Merge pull request #754 from uclahs-cds/czhu-add-badges

Version bump to 1.0.0 and documentation updated
uclahs-cds · Jun 20, 2023 · 0c8489d · 0c8489d
2 parents d6b6092 + 0caf577
commit 0c8489d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
-## [0.12.0] - 2023-04-18
+## [1.0.0] - 2023-06-15
 
 ### Added
 

diff --git a/README.md b/README.md
@@ -2,8 +2,11 @@
 
 <!-- badges: start -->
 
+[![Lifecycle:Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)
 [![Tests](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml)
-[![Docs](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/docs.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/docs.yaml)
+[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/private-moPepGen/pkgs/container/mopepgen)
+[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](https://uclahs-cds.github.io/private-moPepGen/)
+[![License](https://img.shields.io/badge/License-GPL_v2-blue)](./LICENSE.txt)
 
 <!-- badges: end -->
 

diff --git a/docs/vignette.md b/docs/vignette.md
@@ -59,6 +59,10 @@ Single nucleotide variants (SNVs/SNPs) and small insertions/deletions (INDELs) c
 
 Note that, the VEP cache files must be downloaded prior to running VEP (see [here](https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html)). The VEP developers recommend downloading the VEP cache version which corresponds to the Ensembl VEP installation. We also strongly recommend explicitly providing the exact reference genome and GTF file used in moPepGen to VEP to ensure the consistency of transcript IDs (i.e., using `--custom ${ANNOTATION_GTF},${REFERENCE_VERSION},gtf`). The exact genome FASTA and annotation GTF files should be used later when calling for variant peptides.
 
+!!! warning
+
+    If you use `--chr` to limit the chromosomes to annotate, make sure the style matches with your VCF/BED file. For example, if the chromosomes have the 'chr' prefix in your VCF file (*i.e.*, chr1, chr2, ...), you must include the prefix as well (*i.e.*, `--chr chr1,chr2,chr3`).
+
 The example data does not work for VEP.
 
 ```shell

diff --git a/moPepGen/__init__.py b/moPepGen/__init__.py
@@ -5,7 +5,7 @@
 from typing import Iterable, IO
 
 
-__version__ = '0.12.0'
+__version__ = '1.0.0'
 
 ## Error messages
 ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'