From 46e4c66b930a3b46e42cf960c64349f4d9d71eee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marek=20Wieiw=C3=B3rka?= Date: Fri, 10 Jan 2025 19:26:55 +0100 Subject: [PATCH] chore: Doc upgrades --- README.md | 7 ++++--- docs/cookbook.md | 1 + docs/features.md | 6 ++++++ docs/index.md | 1 + mkdocs.yml | 2 ++ 5 files changed, 14 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 3cef5ca..b051212 100644 --- a/README.md +++ b/README.md @@ -14,11 +14,12 @@ It provides a DataFrame API for genomics data and is designed to be blazing fast, memory efficient and easy to use. ## Key Features -* optimized for [peformance](docs/performance.md#results-summary-) and large-scale genomics datasets -* popular genomics [operations](docs/features.md#genomic-ranges-operations) with a DataFrame API (both [Pandas](https://pandas.pydata.org/) and [polars](https://pola.rs/)) +* optimized for [peformance](https://biodatageeks.org/polars-bio/performance/) and large-scale genomics datasets +* popular genomics [operations](https://biodatageeks.org/polars-bio/features/#genomic-ranges-operations) with a DataFrame API (both [Pandas](https://pandas.pydata.org/) and [polars](https://pola.rs/)) * native parallel engine powered by Apache DataFusion and [sequila-native](https://github.com/biodatageeks/sequila-native) -* [out-of-core](docs/features.md#streaming-out-of-core-processing-exeprimental) processing (for data too large to fit into a computer's main memory) with [Apache DataFusion](https://datafusion.apache.org/) and [polars](https://pola.rs/) +* [out-of-core](https://biodatageeks.org/polars-bio/features#streaming-out-of-core-processing-exeprimental) processing (for data too large to fit into a computer's main memory) with [Apache DataFusion](https://datafusion.apache.org/) and [polars](https://pola.rs/) * zero-copy data exchange with [Apache Arrow](https://arrow.apache.org/) +* bioinformatics file [formats](https://biodatageeks.org/polars-bio/features.md#file-formats-support) with [exon](https://github.com/wheretrue/exon) * pre-built wheel packages for *Linux*, *Windows* and *MacOS* (*arm64* and *x86_64*) available on [PyPI](https://pypi.org/project/polars-bio/#files) diff --git a/docs/cookbook.md b/docs/cookbook.md index e707ceb..e2145f1 100644 --- a/docs/cookbook.md +++ b/docs/cookbook.md @@ -12,3 +12,4 @@ [//]: # (## How to set logging level) +[//]: # (## How to read from object storage) \ No newline at end of file diff --git a/docs/features.md b/docs/features.md index 365dc81..bc9035c 100644 --- a/docs/features.md +++ b/docs/features.md @@ -37,6 +37,12 @@ polars-bio supports out-of-core processing with Polars LazyFrame [streaming](htt | expand | :white_check_mark: | :construction: | :white_check_mark: | :white_check_mark: | | :white_check_mark: | | sort | :white_check_mark: | :construction: | :white_check_mark: | :white_check_mark: | | :white_check_mark: | + +## File formats support + + + + ## API comparison between libraries There is no standard API for genomic ranges operations in Python. This table compares the API of the libraries. The table is not exhaustive and only shows the most common operations used in benchmarking. diff --git a/docs/index.md b/docs/index.md index 4c45c7c..b621c80 100644 --- a/docs/index.md +++ b/docs/index.md @@ -13,6 +13,7 @@ It is designed to be easy to use, fast and memory efficient with a focus on geno * native parallel engine powered by Apache DataFusion and [sequila-native](https://github.com/biodatageeks/sequila-native) * [out-of-core](features.md#streaming-out-of-core-processing) processing (for data too large to fit into a computer's main memory) with [Apache DataFusion](https://datafusion.apache.org/) and [polars](https://pola.rs/) * zero-copy data exchange with [Apache Arrow](https://arrow.apache.org/) +* bioinformatics file [formats](features.md#file-formats-support) with [exon](https://github.com/wheretrue/exon) * pre-built wheel packages for *Linux*, *Windows* and *MacOS* (*arm64* and *x86_64*) available on [PyPI](https://pypi.org/project/polars-bio/#files) [//]: # (* support for common genomics file formats (VCF, BAM and FASTQ)) diff --git a/mkdocs.yml b/mkdocs.yml index cb3790d..9382a41 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -11,6 +11,7 @@ nav: - 📚 Tutorial: notebooks/tutorial.ipynb - 🚀 Performance: performance.md - ⚙️ API reference: api.md + - ❓ FAQ : faq.md - Quick start: quickstart.md @@ -18,6 +19,7 @@ nav: - Cookbook: cookbook.md - Tutorial: notebooks/tutorial.ipynb - Performance: performance.md + - API reference: api.md plugins: - search