adding website template

.codespellignore

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+hsa
+slippy

.editorconfig

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+# https://EditorConfig.org
+
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_style = space
+indent_size = 4
+
+[*.ipynb]
+# Content is json, but it seems to be minimally formatted
+indent_size = unset
+
+[*.js]
+indent_size = 2
+
+[*.json]
+indent_size = 2
+
+[*.md]
+indent_size = unset
+
+[*.py]
+# yapf and black will use indents other than 4 spaces
+indent_size = unset
+
+[*.rst]
+indent_size = unset
+
+[*.{yml,yaml}]
+indent_size = 2
+max_line_length = 100

.github/actions/buildresources/action.yaml

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+name: 'Build Jupyterbook'
+description: 'Build the Jupyterbook with desired run features'
+
+inputs:
+  jb-cache:
+    description: “Set up the Jupyterbook Cache (boolean)”
+    required: true
+  publish-to-gh:
+    description: “Publish to GitHub Pages (boolean)”
+    required: true
+  jb-save:
+    description: "Save the Jupyterbook Build (boolean)"
+    required: true
+  token:
+    description: 'A GitHub Personal Access Token (for publishing)'
+    required: false
+    default: '0'
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup JupyterBook Cache
+      if: inputs.jb-cache == 'true'
+      uses: actions/cache@v4
+      with:
+        path: ./book/_build
+        # NOTE: change key to "jupyterbook-N+1" to force rebuilding cache
+        key: jupyterbook-0
+
+    - uses: ./.github/actions/setupconda
+
+    - name: Build JupyterBook
+      shell: bash -l {0}
+      run: |
+        ./scripts/build_resources.sh
+
+    - name: Dump Build Logs
+      if: always()
+      shell: bash -l {0}
+      run: |
+        if (test -a book/_build/html/reports/*log); then cat book/_build/html/reports/*log ; fi
+
+    - name: Upload Pages HTML
+      if: inputs.publish-to-gh == 'true'
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: book/_build/html
+
+    - name: Setup GitHub Pages
+      if: inputs.publish-to-gh == 'true'
+      uses: actions/configure-pages@v5
+
+    - name: Deploy to GitHub Pages
+      if: inputs.publish-to-gh == 'true'
+      id: deployment
+      uses: actions/deploy-pages@v4
+
+    - name: Upload Complete Build Folder
+      if: ${{ always() && inputs.jb-save == 'true'}}
+      uses: actions/upload-artifact@v4
+      with:
+        name: build-${{ runner.os }}
+        path: book/_build/
+

.github/actions/setupconda/action.yaml

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+name: 'Setup Conda'
+description: 'Create conda environment for GitHub Action Job'
+
+runs:
+  using: "composite"
+  steps:
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: conda/conda-lock.yml
+        environment-name: bioscape
+        cache-environment: true
+        cache-downloads: true

.github/workflows/build_website.yaml

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+name: Test website build across operating systems
+
+on:
+  schedule:
+    # run this once a week (sunday midnight) to preserve cache
+    # https://docs.github.com/en/actions/guides/caching-dependencies-to-speed-up-workflows#usage-limits-and-eviction-policy
+    - cron:  '0 0 * * 0'
+  pull_request_target:
+    types: [labeled, synchronize]
+    paths:
+      - '.github/**/*'
+      - '{{ cookiecutter.repo_directory }}/**'
+      - 'book/**/*'
+      - 'conda/**'
+      - 'scripts/**'
+      - 'cookiecutter.yaml'
+    branches:
+      - main
+
+jobs:
+  build-and-test:
+    # This workflow accesses secrets (~/.netrc) so only run if labelled by repo owner
+    # https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+    if: contains(github.event.pull_request.labels.*.name, 'preview')
+    name: Build and test on OS - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest", "macos-latest" ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+
+    - uses: ./.github/actions/buildresources
+      with:
+        jb-cache: false
+        publish-to-gh: false
+        jb-save: true

.github/workflows/deploy.yaml

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+name: Deploy
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'book/**'
+      - '{{ cookiecutter.repo_directory }}/**'
+      - 'scripts/**'
+      - '.github/workflows/deploy.yaml'
+      - 'cookiecutter.yaml'
+
+    branches:
+      - main
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - uses: ./.github/actions/buildresources
+      with:
+        jb-cache: false
+        publish-to-gh: true
+        jb-save: true
+        token:  ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ensure_clean_notebooks.py

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+import sys
+from pathlib import Path
+
+import nb_clean as nbc
+import nbformat
+import yaml
+
+with open('./book/_config.yml') as f:
+  data = yaml.safe_load(f)
+
+# Sometimes we use rendered notebooks instead of executing them
+exclude_paths = []
+for pattern in data['execute']['exclude_patterns']:
+    exclude_paths += list(Path('book/tutorials').glob(pattern))
+    exclude_notebooks = [path.as_posix() for path in exclude_paths]
+print('Excluded from execution:\n', '\n'.join(exclude_notebooks))
+
+# Scrub outputs for spellcheck and linkcheck
+for notebook in exclude_notebooks:
+    print(f'Scrubbing outputs: {notebook}...')
+    nb = nbformat.read(notebook, as_version=nbformat.NO_CONVERT)
+    cleaned = nbc.clean_notebook(nb,
+                                 remove_empty_cells=True,
+                                 preserve_cell_metadata=True)
+    nbformat.write(cleaned, notebook)
+
+
+all_ipynbs = [path.as_posix() for path in Path('book/tutorials').rglob('*.ipynb')]
+ipynbs = [p for p in all_ipynbs if not '.ipynb_checkpoints' in p]
+
+results = []
+for notebook in ipynbs:
+    #if not notebook in exclude_notebooks:
+    print(f'Checking {notebook}...')
+    nb = nbformat.read(notebook, as_version=nbformat.NO_CONVERT)
+    result = nbc.check_notebook(nb,
+                                remove_empty_cells=False,
+                                preserve_cell_metadata=True)
+    results.append(result)
+
+if False in results:
+    sys.exit(1)

.github/workflows/manual.yaml

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+name: Build Without Cache
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - uses: ./.github/actions/buildresources
+      with:
+        jb-cache: false
+        publish-to-gh: false
+        jb-save: true

.github/workflows/qaqc.yaml

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+name: QualityControl
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  quality-control:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: ./.github/actions/setupconda
+
+    - name: Install NB-Clean
+      run: |
+        pip install nb-clean==2.0.2
+
+    - name: Ensure clean notebooks
+      run: |
+        python .github/workflows/ensure_clean_notebooks.py
+
+    # NOTE: this isn't a comprehensive spellcheck, just common typos
+    - name: Spellcheck
+      if: always()
+      uses: codespell-project/actions-codespell@master
+      with:
+        check_filenames: true
+        skip: '*.js,*.css,qaqc.yml,*.geojson'
+        ignore_words_file: .codespellignore
+        only_warn: 1
+
+    # borrowed from https://github.com/ProjectPythia/pythia-foundations/blob/main/.github/workflows/link-checker.yaml
+    - name: Disable Notebook Execution Before Linkcheck
+      if: always()
+      shell: python
+      run: |
+        import yaml
+        with open('./book/_config.yml') as f:
+          data = yaml.safe_load(f)
+          data['execute']['execute_notebooks'] = 'off'
+        with open('./book/_config.yml', 'w') as f:
+          yaml.dump(data, f)
+
+    - name: Check External Links
+      continue-on-error: true
+      timeout-minutes: 5
+      if: always()
+      run: |
+        jb build book --builder linkcheck