CI/CD for docs

biodatageeks · Dec 18, 2024 · 82a56f6 · 82a56f6
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commit 82a56f6
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Showing 9 changed files with 67 additions and 13 deletions.
diff --git a/.github/workflows/publish_documentation.yml b/.github/workflows/publish_documentation.yml
@@ -4,21 +4,23 @@ on:
    tags:
      - "*"
   workflow_dispatch:
-
+env:
+  POETRY_VERSION: 1.8.4
 jobs:
   build:
     name: Deploy docs
     runs-on: ubuntu-latest
     steps:
       - name: Checkout main
         uses: actions/checkout@v2
-
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.12
+      - uses: abatilo/actions-poetry@v2
+        with:
+          poetry-version: ${{ env.POETRY_VERSION }}
+      - run: poetry install
       - name: Deploy docs
-        uses: mhausenblas/mkdocs-deploy-gh-pages@master
-        # Or use mhausenblas/mkdocs-deploy-gh-pages@nomaterial to build without the mkdocs-material theme
+        run: mkdocs gh-deploy --remote-branch gh-pages -f mkdocs.yml --verbose
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          CUSTOM_DOMAIN: biodatageeks.org
-          CONFIG_FILE: mkdocs.yml
-          EXTRA_PACKAGES: build-base
-          REQUIREMENTS: docs/requirements.txt
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,4 @@ venv
 .idea
 sandbox/
 .DS_Store
+site/
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/docs/assets/logo-large.png b/docs/assets/logo-large.png
diff --git a/docs/assets/logo.png b/docs/assets/logo.png
diff --git a/docs/features.md b/docs/features.md
@@ -0,0 +1,23 @@
+## Genomic ranges operations
+
+| Features     | Bioframe           | polars-bio          | PyRanges           | Pybedtools         | PyGenomics         | GenomicRanges      |
+|--------------|--------------------|---------------------|--------------------|--------------------|--------------------|--------------------|
+| overlap      | :white_check_mark: | :white_check_mark:  | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+| nearest      | :white_check_mark: | :white_check_mark:  | :white_check_mark: |                    |                    |                    |
+| cluster      | :white_check_mark: |                     |                    |                    |                    |                    |
+| merge        | :white_check_mark: |                     |                    |                    |                    |                    |
+| complement   | :white_check_mark: |                     |                    |                    |                    |                    |
+| select/slice | :white_check_mark: |                     |                    |                    |                    |                    |
+|              |                    |                     |                    |                    |                    |                    |
+| coverage     | :white_check_mark: |                     |                    |                    |                    |                    |
+| expand       | :white_check_mark: |                     |                    |                    |                    |                    |
+| sort         | :white_check_mark: |                     |                    |                    |                    |                    |
+
+
+## Input/Output
+| I/O              | Bioframe           | polars-bio             | PyRanges           | Pybedtools | PyGenomics | GenomicRanges |
+|------------------|--------------------|------------------------|--------------------|------------|------------|---------------|
+| Pandas DataFrame | :white_check_mark: | :white_check_mark:     | :white_check_mark: |            |            |               |
+| Polars DataFrame |                    | :white_check_mark:     |                    |            |            |               |
+| Polars LazyFrame |                    | :white_check_mark:     |                    |            |            |               |
+| Native readers   |                    | :white_check_mark:     |                    |            |            |               |
diff --git a/docs/index.md b/docs/index.md
@@ -1,2 +1,6 @@
-# Welcome to polars-bio's documentation!
+# Next-gen Python DataFrame operations for genomics!
 
+![logo-large.png](assets/logo-large.png)
+
+polars-bio is a :rocket:blazing fast Python DataFrame library for genomics🧬  built on top of [Apache DataFusion](https://datafusion.apache.org/), [Apache Arrow](https://arrow.apache.org/)
+and  [polars](https://pola.rs/).
diff --git a/docs/versions.json b/docs/versions.json
@@ -0,0 +1,9 @@
+[
+  {
+    "version": "0.2.10",
+    "title": "0.2.10",
+    "aliases": [
+      "latest"
+    ]
+  }
+]
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,7 +1,16 @@
 site_name: polars-bio
+site_url: https://biodatageeks.org/polars-bio/
+repo_url: https://github.com/biodatageeks/polars-bio
+repo_name: biodatageeks/polars-bio
 nav:
-  - Home: index.md
-  - Quickstart: quickstart.md
+  - Home:
+      - polars-bio: index.md
+      - 🏃🏼‍♂️ Quick start: quickstart.md
+      - 🔨Features: features.md
+      - 📚 Tutorial: notebooks/tutorial.ipynb
+      - ⚙️ API reference: api.md
+  - Quick start: quickstart.md
+  - Features: features.md
   - Tutorial: notebooks/tutorial.ipynb
   - API reference: api.md
 
@@ -18,6 +27,8 @@ plugins:
           docstring_style: google
 theme:
   name: material
+  logo: assets/logo.png
+  favicon: assets/logo.png
   features:
     - content.code.copy
     - content.code.select
@@ -33,9 +44,13 @@ theme:
     - navigation.tracking
     - navigation.instant
     - content.footnote.tooltips
+  icon:
+    repo: fontawesome/brands/github
 extra:
   version:
     provider: mike
+    default:
+      - latest
 
 markdown_extensions:
   - admonition
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,3 +10,4 @@ venv @@
     .idea
     sandbox/
     .DS_Store
+    site/