Snipe complete reimplementation

.github/workflows/CI.yaml

@@ -0,0 +1,77 @@
+name: CI
+
+# Trigger the workflow on push and pull request events to the main branch
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  # Job 1: Run Tests
+  test:
+    name: Run Tests on Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+
+    # Define a matrix of Python versions to test against
+    strategy:
+      matrix:
+        python-version: [3.11, 3.12]
+
+    steps:
+      # Step 1: Checkout the repository
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      # Step 2: Set up the specified Python version
+      - name: Set Up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Step 3: Install dependencies using Hatch
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+          hatch env create
+          hatch run install
+
+      # Step 4: Run the test suite
+      - name: Run Tests
+        run: hatch run test
+
+  # Job 2: Build and Deploy Documentation
+  build_and_deploy_docs:
+    name: Build and Deploy Documentation
+    runs-on: ubuntu-latest
+    needs: test  # Ensure tests pass before building docs
+
+    steps:
+      # Step 1: Checkout the repository
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      # Step 2: Set up Python (using a specific version for consistency)
+      - name: Set Up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+
+      # Step 3: Install dependencies for building docs
+      - name: Install Documentation Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+          hatch env create docs
+          hatch run docs-build
+
+      # Step 4: Deploy the generated docs to the gh-pages branch
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/site
+          publish_branch: gh-pages

.gitignore

@@ -151,13 +151,18 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
-# pixi environments
 .pixi
 
+*.sig
+*.zip
+*.ipynb
+*.csv
+*.tsv
+*.txt
+*.gz
+playground/
+*.DS_Store
+*.js
+docs/site/*
+docs/site/
+*whl

.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+    "python.analysis.extraPaths": [
+        "./src"
+    ]
+}

README.md

@@ -1,3 +1 @@
-# Snipe (Beta)
 
-**Snipe (WIP)** is an early beta Python API and command-line tool for efficient k-mer-based QC of sequencing datasets.

docs/docs/ReferenceQC.md

@@ -0,0 +1,3 @@
+# Python API Documentation
+
+::: snipe.api.reference_QC

docs/docs/SnipeSig.md

@@ -0,0 +1,3 @@
+# Python API Documentation
+
+::: snipe.api

docs/docs/cli.md

@@ -0,0 +1,7 @@
+# Command Line Interface (CLI) Documentation
+
+Below is the auto-generated CLI documentation from `click`.
+
+```bash
+snipe --help
+```

docs/docs/index.md

@@ -0,0 +1 @@
+# Welcome to MkDocs

docs/mkdocs.yml

@@ -0,0 +1,103 @@
+site_name: Snipe Documentation
+site_url: https://snipe-bio.github.io/snipe
+site_description: Snipe, an ultrafast and memory-efficient alignment-free sequencing quality control tool.
+site_author: "Mohamed Abuelanin"
+
+theme:
+  name: material
+  palette:
+    - scheme: default
+      media: "(prefers-color-scheme: light)"
+      primary: deep purple
+      accent: teal
+      toggle:
+        icon: material/weather-sunny
+        name: Switch to dark mode
+    - scheme: slate
+      media: "(prefers-color-scheme: dark)"
+      primary: deep purple
+      accent: teal
+      toggle:
+        icon: material/weather-night
+        name: Switch to light mode
+  font:
+    text: Open Sans
+    code: Fira Code
+  # logo: assets/logo.svg
+  # favicon: assets/logo.svg
+  features:
+    - content.code.copy
+    - navigation.tabs
+    - navigation.tabs.sticky
+    - math
+    - mathjax
+
+
+markdown_extensions:
+  - toc:
+      permalink: true
+  - tables
+  - admonition
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - footnotes
+  - abbr
+  - admonition
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.critic
+  - pymdownx.caret
+  - pymdownx.keys
+  - pymdownx.mark
+  - pymdownx.tilde
+  - attr_list
+  - md_in_html
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          # format: !!python/name:pymdownx.superfences.fence_code_format
+  - pymdownx.tabbed:
+      alternate_style: true 
+  - pymdownx.arithmatex:
+      generic: true
+
+
+plugins:
+  - search
+  - mkdocstrings:
+      handlers:
+        python:
+          options:
+            show_signature: true
+  - git-revision-date-localized:
+      enable_creation_date: true  
+nav:
+  - Home: index.md
+  - API:
+      - SnipeSig: SnipeSig.md
+      - ReferenceQC: ReferenceQC.md
+  - CLI: cli.md
+
+
+
+extra_css:
+  - stylesheets/extra.css
+
+
+extra_javascript:
+  - javascripts/mathjax.js
+  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
+
+
+copyright: Copyright &copy; 2024 <a href='https://www.mr-eyes.com/'>Mohamed Abuelanin</a>, Tamer Mansour
+
+extra:
+  analytics:
+    provider: google
+    property: GTM-N5RW3TB3

docs/stylesheets/extra.css

@@ -0,0 +1,28 @@
+.cmd {
+    display: inline-block;
+    background-color: #c4c4c49d;
+    color: #040404;
+    font-family: 'Courier New', monospace;
+    padding: 5px 10px;
+    border-radius: 5px;
+    /* white-space: pre-line; */
+    overflow: auto;
+    max-width: 100%;
+    font-size: small;
+    border: 1px solid #444;
+    font-weight: bolder;
+}
+
+.fancy-hr {
+    border: 0; /* Removes default line */
+    height: 1.3px; /* Specifies the height of the HR */
+    background: #333; /* Sets the color of the line */
+    background-image: linear-gradient(to right, #ccc, #333, #ccc); /* Creates a gradient effect from left to right */
+    margin: 20px 0; /* Provides some space before and after the HR */
+}
+
+/* Custom CSS for equations */
+.math-block {
+    overflow-x: auto;
+    white-space: nowrap;
+}