Complete reviewed DotMatch 0.3.0 integrations

[dnncha]

Summary

Completes the reviewed 0.3.0 candidate after #91 merged its earlier head.

• adds reproducible, checksummed assay handoff bundles without copying raw reads
• updates supported GitHub Actions and site type-checking dependencies
• aligns the Pages readiness checker with actions/deploy-pages@v5
• adds literal-alphabet indexed-vs-scan fuzz coverage
• aligns the site lockfile version with 0.3.0

This carries the compatible changes reviewed from #75, #76, and #85, plus the bounded native regression test from #84. It does not merge broader planning or unvalidated claim material.

Verification

• initial 0.3.0 candidate: native, CLI, ASan/UBSan, 614 Python tests (2 skipped), package install smoke, documentation-as-errors, repository/release/scientific/evidence gates, and coverage all passed before the site toolchain precondition
• focused integrated checks: 3 handoff tests, 28 repository-readiness tests, native tests, TypeScript lint, site asset checks, static site build, and npm audit passed
• exact-head CI and workflow-ecosystem runs are in progress for 53242f1499b8089e71b70e337f54f7b2c3430894

The local full rerun was stopped cleanly at 563 passed / 2 skipped under the shared low-disk hold. No source was lost; exact-head remote CI is the completion authority while local disk remains near the 10 GiB hard floor.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-08-29T22:38:11.708541Z	53242f1	PR opened

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[chatgpt-codex-connector]

💡 Codex Review

dotmatch/python/dotmatch/assayspec.py

Line 2280 in 53242f1

("reads", str(assay.data["reads"])),

Collect both FASTQs in paired-assay handoffs

When a completed pair-count AssaySpec uses the newly supported left_reads/right_reads layout, reads is absent, so this lookup raises KeyError and dotmatch assay handoff fails after partially creating its output directory. Build the input list from both mate paths when the spec has no single reads entry.

---

dotmatch/examples/workflows/galaxy/dotmatch_crispr_count.xml

Lines 17 to 20 in 53242f1

	#set $sample_label = re.sub(r'(?i)\.(?:fastq|fastqsanger)(?:\.gz)?$', '', str($sample.element_identifier))
	#set $sample_id = re.sub(r'[^\w.-]', '_', str($sample_label))
	#if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'):
	#set $fastq_name = $sample_id + '.fastq.gz'

Make generated Galaxy sample IDs unique

When two selected Galaxy datasets have names that become identical after suffix removal and sanitization—for example sample a.fastq and sample@a.fastq—both produce the same sample ID and staged FASTQ name. The second ln -s then fails because the destination already exists; even without that collision, crispr-count rejects duplicate sample labels. Add a deterministic unique suffix or reject collisions with a clear validation error.

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