v1.0.0 Release

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  rust:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - name: Install pinned Rust toolchain
+        run: rustup toolchain install 1.98.0 --profile minimal --component rustfmt --component clippy --target wasm32-unknown-unknown
+      - run: cargo fmt --all --check
+      - run: cargo clippy --workspace --all-targets -- -D warnings
+      - run: cargo test --workspace
+      - run: cargo check -p moddotplot-wasm --target wasm32-unknown-unknown
+
+  web:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - name: Install pinned Rust toolchain
+        run: rustup toolchain install 1.98.0 --profile minimal --target wasm32-unknown-unknown
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
+        with:
+          node-version-file: .node-version
+          cache: npm
+          cache-dependency-path: web/package-lock.json
+      - name: Install pinned wasm-pack
+        run: cargo install wasm-pack --version 0.15.0 --locked
+      - run: npm ci
+        working-directory: web
+      - run: npm run build:release
+        working-directory: web
+      - run: git diff --exit-code -- SBOM.cdx.json THIRD_PARTY_LICENSES.txt
+      - run: npx playwright install --with-deps chromium firefox webkit
+        working-directory: web
+      - name: Run browser end-to-end tests
+        run: xvfb-run --auto-servernum npm run test:e2e
+        working-directory: web

.github/workflows/pages.yml

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+name: Deploy GitHub Pages
+
+on:
+  push:
+    branches:
+      - develop
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: github-pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - name: Install pinned Rust toolchain
+        run: rustup toolchain install 1.98.0 --profile minimal --target wasm32-unknown-unknown
+      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4.4.0
+        with:
+          node-version-file: .node-version
+          cache: npm
+          cache-dependency-path: web/package-lock.json
+      - name: Install pinned wasm-pack
+        run: cargo install wasm-pack --version 0.15.0 --locked
+      - id: pages
+        uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5
+        with:
+          enablement: true
+      - run: npm ci
+        working-directory: web
+      - run: npm test
+        working-directory: web
+      - run: npm run build:wasm
+        working-directory: web
+      - run: npm run build:ui
+        working-directory: web
+        env:
+          MODDOTPLOT_BASE_PATH: /${{ github.event.repository.name }}/
+      - run: npm run docs:check
+        working-directory: web
+      - uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3
+        with:
+          path: web/dist
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4

.gitignore

@@ -0,0 +1,13 @@
+/target/
+/node_modules/
+/web/dist/
+/web/node_modules/
+/web/public/examples/Col-CEN_v1.2.fasta
+/web/src/wasm/
+/web/playwright-report/
+/web/test-results/
+/release-artifacts/
+*.log
+.DS_Store
+.idea/
+.vscode/

.node-version

@@ -0,0 +1 @@
+25.9.0

CITATION.cff

@@ -0,0 +1,225 @@
+cff-version: 1.2.0
+message: >-
+  If you use ModDotPlot Browser, please cite the original ModDotPlot paper listed as the
+  preferred citation and credit the relevant method papers listed in references.
+title: "ModDotPlot Browser"
+type: software
+version: 1.0.0
+date-released: 2026-10-04
+repository-code: "https://github.com/marbl/ModDotPlot-Browser"
+license: MIT-0
+abstract: >-
+  Browser-native genomic dotplot software written by ChatGPT 5.6 Sol under the
+  direction of Adam Phillippy.
+authors:
+  - name: "ChatGPT 5.6 Sol"
+  - family-names: "Phillippy"
+    given-names: "Adam M."
+
+preferred-citation:
+  type: article
+  title: "ModDotPlot-rapid and interactive visualization of tandem repeats"
+  authors:
+    - family-names: "Sweeten"
+      given-names: "Alexander P."
+    - family-names: "Schatz"
+      given-names: "Michael C."
+    - family-names: "Phillippy"
+      given-names: "Adam M."
+  journal: "Bioinformatics"
+  year: 2024
+  month: 8
+  volume: 40
+  issue: 8
+  pages: "btae493"
+  doi: "10.1093/bioinformatics/btae493"
+  url: "https://pubmed.ncbi.nlm.nih.gov/39110522/"
+  notes: "PMID: 39110522; PMCID: PMC11321072."
+
+references:
+  - type: article
+    title: "Mash: fast genome and metagenome distance estimation using MinHash"
+    authors:
+      - family-names: "Ondov"
+        given-names: "Brian D."
+      - family-names: "Treangen"
+        given-names: "Todd J."
+      - family-names: "Melsted"
+        given-names: "Páll"
+      - family-names: "Mallonee"
+        given-names: "Adam B."
+      - family-names: "Bergman"
+        given-names: "Nicholas H."
+      - family-names: "Koren"
+        given-names: "Sergey"
+      - family-names: "Phillippy"
+        given-names: "Adam M."
+    journal: "Genome Biology"
+    year: 2016
+    volume: 17
+    issue: 1
+    pages: "132"
+    doi: "10.1186/s13059-016-0997-x"
+    url: "https://pubmed.ncbi.nlm.nih.gov/27323842/"
+
+  - type: article
+    title: "A fast approximate algorithm for mapping long reads to large reference databases"
+    authors:
+      - family-names: "Jain"
+        given-names: "Chirag"
+      - family-names: "Dilthey"
+        given-names: "Alexander"
+      - family-names: "Koren"
+        given-names: "Sergey"
+      - family-names: "Aluru"
+        given-names: "Srinivas"
+      - family-names: "Phillippy"
+        given-names: "Adam M."
+    journal: "Journal of Computational Biology"
+    year: 2018
+    volume: 25
+    issue: 7
+    pages: "766-779"
+    doi: "10.1089/cmb.2018.0036"
+    url: "https://pubmed.ncbi.nlm.nih.gov/29708767/"
+
+  - type: article
+    title: "Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation"
+    authors:
+      - family-names: "Kille"
+        given-names: "Bryce"
+      - family-names: "Garrison"
+        given-names: "Erik"
+      - family-names: "Treangen"
+        given-names: "Todd J."
+      - family-names: "Phillippy"
+        given-names: "Adam M."
+    journal: "Bioinformatics"
+    year: 2023
+    volume: 39
+    issue: 9
+    pages: "btad512"
+    doi: "10.1093/bioinformatics/btad512"
+    url: "https://academic.oup.com/bioinformatics/article/39/9/btad512/7246743"
+
+  - type: article
+    title: "ntHash2: recursive spaced seed hashing for nucleotide sequences"
+    authors:
+      - family-names: "Kazemi"
+        given-names: "Parham"
+      - family-names: "Wong"
+        given-names: "Johnathan"
+      - family-names: "Nikolić"
+        given-names: "Vladimir"
+      - family-names: "Mohamadi"
+        given-names: "Hamid"
+      - family-names: "Warren"
+        given-names: "René L."
+      - family-names: "Birol"
+        given-names: "Inanç"
+    journal: "Bioinformatics"
+    year: 2022
+    volume: 38
+    issue: 20
+    pages: "4812-4813"
+    doi: "10.1093/bioinformatics/btac564"
+    url: "https://academic.oup.com/bioinformatics/article/38/20/4812/6674501"
+
+  - type: conference-paper
+    title: "b-Bit minwise hashing"
+    authors:
+      - family-names: "Li"
+        given-names: "Ping"
+      - family-names: "König"
+        given-names: "Arnd Christian"
+    collection-title: "Proceedings of the 19th International Conference on World Wide Web"
+    year: 2010
+    pages: "671-680"
+    doi: "10.1145/1772690.1772759"
+    url: "https://doi.org/10.1145/1772690.1772759"
+
+  - type: conference-paper
+    title: "One permutation hashing"
+    authors:
+      - family-names: "Li"
+        given-names: "Ping"
+      - family-names: "Owen"
+        given-names: "Art B."
+      - family-names: "Zhang"
+        given-names: "Cun-Hui"
+    collection-title: "Advances in Neural Information Processing Systems 25"
+    year: 2012
+    pages: "3122-3130"
+    url: "https://papers.nips.cc/paper_files/paper/2012/hash/eaa32c96f620053cf442ad32258076b9-Abstract.html"
+
+  - type: conference-paper
+    title: "HyperLogLog: the analysis of a near-optimal cardinality estimation algorithm"
+    authors:
+      - family-names: "Flajolet"
+        given-names: "Philippe"
+      - family-names: "Fusy"
+        given-names: "Éric"
+      - family-names: "Gandouet"
+        given-names: "Olivier"
+      - family-names: "Meunier"
+        given-names: "Frédéric"
+    collection-title: "Discrete Mathematics and Theoretical Computer Science Proceedings, Analysis of Algorithms 2007"
+    year: 2007
+    volume: "AH"
+    pages: "127-146"
+    url: "https://algo.inria.fr/flajolet/Publications/FlFuGaMe07.pdf"
+
+  - type: conference-paper
+    title: "On the resemblance and containment of documents"
+    authors:
+      - family-names: "Broder"
+        given-names: "Andrei Z."
+    collection-title: "Compression and Complexity of Sequences 1997"
+    year: 1997
+    pages: "21-29"
+    doi: "10.1109/SEQUEN.1997.666900"
+    url: "https://doi.org/10.1109/SEQUEN.1997.666900"
+
+  - type: software
+    title: "ModDotPlot"
+    authors:
+      - family-names: "Sweeten"
+        given-names: "Alexander P."
+      - family-names: "Schatz"
+        given-names: "Michael C."
+      - family-names: "Phillippy"
+        given-names: "Adam M."
+    repository-code: "https://github.com/marbl/moddotplot"
+
+  - type: software
+    title: "MashMap"
+    authors:
+      - name: "MashMap contributors"
+    repository-code: "https://github.com/marbl/MashMap"
+    commit: "1a07d0e"
+
+  - type: software
+    title: "ntHash"
+    authors:
+      - name: "BCGSC ntHash contributors"
+    repository-code: "https://github.com/bcgsc/ntHash"
+    commit: "c26bd4572a19de81e30d55042dbd33c1fd21d4b6"
+
+  - type: software
+    title: "SMHasher and the MurmurHash3 reference implementation"
+    authors:
+      - family-names: "Appleby"
+        given-names: "Austin"
+    url: "https://github.com/aappleby/smhasher/blob/master/src/MurmurHash3.cpp"
+
+  - type: software
+    title: "ColorBrewer 2"
+    version: "2.0"
+    authors:
+      - family-names: "Brewer"
+        given-names: "Cynthia"
+      - family-names: "Harrower"
+        given-names: "Mark"
+      - name: "The Pennsylvania State University"
+    repository-code: "https://github.com/axismaps/colorbrewer"
+    url: "https://colorbrewer2.org/"