✨ Mkdocs starter kit for Github Pages

.github/workflows/docs.yml

@@ -0,0 +1,20 @@
+name: docs
+on:
+  push:
+    branches:
+      - master 
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with: 
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - run: pip install mkdocs mkdocs-material mkdocs-markdownextradata-plugin mkdocs-git-revision-date-localized-plugin "mkdocstrings[python]"
+      - run: mkdocs gh-deploy --force

docs/examples.md

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+## Needleman-Wunsch
+
+```python
+seq_a = ["G", "A", "T", "T", "A", "C", "A"]
+seq_b = ["G", "C", "A", "T", "G", "C", "G"]
+
+aligned_seq_a, aligned_seq_b = needleman_wunsch(
+    seq_a,
+    seq_b,
+    match_score=1.0,
+    mismatch_score=-1.0,
+    indel_score=-1.0,
+    gap="_",
+)
+
+# Expects ["G", "_", "A", "T", "T", "A", "C", "A"]
+print(aligned_seq_a)
+
+# Expects ["G", "C", "A", "_", "T", "G", "C", "G"]
+print(aligned_seq_b)
+```
+
+
+## Hirschberg
+
+```python
+seq_a = ["A", "G", "T", "A", "C", "G", "C", "A"]
+seq_b = ["T", "A", "T", "G", "C"]
+
+aligned_seq_a, aligned_seq_b = hirschberg(
+    seq_a,
+    seq_b,
+    match_score=2.0,
+    mismatch_score=-1.0,
+    indel_score=-2.0,
+    gap="_",
+)
+
+# Expects ["A", "G", "T", "A", "C", "G", "C", "A"]
+print(aligned_seq_a)
+
+# Expects ["_", "_", "T", "A", "T", "G", "C", "_"]
+print(aligned_seq_b)
+```

docs/index.md

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+## Introduction
+
+Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.
+
+## Installation
+
+```bash
+pip install sequence_align
+```
+
+## Quickstart
+
+```python
+seq_a = ["G", "A", "T", "T", "A", "C", "A"]
+seq_b = ["G", "C", "A", "T", "G", "C", "G"]
+
+aligned_seq_a, aligned_seq_b = needleman_wunsch(
+    seq_a,
+    seq_b,
+    match_score=1.0,
+    mismatch_score=-1.0,
+    indel_score=-1.0,
+    gap="_",
+)
+```

mkdocs.yml

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+site_name: sequence_align
+
+theme:
+  name: "material"
+  features:
+    # - navigation.indexes
+    - navigation.sections
+    - navigation.tabs
+    - navigation.expand
+    - navigation.top
+  palette:
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: blue-grey
+      toggle:
+        icon: material/brightness-7
+        name: Switch to dark mode
+
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: blue-grey
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+
+repo_name: PPPModels
+repo_url: https://github.com/kensho-technologies/sequence_align
+edit_uri: blob/main/docs/
+site_url: https://kensho-technologies.github.io/sequence_align/
+
+extra: 
+  homepage: https://kensho-technologies.github.io/
+  social:
+    - icon: fontawesome/brands/github
+      link: https://github.com/kensho-technologies/sequence_align
+
+nav:
+  - Overview: index.md
+  - Methodology: methodology.md
+  - Examples: examples.md
+
+plugins:
+  - search
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            docstring_style: google
+
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - pymdownx.arithmatex: 
+      generic: true
+  - pymdownx.details
+  - admonition
+
+extra_javascript: 
+  - https://polyfill.io/v3/polyfill.min.js?features=es6
+  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js 
+

pyproject.toml

@@ -50,6 +50,9 @@ dev = [
     "pyyaml",
     "types-psutil",
     "types-pyyaml",
+    "mkdocs",
+    "mkdocs-material",
+    "mkdocstrings",
 ]
 
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