Introduce AssayCode and the DotMatch 0.2.0 assay platform

[dnncha]

Outcome

This draft introduces AssayCode as the assay-level platform while preserving
DotMatch as the matching engine, Python/Bioconda distribution, native ABI,
DOI, and scientific citation. This is an additive identity, not a destructive
package rename.

Implemented

• Adds the assaycode CLI and Python namespace alongside all existing
  dotmatch interfaces.
• Adds experimental AssayScript v2 compilation for R1/R2/I1/I2 segments,
  anchors or fixed windows, jitter/orientation, target-library safety analysis,
  allowed combinations, input fingerprints, deterministic strategy selection,
  and portable compiled plans.
• Adds experimental calibrated selective decoding, per-cycle/substitution error
  fitting, allowed-tuple joint decoding, calibration diagnostics, empirical FDR
  threshold selection, and strict smoothed priors.
• Adds an experimental deterministic panel digital twin reporting usable yield,
  ambiguity, no-calls, confusion, and false-discovery rate under declared
  substitution-error models.
• Adds bounded-memory sequential QC via assaycode watch with Wilson intervals
  and machine-readable on-track/review/insufficient-data decisions.
• Rewrites the manuscript around ambiguity-aware known-target assignment and
  auditable assay workflows, with explicit supported/experimental boundaries.
• Rebrands the public product surface and reserves AssayCode/AssayScript naming
  while keeping compatibility language visible.
• Prepares the DotMatch 0.2.0 PyPI/Bioconda metadata and release gates.
• Adds a separate assaycode Bioconda metapackage pinned to the matching
  dotmatch engine release, preserving old installs while creating the new
  flagship package coordinate.
• Adds a deterministic handoff renderer that computes the tagged archive SHA-256
  and emits ready-to-copy recipes/dotmatch/ and recipes/assaycode/.
• Extends post-release verification to require both clean Conda installs,
  command identities, and Python engine identity.

Scientific boundary

The deterministic DotMatch assignment paths remain authoritative. AssayScript
v2 execution, calibrated decoding, simulation, and sequential monitoring are
labeled experimental until their dedicated public-data correctness,
calibration, and throughput gates pass. No universal assay runtime, sequencing
platform model, or superiority claim is made.

Verification

Passing on an independent Linux checkout:

• 546 Python tests
• native C tests and allocation regression
• end-to-end native CLI fixtures
• DotMatch and AssayCode Bioconda recipe validators
• two-recipe checksum/handoff rendering tests
• AssayCode readiness gate
• warning-free Sphinx documentation build
• website asset and positioning gate
• JOSS manuscript gate (1,400 words)
• wheel build/install/import/CLI smoke test
• sdist build/install/import/CLI smoke test
• direct assaycode simulate JSON smoke test

GitHub Actions CI, workflow-ecosystem, and CodeQL remain the external hosted
gates. The PR remains draft and the release record remains not_released.

Bioconda handoff

The distribution strategy is intentionally dual-coordinate:

• dotmatch: engine, native artifacts, compatibility CLI, and uninterrupted
  upgrade path.
• assaycode: flagship noarch metapackage pinned to the matching DotMatch
  release.

A Bioconda 0.2.0 PR still requires the immutable v0.2.0 archive. After the
tag, scripts/prepare_bioconda_handoff.py inserts its real SHA-256 and emits
both upstream recipes for a joint submission. No placeholder-checksum PR will
be presented as releasable.

[chatgpt-codex-connector]

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[dnncha]

Applied in commit 989365c94daa1b80ef4d72e8535ce71d13380474:

• strict .fastq, .fq, .fastq.gz, and .fq.gz validation for crispr quickstart
• refuse to overwrite an existing sibling staging path
• keep review-only quickstarts and their generated run.sh in draft status
• fix the release container OCI-label smoke test to expect 0.2.0
• add a release-readiness regression test so stale workflow version assertions fail early

Local evidence: 549 PR54 tests, release/readiness and packaging gates, wheel and sdist clean-install identity checks, and both Bioconda recipe validators pass. The new hosted CI/CodeQL/workflow-ecosystem runs are still in progress; the unrelated Vercel status remains failing.