Prepare DotMatch 0.2.0

.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

.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

.github/PULL_REQUEST_TEMPLATE.md

@@ -13,13 +13,20 @@
 - [ ] `make repository-ready` if governance, security, licensing, trademark, public docs, or commercial-boundary wording changed.
 - [ ] Relevant benchmark/report gate, if claims or artifacts changed:
 
-## Claim Boundary
+## Validated Scope
 
 - [ ] This PR does not broaden README/docs claims beyond checked evidence.
 - [ ] New benchmark wording links to raw artifacts, commands, and validation status.
 - [ ] 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 until `docs/workflow-adoption.json` records it.
+- [ ] Distribution, registry, and workflow-integration wording matches the current machine-readable status files.
+- [ ] Broad replacement wording or launch copy was removed or avoided.
+- [ ] `make reviewer-readiness-ready` was run if public docs, registry metadata, workflow handoff, evaluation, or public-use record materials changed.
+
 ## Acceptance Criteria
 
 - 

.github/workflows/ci.yml

@@ -11,7 +11,7 @@ jobs:
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
@@ -40,7 +40,7 @@ jobs:
           make release-ready
           make assay-evidence-ready
           make joss-paper-ready
-      - uses: actions/setup-node@v6
+      - uses: actions/setup-node@v7
         if: runner.os == 'Linux'
         with:
           node-version: 22
@@ -106,7 +106,7 @@ jobs:
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
@@ -121,7 +121,7 @@ jobs:
     name: Reviewer reproducibility packet
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"

.github/workflows/codeql.yml

@@ -26,7 +26,7 @@ jobs:
           - language: javascript-typescript
             build-mode: none
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: github/codeql-action/init@v4
         with:

.github/workflows/pages.yml

@@ -19,8 +19,8 @@ jobs:
     name: Build static site
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
-      - uses: actions/setup-node@v6
+      - uses: actions/checkout@v7
+      - uses: actions/setup-node@v7
         with:
           node-version: 22
           cache: npm
@@ -46,87 +46,6 @@ jobs:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     steps:
-      - id: deployment
-        name: Deploy to GitHub Pages
-        env:
-          GH_TOKEN: ${{ github.token }}
-        run: |
-          set -euo pipefail
-
-          artifact_id="$(
-            gh api "repos/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}/artifacts" \
-              --jq '.artifacts[] | select(.name == "github-pages") | .id' \
-              | head -n 1
-          )"
-
-          if [ -z "${artifact_id}" ]; then
-            echo "No github-pages artifact found for run ${GITHUB_RUN_ID}" >&2
-            exit 1
-          fi
-
-          owner_lc="${GITHUB_REPOSITORY_OWNER,,}"
-          oidc_token="$(
-            curl -fsSL \
-              -H "Authorization: bearer ${ACTIONS_ID_TOKEN_REQUEST_TOKEN}" \
-              "${ACTIONS_ID_TOKEN_REQUEST_URL}&audience=https://github.com/${owner_lc}" \
-              | jq -r '.value'
-          )"
-
-          if [ -z "${oidc_token}" ] || [ "${oidc_token}" = "null" ]; then
-            echo "Failed to request a GitHub Pages OIDC token" >&2
-            exit 1
-          fi
-
-          payload="$(
-            jq -n \
-              --argjson artifact_id "${artifact_id}" \
-              --arg build_version "${GITHUB_SHA}" \
-              --arg oidc_token "${oidc_token}" \
-              '{artifact_id: $artifact_id, pages_build_version: $build_version, oidc_token: $oidc_token}'
-          )"
-
-          deployment="$(
-            gh api \
-              --method POST \
-              "repos/${GITHUB_REPOSITORY}/pages/deployments" \
-              --input - <<< "${payload}"
-          )"
-
-          page_url="$(jq -r '.page_url // empty' <<< "${deployment}")"
-          deployment_id="$(jq -r '.id // (.status_url // "" | split("/")[-1]) // empty' <<< "${deployment}")"
-
-          if [ -z "${page_url}" ]; then
-            page_url="https://${owner_lc}.github.io/${{ github.event.repository.name }}/"
-          fi
-          echo "page_url=${page_url}" >> "${GITHUB_OUTPUT}"
-
-          if [ -z "${deployment_id}" ]; then
-            echo "Pages deployment response did not include a deployment id" >&2
-            echo "${deployment}" | jq .
-            exit 1
-          fi
-
-          for _ in {1..120}; do
-            status="$(
-              gh api \
-                "repos/${GITHUB_REPOSITORY}/pages/deployments/${deployment_id}" \
-                --jq '.status'
-            )"
-
-            case "${status}" in
-              succeed)
-                echo "Pages deployment succeeded: ${page_url}"
-                exit 0
-                ;;
-              deployment_failed|deployment_content_failed|deployment_cancelled|deployment_lost)
-                echo "Pages deployment failed with status: ${status}" >&2
-                exit 1
-                ;;
-            esac
-
-            echo "Pages deployment status: ${status}"
-            sleep 5
-          done
-
-          echo "Timed out waiting for Pages deployment ${deployment_id}" >&2
-          exit 1
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
     name: Release preflight gates
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
@@ -49,7 +49,7 @@ jobs:
             label: macOS
             artifact_name: dotmatch-wheel-macos
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
@@ -67,12 +67,12 @@ jobs:
     runs-on: ubuntu-latest
     needs: [preflight]
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
       - name: Build and test repaired Linux wheels
-        uses: pypa/cibuildwheel@v3.4.1
+        uses: pypa/cibuildwheel@v4.1.0
         env:
           CIBW_PLATFORM: linux
         with:
@@ -89,7 +89,7 @@ jobs:
     needs: [preflight]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
@@ -107,16 +107,16 @@ jobs:
     needs: [preflight]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: docker/setup-buildx-action@v4
       - name: Build local smoke-test image
         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:

.github/workflows/workflow-ecosystem.yml

@@ -26,11 +26,11 @@ jobs:
     name: Nextflow, nf-test, Snakemake, Galaxy, MultiQC
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: mamba-org/setup-micromamba@v3
         with:
           environment-name: dotmatch-workflows
           create-args: >-

.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": [
     {