Create issue templates for more structured collaboration#52
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conradbzura wants to merge 27 commits intomasterfrom
Open
Create issue templates for more structured collaboration#52conradbzura wants to merge 27 commits intomasterfrom
conradbzura wants to merge 27 commits intomasterfrom
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* Initialize project * Implement binary predicate operators and genomic interval notation parser * Rename OVERLAPS to INTERSECTS to align with bedtools and eliminate conflict with existing OVERLAPS keyword * Implement expected schema and dialect parser * Implement GIQL to SQL transpiler * Implement GIQL query engine * Make all imports absolute * Fix bug preventing GIQL operators from being used alongside standard SQL operators and in CTEs * Add bedtools intersect-like recipes to readme * Add documentation * Implement CLUSTER and MERGE UDFs * Quote customizable field names to avoid collisions with protected SQL keywords * Fully implement custom schema support * Implement "giql intersect" CLI command mirroring "bedtools intersect" API and functionality * Replace GIQLEngine.query() with new a execute() method that returns a PEP 249-like cursor * Add transpile() method to GIQLEngine class and update docs * Update README to include installation instructions * Fix bug in MERGE and CLUSTER queries that incorporate CTEs; Add demo notebook with various usage examples * Drafted GIQL's governing project constitution * Created feature specification for "DISTANCE" operator * Implement DISTANCE UDF for caluculating the distance(s) between intervals * Update demo.ipynb with DISTANCE examples * Update DISTANCE operator to remove "signed" parameter and change behavior of "stranded" parameter when intervals are on opposite strands * Create feature specification for "NEAREST" operator * Implement NEAREST operator * Fix formatting * Implement integration test suite evaluating GIQL behavior against bedtools (#5) * Update core principle I Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> * Update rules for core principle I Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> * Update core principle II Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> * Update core principle III Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> * Update rationale for core principle III Co-authored-by: Nezar Abdennur <nabdennur@gmail.com> * Clean up speckit artifacts we don't want to track * Refactor documentation * Changed default genomic column name from "position" to "interval" * Update readme * Implement CICD * Update project authors and maintainers * Implement build hook for dynamic version resolution from git tag * Update readme * Add hypothesis to dev dependencies * Add pybedtools to dev dependencies * Update test workflow to use pixi * Update test workflow to install GIQL in editable mode * Lower code coverage target for now * Describe tags of head branch when tagging new version in publish-release workflow * Separate bump and tag version jobs in publish-release workflow --------- Co-authored-by: Nezar Abdennur <nabdennur@gmail.com>
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- Add new public API: `transpile()` function and `Table` dataclass - Replace SchemaInfo/TableSchema/ColumnInfo with simpler Table/Tables types - Remove GIQLEngine, CLI, and dialect-specific generators - Delete integration tests that depended on execution engine - Update all generators and transformers to use new Table types
- Add required `name` field to Table dataclass - Rename default columns: chromosome→chrom, start_pos→start, end_pos→end - Simplify `tables` parameter from `list[str] | dict[str, Table]` to `list[str | Table]` - Update README to reflect transpile-only API with usage examples
Remove execution engine and refactor to transpile-only API
doc: Rewrite documentation
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Created some simple issue templates for creating bug reports, feature requests, etc.