diff --git a/.github/workflows/publish_documentation.yml b/.github/workflows/publish_documentation.yml index e772e0f..8b40462 100644 --- a/.github/workflows/publish_documentation.yml +++ b/.github/workflows/publish_documentation.yml @@ -4,7 +4,8 @@ on: tags: - "*" workflow_dispatch: - +env: + POETRY_VERSION: 1.8.4 jobs: build: name: Deploy docs @@ -12,13 +13,14 @@ jobs: 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 \ No newline at end of file + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/.gitignore b/.gitignore index 86e99f0..0d1e961 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ venv .idea sandbox/ .DS_Store +site/ \ No newline at end of file diff --git a/Cargo.lock b/Cargo.lock index 8143815..8001154 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -2734,7 +2734,7 @@ checksum = "953ec861398dccce10c670dfeaf3ec4911ca479e9c02154b3a215178c5f566f2" [[package]] name = "polars_bio" -version = "0.2.0" +version = "0.2.10" dependencies = [ "arrow", "datafusion", diff --git a/docs/assets/logo-large.png b/docs/assets/logo-large.png new file mode 100644 index 0000000..006cdf6 Binary files /dev/null and b/docs/assets/logo-large.png differ diff --git a/docs/assets/logo.png b/docs/assets/logo.png new file mode 100644 index 0000000..7718ace Binary files /dev/null and b/docs/assets/logo.png differ diff --git a/docs/features.md b/docs/features.md new file mode 100644 index 0000000..1361c2c --- /dev/null +++ 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 index ec1d088..9b0f3ed 100644 --- 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 new file mode 100644 index 0000000..d658e51 --- /dev/null +++ b/docs/versions.json @@ -0,0 +1,9 @@ +[ + { + "version": "0.2.10", + "title": "0.2.10", + "aliases": [ + "latest" + ] + } +] \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 0bfbd9e..0983540 100644 --- 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