Scaffold museomics/methods site (Jekyll + client-side filtering)

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Contribute directly (pull request)
+    url: https://github.com/museomics/methods/blob/main/CONTRIBUTING.md
+    about: Comfortable with GitHub? Add an entry by PR instead.

.github/ISSUE_TEMPLATE/suggest-bibliography.yml

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+name: Suggest a bibliography entry
+description: Propose a paper or SOP to add to the Bibliography page.
+title: "[Bibliography] "
+labels: ["type: bibliography-suggestion"]
+# NOTE: tag options mirror _data/tags.yml — update both together.
+body:
+  - type: markdown
+    attributes:
+      value: "Fields marked * are required."
+  - type: dropdown
+    id: type
+    attributes:
+      label: Type*
+      options: [paper, sop]
+    validations:
+      required: true
+  - type: input
+    id: title
+    attributes:
+      label: Title*
+    validations:
+      required: true
+  - type: input
+    id: authors
+    attributes:
+      label: Authors or institution*
+    validations:
+      required: true
+  - type: input
+    id: year
+    attributes:
+      label: Year / date*
+      placeholder: e.g. 2024
+    validations:
+      required: true
+  - type: input
+    id: link
+    attributes:
+      label: Link or DOI*
+      placeholder: https://doi.org/10.xxxx/xxxxx
+    validations:
+      required: true
+  - type: dropdown
+    id: tags
+    attributes:
+      label: Relevant method tags
+      multiple: true
+      options:
+        - silica-column
+        - magnetic-bead
+        - phenol-chloroform
+        - ctab
+        - chelex
+        - tagmentation
+        - ligation
+        - single-stranded
+        - pcr-free
+        - hybridization-capture
+        - genome-skimming
+        - shotgun-wgs
+        - target-capture
+        - metabarcoding
+        - rad-seq
+        - sanger
+    validations:
+      required: false
+  - type: input
+    id: notes
+    attributes:
+      label: Relevance note
+      description: Optional one-line note on why it's relevant.
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/suggest-method.yml

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+name: Suggest a method
+description: Propose a working museomics method to add to the Methods page.
+title: "[Method] "
+labels: ["type: method-suggestion"]
+# NOTE: the dropdown options below mirror _data/tags.yml. GitHub Issue Forms
+# cannot read that file, so if you add a vocabulary term there, add it here too.
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for contributing! Fill in what you can. A maintainer will review
+        and add it to the site. Fields marked * are required.
+  - type: input
+    id: title
+    attributes:
+      label: Title*
+      placeholder: e.g. Genome skimming from a 40-year-old pinned beetle
+    validations:
+      required: true
+  - type: input
+    id: summary
+    attributes:
+      label: One-line summary*
+      description: Shown on the collapsed card.
+    validations:
+      required: true
+  - type: dropdown
+    id: kingdom
+    attributes:
+      label: Kingdom*
+      multiple: true
+      options: [Animalia, Plantae, Fungi, Chromista, Bacteria, Archaea]
+    validations:
+      required: true
+  - type: dropdown
+    id: phylum
+    attributes:
+      label: Phylum / Division*
+      multiple: true
+      options:
+        - Chordata
+        - Arthropoda
+        - Mollusca
+        - Annelida
+        - Echinodermata
+        - Cnidaria
+        - Nematoda
+        - Platyhelminthes
+        - Porifera
+        - Tracheophyta
+        - Bryophyta
+        - Ascomycota
+        - Basidiomycota
+        - "Other (describe in detail box)"
+    validations:
+      required: true
+  - type: dropdown
+    id: preservation
+    attributes:
+      label: Preservation type*
+      multiple: true
+      options:
+        - dry-pinned
+        - study-skin
+        - herbarium-pressed
+        - fluid-ethanol
+        - fluid-formalin
+        - frozen
+        - dried-tissue
+        - bone-subfossil
+        - "Other (describe in detail box)"
+    validations:
+      required: true
+  - type: dropdown
+    id: extraction
+    attributes:
+      label: Extraction method*
+      multiple: true
+      options:
+        - silica-column
+        - magnetic-bead
+        - phenol-chloroform
+        - ctab
+        - chelex
+        - "Other (describe in detail box)"
+    validations:
+      required: true
+  - type: dropdown
+    id: library
+    attributes:
+      label: Library prep method*
+      multiple: true
+      options:
+        - tagmentation
+        - ligation
+        - single-stranded
+        - pcr-free
+        - hybridization-capture
+        - "Other (describe in detail box)"
+    validations:
+      required: true
+  - type: dropdown
+    id: sequencing
+    attributes:
+      label: Sequencing / downstream method*
+      multiple: true
+      options:
+        - genome-skimming
+        - shotgun-wgs
+        - target-capture
+        - metabarcoding
+        - rad-seq
+        - sanger
+        - "Other (describe in detail box)"
+    validations:
+      required: true
+  - type: dropdown
+    id: outcome
+    attributes:
+      label: Outcome
+      description: How well did it work?
+      options:
+        - worked-well
+        - worked-with-caveats
+        - exploratory
+    validations:
+      required: false
+  - type: input
+    id: doi
+    attributes:
+      label: DOI or link to paper
+      description: Optional — leave blank for unpublished / in-house methods.
+      placeholder: 10.xxxx/xxxxx
+    validations:
+      required: false
+  - type: textarea
+    id: detail
+    attributes:
+      label: Detail / notes
+      description: Protocol notes, yields, caveats. Becomes the expanded card body. Markdown OK.
+    validations:
+      required: false
+  - type: input
+    id: contributor
+    attributes:
+      label: Your name (for attribution)
+    validations:
+      required: false

.github/workflows/ci.yml

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+name: CI
+
+on:
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  validate-and-build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.3"
+          bundler-cache: true
+      - name: Validate entries against controlled vocabulary
+        run: ruby scripts/validate_entries.rb
+      - name: Build with Jekyll (catches broken front-matter / Liquid)
+        run: bundle exec jekyll build
+        env:
+          JEKYLL_ENV: production

.github/workflows/deploy.yml

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+name: Build & deploy to GitHub Pages
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow one concurrent deployment; don't cancel an in-progress production deploy.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.3"
+          bundler-cache: true
+      - name: Validate entries against controlled vocabulary
+        run: ruby scripts/validate_entries.rb
+      - id: pages
+        uses: actions/configure-pages@v5
+      - name: Build with Jekyll
+        run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          JEKYLL_ENV: production
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: _site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

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+_site/
+.jekyll-cache/
+.jekyll-metadata
+vendor/
+.sass-cache/

CONTRIBUTING.md

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+# Contributing to museomics/methods
+
+Two ways to contribute: a **GitHub issue form** (no coding), or a **pull
+request** (add a Markdown file directly). Either way, a maintainer reviews
+before it goes live.
+
+## Option A — Issue form (easiest)
+
+- [Suggest a method](https://github.com/museomics/methods/issues/new?template=suggest-method.yml)
+- [Suggest a bibliography entry](https://github.com/museomics/methods/issues/new?template=suggest-bibliography.yml)
+
+A maintainer transcribes accepted issues into entry files.
+
+## Option B — Pull request
+
+Add one Markdown file per entry, then open a PR. CI validates it automatically.
+
+### Method entry — `_methods/<short-slug>.md`
+
+```yaml
+---
+title: "Genome skimming from a 40-year-old pinned beetle"
+kingdom: [Animalia]           # one or more, from _data/tags.yml
+phylum: [Arthropoda]          # "Phylum / Division", from _data/tags.yml
+preservation: [dry-pinned]
+extraction: [silica-column]
+library: [tagmentation]
+sequencing: [genome-skimming]
+outcome: worked-well          # optional: worked-well | worked-with-caveats | exploratory
+contributor: "Your Name"
+date: 2026-07-19
+summary: "One-line outcome, shown on the collapsed card."
+doi: "10.xxxx/xxxxx"          # optional — omit for unpublished methods
+---
+
+Full detail in Markdown. Renders when the card is expanded: protocol notes,
+yields, caveats, links to SOPs in the bibliography, etc.
+```
+
+Required: `title`, `kingdom`, `phylum`, `preservation`, `extraction`,
+`library`, `sequencing`, `summary`, `contributor`, `date`.
+Optional: `outcome`, `doi`, body.
+
+### Bibliography entry — `_bibliography/<short-slug>.md`
+
+```yaml
+---
+type: paper                   # paper | sop
+title: "..."
+authors_or_institution: "..."
+year_or_date: 2025
+link: "https://doi.org/10.xxxx/xxxxx"
+tags: [extraction, silica-column]   # optional, from _data/tags.yml
+notes: "Optional one-line relevance note"
+---
+```
+
+Required: `type`, `title`, `authors_or_institution`, `year_or_date`, `link`.
+
+## The controlled vocabulary
+
+All tag values live in [`_data/tags.yml`](_data/tags.yml) — the single source of
+truth. CI (`scripts/validate_entries.rb`) fails the build if an entry uses a
+value that isn't listed there, which keeps filtering consistent and stops typos
+fragmenting the taxonomy.
+
+**Need a new tag value?** Add it to `_data/tags.yml` in the same PR. If that
+value is also offered as a dropdown in an issue form, add it to the matching
+list in `.github/ISSUE_TEMPLATE/*.yml` too — the forms can't read `tags.yml`
+automatically. The maintainer curates this vocabulary.
+
+## Local preview
+
+```sh
+bundle install
+bundle exec jekyll serve
+# then open http://localhost:4000/methods/
+```
+
+Run `ruby scripts/validate_entries.rb` before pushing to catch schema errors.
+
+## Licence
+
+Entry content is contributed under [CC BY 4.0](LICENSE-CONTENT.md). Site code is
+MIT ([LICENSE](LICENSE)).

Gemfile

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+source "https://rubygems.org"
+gem "jekyll", "~> 4.3"
+group :jekyll_plugins do
+  gem "jekyll-sitemap"
+end