to 4.25.0 (dependabot via 110)
- Enable Dependabot updates to Poetry lockfile (d33bs via 109)
- Add presentation section to docsite (d33bs via 106)
- Disable docs builds for dependabot (d33bs via 105)
- Turn off automatic notebook execution for docs builds (d33bs via 103)
- Format `pyproject.toml` file with `pyproject-fmt` using pre-commit (d33bs via 102)
- Bump actions/setup-python from 4 to 5 (dependabot via 100)
- Enable Dependabot updates for GitHub Actions (d33bs via 99)
- Add poster content for 2024 SBI2 conference (d33bs via 67)

Changes

- Correct post build doctree removal path (d33bs via 95)
- Reduce UMAP rendered notebook size and avoid docsite `.doctree` files for publishing (d33bs via 94)
- Add example notebook with JUMP UMAP processing (d33bs via 88)
- Add nuclear speckles data with tests (d33bs via 84)
- Fix docs logo link and customize other links (d33bs via 82)
- Add `find_outliers` percentage of total (d33bs via 81)
- Bump jupyterlab from 4.2.3 to 4.2.5 (dependabot via 80)
- Remove python 3.8 from tests (d33bs via 78)
- Add docsite html for base path redirection (d33bs via 74)
- Add docsite (d33bs via 73)
- Add label and identify functions to init file (jenna-tomkinson via 71)
- Update pull request template (d33bs via 68)

Changes

- Fix for nuclear speckle image display in CytoDataFrame (d33bs via 64)

Changes

- Add code coverage badge through coverage.py (d33bs via 63)