dnncha · dnncha · Jul 13, 2026 · Jul 13, 2026 · Jul 13, 2026 · Jul 13, 2026
diff --git a/.github/ISSUE_TEMPLATE/pilot_feedback.yml b/.github/ISSUE_TEMPLATE/pilot_feedback.yml
@@ -0,0 +1,62 @@
+name: Evaluation feedback
+description: Record scoped feedback from a DotMatch technical evaluation.
+title: "[Evaluation]: "
+labels: ["evaluation", "feedback", "needs-triage"]
+body:
+  - type: dropdown
+    id: assay_context
+    attributes:
+      label: Assay Context
+      options:
+        - CRISPR guide counting
+        - Inline barcode demultiplexing
+        - Feature barcode assignment
+        - Perturb-seq guide capture
+        - Amplicon or panel target assignment
+        - Oligo or adapter-prefix assignment
+        - Other known-target workflow
+    validations:
+      required: true
+  - type: textarea
+    id: install_path
+    attributes:
+      label: Install Path
+      description: State PyPI, Bioconda, source checkout, container, or workflow wrapper version.
+    validations:
+      required: true
+  - type: textarea
+    id: inputs
+    attributes:
+      label: Inputs
+      description: Describe the target table and read window without sharing private raw data.
+    validations:
+      required: true
+  - type: checkboxes
+    id: outputs_reviewed
+    attributes:
+      label: Outputs Reviewed
+      options:
+        - label: sample_qc.tsv
+        - label: summary.json
+        - label: assignments.tsv
+        - label: top_unmatched.tsv
+        - label: HTML report
+        - label: methods.md / CITATION.bib / software_versions.yml
+  - type: textarea
+    id: findings
+    attributes:
+      label: Findings
+      description: What became clearer or blocked the evaluation?
+    validations:
+      required: true
+  - type: dropdown
+    id: public_use_permission
+    attributes:
+      label: Public Use Permission
+      options:
+        - No public use record approved
+        - Anonymized summary approved
+        - Public project name approved
+        - Approved public use record text and URL
+    validations:
+      required: true
diff --git a/.github/ISSUE_TEMPLATE/workflow_integration.yml b/.github/ISSUE_TEMPLATE/workflow_integration.yml
@@ -0,0 +1,54 @@
+name: Workflow integration review
+description: Propose or review an external DotMatch workflow integration.
+title: "[Integration]: "
+labels: ["workflow", "integration", "needs-triage"]
+body:
+  - type: dropdown
+    id: workflow_manager
+    attributes:
+      label: Workflow Manager
+      options:
+        - nf-core / Nextflow
+        - MultiQC
+        - Galaxy / IUC
+        - Snakemake
+        - bio.tools
+        - Institutional workflow
+    validations:
+      required: true
+  - type: textarea
+    id: workflow_context
+    attributes:
+      label: Workflow Context
+      description: Which known-target assay workflow would this integration support?
+    validations:
+      required: true
+  - type: textarea
+    id: source_assets
+    attributes:
+      label: Source Assets
+      description: Link the local module, wrapper, fixture, parser, schema, or registry draft.
+    validations:
+      required: true
+  - type: textarea
+    id: expected_outputs
+    attributes:
+      label: Expected Outputs
+      description: List the TSV, JSON, FASTQ, HTML, MultiQC, or citation artifacts the integration should expose.
+    validations:
+      required: true
+  - type: textarea
+    id: review_evidence
+    attributes:
+      label: Review Evidence
+      description: Include commands, CI links, fixture paths, lint output, or external review links.
+      render: bash
+    validations:
+      required: false
+  - type: textarea
+    id: validated_scope
+    attributes:
+      label: Validated Scope
+      description: State what the integration supports and what it must not imply.
+    validations:
+      required: true
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -20,6 +20,12 @@
 - [ ] Large generated datasets or scratch outputs are not committed.
 - [ ] No real FASTQ/BAM/BCL/customer assay data is committed; examples are synthetic, minimized, or public and scoped.
 
+## Public Language and Reviewer Readiness
+
+- [ ] This PR does not imply accepted external workflow integration.
+- [ ] Broad replacement wording or launch copy was removed or avoided.
+- [ ] Public-facing claims link to a checked artifact, gate, or scoped status record.
+
 ## Acceptance Criteria
 
 - 

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -113,10 +113,10 @@ jobs:
         run: docker build -t dotmatch:ci .
       - name: Smoke test container
         run: |
-          docker run --rm dotmatch:ci --version | grep '^dotmatch 0.1.8$'
+          docker run --rm dotmatch:ci --version | grep '^dotmatch 0.2.0$'
           docker run --rm dotmatch:ci dist ACGT AGGT | grep '^1$'
           docker run --rm dotmatch:ci leq 1 ACGT AGGT | grep '^true$'
-          docker image inspect dotmatch:ci --format '{{ index .Config.Labels "org.opencontainers.image.version" }}' | grep '^0.1.8$'
+          docker image inspect dotmatch:ci --format '{{ index .Config.Labels "org.opencontainers.image.version" }}' | grep '^0.2.0$'
       - uses: docker/metadata-action@v6
         id: meta
         with:

diff --git a/.zenodo.json b/.zenodo.json
@@ -1,7 +1,7 @@
 {
   "title": "DotMatch: deterministic known-target short-DNA assignment for sequencing workflows",
   "upload_type": "software",
-  "version": "0.1.8",
+  "version": "0.2.0",
   "conceptdoi": "10.5281/zenodo.20541628",
   "creators": [
     {

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,7 +2,19 @@
 
 All notable user-facing changes are tracked here. Public statements in release notes must stay aligned with `docs/scientific-claims.md`.
 
-## Unreleased / Next (post 0.1.7)
+## 0.2.0 - Unreleased
+
+- Added a compatibility-safe AssayCode Bioconda metapackage template and a deterministic two-recipe release-handoff generator while preserving `dotmatch` as the engine package.
+
+- Added a deterministic experimental panel simulator for pre-sequencing yield, ambiguity, no-call, confusion, and FDR analysis.
+### AssayCode platform
+
+- Added the additive `assaycode` CLI and Python namespace while preserving the `dotmatch` package, executable, ABI, DOI, schemas, and citation contract.
+- Added AssayScript v2 compilation for R1/R2/I1/I2 segment declarations, fixed or anchored extraction, positional jitter, orientation, per-segment matching policies, allowed-combination tables, source and library fingerprints, bounded safety findings, deterministic strategy selection, and portable JSON plans.
+- Added `assaycode compile`, `assaycode inspect`, and compatibility-safe assay workflow shortcuts.
+- Added an explicitly experimental calibration module with per-cycle error fitting, Phred shrinkage, selective posterior calls, likelihood-ratio abstention, joint decoding over permitted tuples, Brier score, expected calibration error, held-out FDR threshold selection, and smoothed abundance priors.
+- Added `assaycode watch`, a bounded-memory JSONL monitor that emits assignment-rate confidence intervals and threshold-based sequential QC decisions.
+- Added a release-blocking AssayCode readiness gate, focused tests, updated scientific claim boundaries, a rewritten paper, and Bioconda smoke tests for both command identities.
 
 ### Added
 - `dotmatch.tl` submodule: scverse/scanpy-style tools (`tl.assign_features`, `tl.feature_counts`, aliases for CRISPR/feature barcodes). In-place modification or copy, with provenance in `.uns`. Excellent UX for AnnData-centric workflows.

diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ authors:
     orcid: "https://orcid.org/0009-0003-5012-7229"
 repository-code: "https://github.com/dnncha/dotmatch"
 license: Apache-2.0
-version: "0.1.8"
+version: "0.2.0"
 doi: 10.5281/zenodo.20541628
 abstract: "DotMatch is a deterministic known-target short-DNA assignment engine for CRISPR guide counting, barcode demultiplexing, and fixed-target FASTQ workflows."
 keywords:
@@ -21,7 +21,7 @@ keywords:
   - edit distance
 preferred-citation:
   type: article
-  title: "DotMatch: deterministic known-target short-DNA assignment for sequencing workflows"
+  title: "DotMatch: ambiguity-aware known-target DNA assignment and auditable assay workflows"
   authors:
     - given-names: "Donncha"
       family-names: "O'Toole"

diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@ LABEL org.opencontainers.image.title="DotMatch" \
       org.opencontainers.image.source="https://github.com/dnncha/dotmatch" \
       org.opencontainers.image.url="https://dotmatch.readthedocs.io/" \
       org.opencontainers.image.documentation="https://dotmatch.readthedocs.io/" \
-      org.opencontainers.image.version="0.1.8" \
+      org.opencontainers.image.version="0.2.0" \
       org.opencontainers.image.licenses="Apache-2.0" \
       org.opencontainers.image.authors="Donncha O'Toole"
 

diff --git a/Makefile b/Makefile
@@ -454,7 +454,7 @@ repository-ready:
 	python3 scripts/check_evidence_gallery.py
 	$(MAKE) docs-ready
 
-release-ready: python-test python-package-test docs-ready scientific-readiness-ready assay-evidence-ready alphabet-policy-ready citation-metadata-ready native-comparator-scope-ready workflow-examples-ready evidence-gallery-ready distribution-record-ready bioconda-recipe-ready gpu-evidence-gate native-exact-gate public-crispr-evidence-gate crispr-comparison-gate barcode-comparison-gate feature-barcode-public-gate perturb-seq-public-gate amplicon-panel-public-gate bcl-tiny-public-gate oligo-adapter-public-gate
+release-ready: python-test python-package-test docs-ready scientific-readiness-ready assay-evidence-ready alphabet-policy-ready citation-metadata-ready native-comparator-scope-ready workflow-examples-ready evidence-gallery-ready distribution-record-ready bioconda-recipe-ready gpu-evidence-gate native-exact-gate public-crispr-evidence-gate crispr-comparison-gate barcode-comparison-gate feature-barcode-public-gate perturb-seq-public-gate amplicon-panel-public-gate bcl-tiny-public-gate oligo-adapter-public-gate reviewer-readiness-ready adoption-metrics-ready assaycode-readiness-ready
 	python3 scripts/check_release_readiness.py
 
 pretag-ready:
@@ -498,12 +498,25 @@ workflow-integration-test: dotmatch shared
 workflow-adoption-status:
 	python3 scripts/check_workflow_adoption.py
 
+.PHONY: reviewer-readiness-ready
+reviewer-readiness-ready:
+	python3 scripts/check_reviewer_readiness_assets.py
+
+.PHONY: adoption-metrics-ready
+adoption-metrics-ready:
+	python3 scripts/check_adoption_metrics.py
+
 distribution-record-ready:
 	python3 scripts/check_distribution_record.py
 
+.PHONY: assaycode-readiness-ready
+assaycode-readiness-ready:
+	python3 scripts/check_assaycode_readiness.py
+
 
 bioconda-recipe-ready:
 	python3 scripts/check_bioconda_recipe.py
+	python3 scripts/check_assaycode_bioconda_recipe.py
 
 distribution-channels:
 	python3 scripts/check_distribution_channels.py