From da98790bdc0daf736021f20853ab9e944e2122ed Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 1 Jul 2024 17:52:15 +0200 Subject: [PATCH 1/3] swap coveralls image for codecov --- README.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 01a189e..a956414 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,5 @@ # Stranger ![Build Status - GitHub][actions-build-status] -[![Coverage Status][coveralls-image]][coveralls-url] [![PyPI Version][pypi-img]][pypi-url] [![DOI][doi-image]][doi-url] ![GitHub Release Date][github-release-date] @@ -45,7 +44,7 @@ Options: The repeats are called with Expansion Hunter as mentioned earlier. ExpansionHunter will annotate the number of times that a repeat has been seen in the bam files of each individual and what repeat id the variant has. Stranger will annotate the level of pathogenicity for the repeat number. The intervals that comes with the package are manually collected from the literature since there is no single source where this information can be collected. -You can find a demo repeat definitions json file that comes with Stranger [here](https://github.com/Clinical-Genomics/stranger/blob/master/stranger/resources/variant_catalog_grch37.json). It is based on the ExpansionHunter variant catalog, but extended with a few disease locus relevant keys: +You can find a demo repeat definitions json file that comes with Stranger [here](https://github.com/Clinical-Genomics/stranger/blob/main/stranger/resources/variant_catalog_grch37.json). It is based on the ExpansionHunter variant catalog, but extended with a few disease locus relevant keys: It is advisable to use an up to date file, perhaps based on a curated public repostitory such as [STRchive][strchive] or [STRipy][stripy]. The ones we use in our routine pipelines can be found at our [Reference-files repository][reference-files] and include our literature curation. | Column/Key | Content/Value | @@ -219,8 +218,8 @@ and [pypi-img]: https://img.shields.io/pypi/v/stranger.svg?style=flat-square [pypi-url]: https://pypi.python.org/pypi/stranger/ -[coveralls-url]: https://coveralls.io/github/moonso/stranger -[coveralls-image]: https://coveralls.io/repos/github/moonso/stranger/badge.svg?branch=master +[codecov-img]: https://codecov.io/gh/Clinical-Genomics/stranger/branch/main/graph/badge.svg +[codecov-url]: https://codecov.io/gh/Clinical-Genomics/stranger [doi-image]: https://zenodo.org/badge/158848858.svg [doi-url]: https://zenodo.org/badge/latestdoi/158848858 [github-release-date]: https://img.shields.io/github/release-date/Clinical-Genomics/scout From 5b2fffd2ffb5c545f8a362664b0e542c497c6bf6 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 1 Jul 2024 17:40:04 +0200 Subject: [PATCH 2/3] Release 0.9.1 - TRGT missing MC fallback fix --- CHANGELOG.md | 3 +-- stranger/__version__.py | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2bcc795..27eba86 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,14 +2,13 @@ All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). -## [unreleased] +## [0.9.1] ### Added - Added github action test and release workflows ### Fixed - Docs for TRGT annotation - Fallback setting allele size to 0 if MC is only set to "." and TRGT annotation requested - ## [0.9.0] - Add Docker image - Parse TRGT VCFs - in particular, decompose and parse FORMAT.MC diff --git a/stranger/__version__.py b/stranger/__version__.py index 3e2f46a..d69d16e 100644 --- a/stranger/__version__.py +++ b/stranger/__version__.py @@ -1 +1 @@ -__version__ = "0.9.0" +__version__ = "0.9.1" From e7262d4a93f1b45983529fb0568a64a0687294b1 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 1 Jul 2024 17:56:00 +0200 Subject: [PATCH 3/3] changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 27eba86..32dc437 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). +## [unreleased] +### Fixed +- Use codecov badge on README page + ## [0.9.1] ### Added - Added github action test and release workflows