test: complete test-suite overhaul (phases 1-7) by d-laub · Pull Request #194 · mcvickerlab/GenVarLoader

d-laub · 2026-05-24T21:27:19Z

Summary

Completes the test-suite overhaul across all 7 phases. The tree is now split into a fast unit tier (no project fixtures) and an integration tier (real on-disk artifacts), with a CI job publishing coverage HTML on every PR.

Phase 1 (bootstrap): added pytest-cov config + test-cov pixi task; scaffolded tests/unit/, tests/integration/, tests/_builders/; relocated all existing tests under tests/integration/.
Phase 2 (conftest): centralized 17 session-scoped path fixtures in tests/conftest.py (ref_fasta, phased_{vcf,pgen,svar}_gvl, kg_*, source_*, issue_153_*, vcf_dir, pgen_dir, bigwig_dir, consensus_dir, filtered_svar); migrated every integration file to use them.
Phase 3 (audit): captured coverage baseline (63%); produced docs/superpowers/specs/2026-05-24-test-audit.md classifying 137 functions across 35 files (Delete: 5, Port: 77, Keep: 55).
Phase 4 (delete pass): removed dead/tautological/skip-only tests (test_filter_af.py, test_rs_indexing 147-case cross-product, test_interval_track.py, etc.).
Phase 5 (ports — by component):
- Prelude + ragged builders (make_ragged_seqs, make_ragged_intervals)
- Reconstruct (make_tracks builder + 19-test insertion-fill extraction)
- Variants (info-fields + choose_exonic_variants)
- Splice (get_splice_bed + RefDataset settings/validation)
- SVAR-link (pydantic-model tests)
- Utility (test_utils.py whole-file)
- Tracks (broader): test_random_nonoverlapping + sibling utils.py, test_write_tracks atomic split (integration renamed _e2e for basename-collision avoidance), test_table.py whole-file
- Ref/FASTA: session-scoped reference fixture promoted to conftest with docstring carve-out (metadata-only Reference is cheap); test_fasta.py + test_ref_ds.py whole-file moves
- Dataset polymorphism (minimal): test_with_insertion_fill_rejects_when_no_tracks_active extracted; test_ds_indexing deferred (would require a speculative make_dataset builder — YAGNI)
Phase 6 (integration trim): systematic redundancy audit via Explore agent. Found zero strict redundancies — the audit's Port/Delete buckets already captured everything that could move. Closed with no deletions.
Phase 7 (CI coverage): new coverage job in .github/workflows/test.yaml runs test-cov on py312 in parallel with the pytest matrix; publishes htmlcov/ + coverage.xml as GHA artifacts on every PR and main push.

Final state

Unit tier: 167 passed, 2 xfailed (~3.2s)
Integration tier: 184 tests using real on-disk artifacts
Full non-slow suite: 351 passed, 3 skipped, 2 xfailed (62% line+branch coverage)
No production code modified.
Builders: tests/_builders/ exports make_ragged_seqs, make_ragged_intervals, make_tracks.
Deferred: make_dataset + test_ds_indexing port (no consumer beyond one test).

Test Plan

CI: existing pytest matrix (py310–py313) passes on every entry.
CI: new coverage job uploads htmlcov/ and coverage.xml artifacts.
Download htmlcov artifact from the CI run; spot-check the report renders.
Reviewer: skim docs/superpowers/specs/2026-05-24-test-suite-overhaul-status.md (living status snapshot) — "Notable decisions / gotchas" section captures the non-obvious choices (basename collisions, sibling-import preservation, conftest carve-out, etc.).

🤖 Generated with Claude Code

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Moves all test_*.py files and dataset/, tracks/, variants/ subdirs into tests/integration/, preserving subdirectory structure. Increments parents[N] and parent.parent depth references by one to account for the extra nesting level; suite stays at 500 passed, 6 skipped, 3 deselected, 2 xfailed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Audit 35 integration test files (137 test functions) into Delete (5), Port (77), and Keep-as-integration (55) buckets, with a polymorphism-gap section covering 8 axes. Gating document for Phases 4+ (delete pass, unit builders, coverage trim). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…types/

5 pure-utility tests (bed_to_regions, splits_sum_le_value, normalize_contig_name) with no fixture dependencies. Whole-file move per audit classification — all Port, zero Keep. Phase 5 utility component of the test suite overhaul.

Both files move together to preserve the prepend-mode sibling import (`from utils import nonoverlapping_intervals`). 4 parametrized cases; no fixture dependencies; the tested helper is itself a test utility, not library code. Phase 5 tracks (broader) component.

Move test_write_duplicate_track_names_rejected to tests/unit/dataset/test_write_tracks.py (port: input validation fires before disk I/O). Rename the integration file to test_write_tracks_e2e.py to avoid the pytest prepend-mode basename collision (precedent: reconstruct plan). Phase 5 tracks (broader) component.

12 Table tests (init, column_map, from_path format dispatch, count_intervals kernel, contig normalization). All audit-Port, zero Keep. tmp_path is the only fixture used; no project scaffolding. Phase 5 tracks (broader) component — final file.

…next

Add session-scoped reference fixture to tests/conftest.py. Two existing files (test_ref_ds_splicing, test_ref_ds_splice_settings) duplicated the same Reference.from_path(..., in_memory=False) construction; both now consume the conftest fixture. Convention carve-out documented in the fixture docstring — metadata-only construction is cheap enough to warrant centralization. Phase 5 ref/fasta component — fixture pre-work.

3 Fasta.read pad/no-pad boundary tests. Audit-Port whole-file move; only ref_fasta fixture used (already in conftest); no basename collision. Phase 5 ref/fasta component.

2 remaining audit-Port tests (test_getitem, test_padded_slice) move whole-file to tests/unit/dataset/. The local reference fixture is deleted in favor of the conftest fixture promoted in the previous commit. Tidy the pytest_cases import (fixture no longer needed). Phase 5 ref/fasta component — final move.

Follow-up to 8eafb36 — the prior commit landed the rename only; pre-commit's working-tree stash hid the fixture-drop edits. This commit removes the duplicate `reference` fixture from the moved file and tidies the unused `pytest_cases.fixture` import. The moved tests pick up the conftest fixture by name.

Move test_with_insertion_fill_rejects_when_no_tracks_active to tests/unit/dataset/test_with_insertion_fill.py. The test uses gvl.get_dummy_dataset() (gvl-shipped helper, not a project toy- dataset fixture) and only checks API-level rejection behavior. The 2 remaining tests in the integration file exercise the full reconstruction call path and stay in integration. Phase 5 dataset polymorphism component — minimal scope (test_ds_indexing deferred pending a make_dataset consumer; see status doc).

… next

Explore-agent systematic comparison of every remaining integration test against the unit tier found zero strict redundancies. The audit's Port/Delete buckets already captured everything that could move; remaining Keeps exercise write→read roundtrips, byte-comparison against real FASTA, or full reconstruction call paths that no unit test covers. Last component before the overhaul is done: Phase 7 (htmlcov CI upload).

Runs the existing test-cov pixi task on py312 in parallel with the pytest matrix. Publishes htmlcov/ and coverage.xml as separate GitHub Actions artifacts; both upload with if-no-files-found=error so a silently-empty artifact never lands. Closes the test-suite-overhaul Phase 7 (CI report).

d-laub and others added 30 commits May 24, 2026 13:30

test: add pytest-cov configuration

45ab6a5

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: add test-cov pixi task

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: scaffold unit/, integration/, _builders/ directories

ad4cbd4

test: fix path depths in relocated test files

202bd80

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: add centralized path fixtures in tests/conftest.py

5c214ad

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_fasta

70d6bfd

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_interval_track

2b28fb4

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_ref_ds

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_ref_ds_splicing

148a8bf

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_annot_tracks

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_dataset

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_ds_haps

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_ds_haps_1kg

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_write

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_write_tracks

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_jitter

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_issue_153

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_issue_191_var_fields.py

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_open_vs_settings_parity.py

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_rc_packing.py

822ea49

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_splice_plan.py

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_svar_link.py

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_with_settings_var_filter.py

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: use conftest fixtures in test_subset.py

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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

test: capture coverage baseline for audit

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docs(audit): correct spec reference in audit header

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style: apply ruff format and lint fixes

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test: delete dead test_filter_af.py (entirely skipped, missing cases)

39c0dcd

d-laub added 28 commits May 24, 2026 15:42

test: extract _Variants info-field unit tests to unit/variants/

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test: move genotypes/test_choose_exonic_variants to unit/dataset/geno…

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…types/

docs(plan): phase 5 variants component plan

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test: move test_get_splice_bed to unit/splice/

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test: extract RefDataset splice settings tests to unit/splice/

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docs(plan): phase 5 splice component plan

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test: extract svar_link/Metadata pydantic unit tests to unit/dataset/

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docs(plan): phase 5 svar_link component plan

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style: drop unused imports after svar_link unit extraction

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docs(status): test-suite overhaul progress + resume notes

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docs(status): record utility component move; recommend tracks next

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docs(status): record tracks (broader) component; recommend ref/fasta …

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test: move test_fasta.py to unit tier (ref/fasta component)

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3 Fasta.read pad/no-pad boundary tests. Audit-Port whole-file move; only ref_fasta fixture used (already in conftest); no basename collision. Phase 5 ref/fasta component.

docs(status): record ref/fasta component; recommend make_dataset next

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docs(status): close dataset polymorphism (minimal); recommend Phase 6…

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docs(status): test-suite overhaul complete (Phase 7 landed)

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docs(status): bump shipped-commits header to 79

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docs(status): drop stale commit count from What shipped header

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d-laub changed the title ~~test: phases 1-3 of test suite overhaul — relocate + audit~~ test: complete test-suite overhaul (phases 1-7) May 25, 2026

d-laub merged commit 280e06e into main May 25, 2026
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test: complete test-suite overhaul (phases 1-7)#194

test: complete test-suite overhaul (phases 1-7)#194
d-laub merged 81 commits into
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d-laub commented May 24, 2026 •

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d-laub commented May 24, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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d-laub commented May 24, 2026 •

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