From bdbf6b1425b8798f65c07f3a129c597a5c3afcf9 Mon Sep 17 00:00:00 2001 From: Kevin Yamauchi Date: Fri, 19 May 2023 15:21:08 +0200 Subject: [PATCH 1/5] update readme and docs --- README.md | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index a5c9b38a..6741d0c5 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,20 @@ -# spatialdata-io +![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true) + +# spatialdata-io: convenient readers for loading common formats into SpatialData [![Tests][badge-tests]][link-tests] [![Documentation][badge-docs]][link-docs] -[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg -[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml +[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml/badge.svg +[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io -SpatialData IO for common technologies. +SpatialData IO for common technologies. Currently, we provide support for: +- Nanostring CosMx +- mcmicro +- steinbock +- 10X Genomics Visium +- 10X Genomics Xenium ## Getting started @@ -22,32 +29,27 @@ Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/l There are several alternative options to install spatialdata-io: - -1. Install the latest development version: + +2. Install the latest development version: ```bash pip install git+https://github.com/scverse/spatialdata-io.git@main ``` -## Release notes - -See the [changelog][changelog]. - ## Contact For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse]. If you found a bug, please use the [issue tracker][issue-tracker]. ## Citation +[L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1). \* = equal contribution -> t.b.a [scverse-discourse]: https://discourse.scverse.org/ [issue-tracker]: https://github.com/scverse/spatialdata-io/issues From e7287dc6c45428b372138270d9251ad4a4aee6e9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 19 May 2023 13:21:23 +0000 Subject: [PATCH 2/5] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- README.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 6741d0c5..79ece23e 100644 --- a/README.md +++ b/README.md @@ -10,11 +10,12 @@ [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io SpatialData IO for common technologies. Currently, we provide support for: -- Nanostring CosMx -- mcmicro -- steinbock -- 10X Genomics Visium -- 10X Genomics Xenium + +- Nanostring CosMx +- mcmicro +- steinbock +- 10X Genomics Visium +- 10X Genomics Xenium ## Getting started @@ -29,13 +30,12 @@ Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/l There are several alternative options to install spatialdata-io: -1. Install the latest release of `spatialdata-io` from `PyPI `_: +1. Install the latest release of `spatialdata-io` from `PyPI `\_: ```bash pip install spatialdata-io ``` - 2. Install the latest development version: ```bash @@ -48,8 +48,8 @@ For questions and help requests, you can reach out in the [scverse discourse][sc If you found a bug, please use the [issue tracker][issue-tracker]. ## Citation -[L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1). \* = equal contribution +[L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1). \* = equal contribution [scverse-discourse]: https://discourse.scverse.org/ [issue-tracker]: https://github.com/scverse/spatialdata-io/issues From 84c1446bc54e1157fd6f1b4ca6977ed78e927505 Mon Sep 17 00:00:00 2001 From: Kevin Yamauchi Date: Fri, 19 May 2023 15:22:47 +0200 Subject: [PATCH 3/5] Update template_usage.md --- docs/template_usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/template_usage.md b/docs/template_usage.md index 324fe4c3..bf8152f6 100644 --- a/docs/template_usage.md +++ b/docs/template_usage.md @@ -1,4 +1,4 @@ -# Using this template +# Developer guide Welcome to the developer guidelines! This document is split into two parts: From 8c1915c0d592b1cebb8f8dcc87bed631b8cc52ca Mon Sep 17 00:00:00 2001 From: Kevin Yamauchi Date: Fri, 19 May 2023 15:27:36 +0200 Subject: [PATCH 4/5] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 79ece23e..45ff46b4 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io -SpatialData IO for common technologies. Currently, we provide support for: +This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for: - Nanostring CosMx - mcmicro @@ -30,7 +30,7 @@ Python installed, we recommend installing [Miniconda](https://docs.conda.io/en/l There are several alternative options to install spatialdata-io: -1. Install the latest release of `spatialdata-io` from `PyPI `\_: +1. Install the latest release of `spatialdata-io` from [PyPI](https://pypi.org/project/spatialdata-io/): ```bash pip install spatialdata-io From fb418e73aa4142527554e12992c9af9c77eab3ca Mon Sep 17 00:00:00 2001 From: LucaMarconato <2664412+LucaMarconato@users.noreply.github.com> Date: Fri, 19 May 2023 15:51:46 +0200 Subject: [PATCH 5/5] fix spelling --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 45ff46b4..8e629940 100644 --- a/README.md +++ b/README.md @@ -11,11 +11,11 @@ This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for: -- Nanostring CosMx -- mcmicro -- steinbock -- 10X Genomics Visium -- 10X Genomics Xenium +- NanoString CosMx +- MCMICRO +- Steinbock +- 10x Genomics Visium +- 10x Genomics Xenium ## Getting started