Cytotable

Changes

- Add image filename columns to CellProfiler presets (d33bs via 252)
- Add Python 3.13 compatibility (d33bs via 244)
- Bump cytominer-database from 0.3.4 to 0.3.5 (dependabot via 248)
- Bump sphinxcontrib-mermaid from 0.9.2 to 1.0.0 (dependabot via 246)
- Bump botocore from 1.35.51 to 1.35.54 (dependabot via 247)
- Bump sphinx from 6.2.1 to 7.4.7 (dependabot via 249)
- Bump pytest from 7.4.4 to 8.3.3 (dependabot via 245)
- Update pre-commit hooks and apply linting checks (d33bs via 242)
- Remove python 3.8 compatibility (d33bs via 243)
- Bump botocore from 1.34.142 to 1.35.51 (dependabot via 241)
- Bump dunamai from 1.19.2 to 1.22.0 (dependabot via 239)
- Bump myst-parser from 2.0.0 to 3.0.1 (dependabot via 237)
- Bump pytest-cov from 4.1.0 to 5.0.0 (dependabot via 236)
- Enable Dependabot updates to Poetry (d33bs via 235)

Changes

- Add tablenumber capabilities to distinguish repeated image numbers from multiple datasets (d33bs via 188)
- Add join concatenation parameter distinction (d33bs via 181)
- Disable DuckDB progress bars (d33bs via 233)
- Format `pyproject.toml` file with `pyproject-fmt` using pre-commit (d33bs via 232)
- Bump pre-commit/action from 3.0.0 to 3.0.1 (dependabot via 231)
- Bump release-drafter/release-drafter from 5 to 6 (dependabot via 229)
- Bump actions/setup-python from 4 to 5 (dependabot via 230)
- Enable Dependabot updates for GitHub Actions (d33bs via 228)
- Bump cryptography from 42.0.5 to 43.0.1 (dependabot via 225)

Changes

- Move to keyset pagination (d33bs via 220)
- Fix dependency resolution issues for non-locked installations of CytoTable in tests (d33bs via 217)

Changes

- Bump zipp from 3.18.1 to 3.19.1 (dependabot via 216)
- Bump certifi from 2024.2.2 to 2024.7.4 (dependabot via 215)
- Bump requests from 2.31.0 to 2.32.2 (dependabot via 213)
- Use real AWS S3 data tests and apply related fixes (d33bs via 212)
- Bump urllib3 from 1.26.18 to 1.26.19 (dependabot via 210)

Changes

- Increase sorting scalability via CytoTable metadata columns (d33bs via 204)
- Bump flask-cors from 4.0.0 to 4.0.1 (dependabot via 207)
- Bump werkzeug from 3.0.1 to 3.0.3 (dependabot via 205)
- Bump jinja2 from 3.1.3 to 3.1.4 (dependabot via 206)
- Enable Parsl app concurrency with futures (d33bs via 194)
- Remove `SECURITY.md` to rely on organization-wide community health file (d33bs via 184)
- Use declarative version specification for Ubuntu GitHub Actions runners (d33bs via 199)
- Avoid `macos-latest` Python version compatibility issues in GitHub Actions runner images (d33bs via 196)

Changes

- Use compartment tables as basis of preset joins (d33bs via 183)
- Add order to limit and offset queries for deterministic results (d33bs via 182)
- Bump idna from 3.6 to 3.7 (dependabot via 186)
- Enable Python 3.12 compatibility through dependency-based updates (d33bs via 174)
- Bump scipy from 1.9.3 to 1.10.0 (dependabot via 173)
- Add python 3.11 to automated tests (d33bs via 172)
- Remove poetry lockfile to better project testing with scheduled trigger (d33bs via 170)
- Changing python's upper limit version to python<3.12 (axiomcura via 158)