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* Implement genomic interval SQL operators * 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> * Treat undefined release cycle as stable --------- Co-authored-by: Nezar Abdennur <nabdennur@gmail.com>
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…logical PBT, harden edge cases Acts on the deferred items from the 10-agent re-review of PR #93. Source changes (src/giql/transformer.py): - Reject 'SELECT a.* AS x' rather than silently dropping the user alias. Most engines reject star-with-alias outright; the dialect now raises ValueError with a message pointing at the two valid alternatives (drop the alias or list columns explicitly). Closes the previously-deferred R4 finding. - Defensive subquery gate at transform_to_sql: if any of GROUP BY / HAVING / ORDER BY embeds a subquery, fall back to the binned plan. The modifier rewriter is not scope-aware, so this prevents a future relaxation from accidentally rewriting columns inside a nested scope. - Document the traversal-order assumption on allocate() and the lexical-scope assumption on _rewrite_modifier_refs (R4 follow-ups). Test tightening (tests/test_duckdb_iejoin.py): - ADD-R-006: test that 'SELECT a.* AS x' raises ValueError naming the unsupported star-with-alias shape. - R6 #19: relax 'assert type(...) is ValueError' to isinstance, so the test doesn't forbid future ValueError subclasses with richer error info. - R6 #20: replace the brittle inner_aliases == {__giql_p0, __giql_p1} assertion with a behavior-level dedup check (a."score" must be allocated to exactly one inner alias regardless of its index). - R6 #21: tighten the multi-key ORDER BY DESC-attachment regex to pin DESC positionally to the second term. - R6 #22: anchor the BETWEEN / IS NULL inline assertions to the SET VARIABLE half of the SQL (the per-chromosome template) and assert the predicate does NOT appear in the outer SELECT wrapper. - R6 #17: rephrase three test docstrings to avoid naming private helpers (_strip_intersects, _can_inline_extras) — describe the behavior in user-visible terms instead. - R7 #9: pivot the near-duplicate cross-side ON test to a genuinely new shape — cross-side predicate in WHERE rather than ON, exercising the WHERE-extras extraction path rather than the JOIN-ON extras path. - R7 #10: tighten the kitchen-sink test's HAVING from the no-op 'COUNT(*) > 0' to 'SUM(a.score) > 40' (now actually filters one group out), add SUM(a.score) to the SELECT list so multiple aggregates coexist, and document the row-by-row truth table in the docstring. - R7 #11: add a Python-native expected list to the coord-system parametric test so a regression where both plans share the same bug can't silently pass. - R8 #12: add an executing AVG-equivalence example test (test_query_should_match_binned_plan_avg_aggregate_when_dialect_is_duckdb) that compares binned vs dialect AVG values with pytest.approx — fills the gap the aggregate PBT intentionally leaves. - R8 #13: fix the 'is_null' PBT tautology. The score strategy now draws st.one_of(st.none(), st.integers(0, 50)) so WHERE a.score IS NULL / IS NOT NULL are no longer tautologically true/false. - R8 #14, #15, #16: full-composite PBT now uses min_size=0 (covers empty-input + Tier 1 stack), max_examples=60 (was 30 — the largest input space deserves more sampling), and limit= st.integers(min_value=0) (LIMIT 0 edge case now exercised). Skip executemany when the parameter list is empty (DuckDB rejects it). Tests: 110 dialect tests pass (was 108). Full suite: 1184 passed, 1 skipped, 90 xfailed (all xfails pre-existing in unrelated modules). Refs #93.
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