Cytotable

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)

Changes

- Move citation.cff validation to pre-commit check (d33bs via 165)
- Remove duplicative all-at-once concatenate with join operations (d33bs via 168)
- Add and apply pre-commit poetry checks (d33bs via 164)

Changes

- Set upper limit on DuckDB version (`<0.10.0`) to avoid Arrow errors (d33bs via 166)
- Add weekly testing for preventative awareness of external changes (d33bs via 167)
- Bump cryptography from 42.0.2 to 42.0.4 (dependabot via 162)
- Bump cryptography from 41.0.6 to 42.0.2 (dependabot via 161)
- Add `pytest` warning filters for `pkg_resource` and `sqlalchemy` (d33bs, kenibrewer via 153)
- Fix source filename ingest for IN Carta data with spaces and inconsistent casing (d33bs via 151)
- Add security community health file (d33bs via 147)

Changes

- Add IN Carta preset and related compatibility changes + testing (d33bs via 145)
- Move from dev-dependencies to poetry group specification (d33bs via 146)
- Define and demonstrate data transform types within documentation (d33bs via 142)
- Bump jinja2 from 3.1.2 to 3.1.3 (dependabot via 144)
- Add IN Carta test data from Colas Lab (d33bs via 141)
- Increase documentation on cloud-based data sources (d33bs via 138)
- Move PR template credit to un-rendered HTML comment (d33bs via 139)
- Add project title definition (d33bs via 135)
- Add version metadata to CytoTable Parquet output (d33bs via 134)
- Add poetry dynamic versioning and update release process (d33bs via 132)
- Bump paramiko from 3.1.0 to 3.4.0 (dependabot via 133)
- Bump cryptography from 41.0.4 to 41.0.6 (dependabot via 131)
- Bump werkzeug from 2.2.3 to 3.0.1 (dependabot via 127)
- Bump flask from 2.2.3 to 2.2.5 (dependabot via 130)
- Bump requests from 2.28.2 to 2.31.0 (dependabot via 129)
- Bump cryptography from 40.0.1 to 41.0.4 (dependabot via 128)
- Bump certifi from 2022.12.7 to 2023.7.22 (dependabot via 126)
- Bump urllib3 from 1.26.15 to 1.26.18 (dependabot via 125)
- Bump pygments from 2.14.0 to 2.15.0 (dependabot via 124)
- Bump PyArrow dependency for CVE-2023-47248 (d33bs via 123)

Changes

- Patch v0.0.3 (d33bs via 121)
- Add related software + paper references to citations (d33bs via 120)
- Update readme with additional installation notes (d33bs via 119)
- Move to offset-based joins (d33bs via 113)
- Add PR author mentions to release drafts (d33bs via 118)
- Fix PyPI readme image reference (d33bs via 117)
- Use Parsl NoDataFlowKernelError for detecting existing Parsl configurations (d33bs via 112)
- Enable DuckDB >= v0.8.0 (d33bs via 114)

Changes

- Update to v0.0.2 with related automated workflows (108)
- Correct SQL preset join references (106)
- Move to Parsl HighThroughputExecutor for default workflow execution (97)
- Add exception on existing `dest_path` to avoid unsafe operation (104)
- Fix GitHub Actions version specification typo (103)
- Update dependencies (101)
- Remove dead code for Dagger-based testing (99)
- Update test for `pandas` 2.0.3 compatibility (98)
- Close database connections (95)
- Reuse existing Parsl configurations (93)
- Update DuckDB to `^v0.8.0` (92)
- Add PyArrow memory mapping improvements and allocator documentation (91)
- Expand source and destination paths (89)
- Move to PyArrow parquet writer for data extraction (87)
- Adding Legacy Presets for CytoTable (46)
- Add SQLite affinity type synonym matching for _sqlite_mixed_type_query_to_parquet (84)
- Resolve test_convert_s3_path_sqlite test failures with explicit local_cache_dir (83)
- Add SQLite mixed-type compatibility for _get_table_columns_and_types (82)
- Add macos testing (80)
- Change drop_nulls default in `convert()` to false (78)
- Fix test_convert_s3_path_sqlite test failure inconsistencies (79)
- Add output data type casting controls for integers and floats (49)
- Add SQLite mixed-type data handling capabilities (50)
- Add logo png (73)
- Fix link in README (72)
- logo (71)
- Enable preset overrides (65)