[theontho]

Summary

Release CLI 0.6.2 from the final validated main branch. This PR changes only the synchronized version declarations in pyproject.toml, pixi.toml, and src/wgsextract_cli/__init__.py.

The stale release-0.6.2 branch is preserved and is not used.

User-facing changes since v0.6.1

• Native Windows execution with Pixi-managed native bioinformatics packages, without WSL or MSYS2 (Native Windows builds of the core tools, as conda packages for Pixi #155, Windows runs natively: tools from Pixi, no WSL or MSYS2 #157).
• Consistent Windows text line endings and UTF-8 logs (Windows: text files end lines with \n, and log output is UTF-8 #156).
• Faster native Windows line reading, BWA suffix-array lookups, and HTS CRAM extraction (Windows getline: lock once per line and preserve atomic reads #160, Batch native BWA suffix-array lookups to overlap memory reads #162, Reduce native Windows CRAM extraction overhead #163).
• Production HTTPS/SHA pins for the exact tested windows-tools-5 HTS packages (Pin native Windows HTS packages to windows-tools-5 #168).
• Threaded CRAM decoding throughout FASTQ extraction (Thread CRAM decoding during FASTQ extraction #165).
• Avoid whole-CRAM sex scans for sex-independent regional calls (Avoid whole-CRAM sex scans for sex-independent regional calls #161).
• Document native BWA-MEM2 selection and its memory-limited BWA fallback (Document native Windows BWA-MEM2 selection #164).
• Correct microarray coordinate conversion, mitochondrial positions, haploid output, allele ordering, and vendor formatting; add current 23andMe, Ancestry, and Nucleus templates (Fix microarray kit bugs and add current chip templates (#167) #169).
• Recognize Ultima Genomics reads, preserve flow-space tags, and select Ultima-aware alignment and variant-calling settings (Ultima Genomics support (#166) #171).
• Improve app-installation validation for current macOS and Windows packages (Install lab: find the runner in current app packages #158, Install lab: exercise the current Tauri macOS app #159, Install lab: test a signed Windows installer without a paid certificate #170).

Validation

• All five matched Windows/Linux VM performance workloads passed at or below 1.20× Linux elapsed time with exact decoded outputs.
• Full installed native-Windows correctness passed: exact full-genome SNP output, exact decoded paired FASTQ SHA-256 values with 339,819,948 records per mate, and full microarray correctness.
• Local evidence (ignored, not GitHub-hosted): out/full-validation/final-installed-correctness.json and out/perf-parity/fastq-threads/matched-vm-final-comparison.json in the rollout worktree.
• Published Windows HTS archives are byte-identical to the tested archives. Green Windows --locked CI verifies the production HTTPS/SHA pins.
• All three feature PRs merged in order (Reduce native Windows CRAM extraction overhead #163 → Pin native Windows HTS packages to windows-tools-5 #168 → Thread CRAM decoding during FASTQ extraction #165) after current-head CI and review gates; final feature-main checks passed before this release branch was created.
• Local release checks passed: Ruff lint and formatting, mypy (124 source files), site/actionlint/Actions validators, applicable pre-commit hooks, and built-wheel package smoke testing. The ordinary suite passed 1,918 tests (30 skipped, 87 remote tests deselected) under a 2-core/2-GiB resource lease, including version synchronization.
• BWA-MEM2 correctness/performance validation covers the chr20 reference, not full-human MEM2 alignment; the existing memory guard selects BWA when needed.

Release boundary

After this PR and its exact main SHA pass CI, tag that verified SHA as v0.6.2. The release workflow must succeed and create a draft release for root review. Do not publish it and do not start GUI rollout work.

Compare: v0.6.1...v0.6.2

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• Repository: theontho/wgsextract-cli
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🟢 Approval recommended

No active review issues block the release-version synchronization.

No open issues 🎉

What changed in this PR

Prepares WGS Extract CLI 0.6.2 for release by synchronizing its package, workspace, and runtime versions. The features described in the release notes were merged previously; this PR changes only version declarations.

Changes:

• Updates all three version declarations from 0.6.1 to 0.6.2.
• Leaves application behavior and dependencies unchanged.

File	Description
src/​wgsextract_cli/​__init__.py	Sets runtime __version__ to 0.6.2.
pyproject.toml	Sets Python package metadata to version 0.6.2.
pixi.toml	Sets the Pixi workspace version to 0.6.2.

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