Merge branch '4.x'

.github/workflows/docker_pkg.yaml

@@ -3,7 +3,10 @@ name: publish docker package
 # Configures this workflow to run every time a change is pushed to the branch called `release`.
 on:
   push:
-    branches: ['master']
+    tags:
+      - "v*"
+  release:
+    types: [published]
 
 # Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
 env:

.github/workflows/testpypi_release.yaml

@@ -3,7 +3,9 @@ name: Test PyPI Release
 on:
   push:
     tags:
-      - "v*"
+      - "v*-alpha*"
+      - "v*-beta*"
+      - "v*-rc*"
 
 # Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
 jobs:

README.md

@@ -1,12 +1,27 @@
-[![dbcan](https://github.com/linnabrown/run_dbcan/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/linnabrown/run_dbcan/actions/workflows/ci.yml)
-[![Documentation Status](https://readthedocs.org/projects/dbcan/badge/?version=latest)](https://dbcan.readthedocs.io/en/latest/?badge=latest)
-[![Package status](https://anaconda.org/bioconda/dbcan/badges/version.svg)](https://anaconda.org/bioconda/dbcan)
-[![GitHub license](https://img.shields.io/badge/license-GNU3.0-blue.svg)](https://github.com/linnabrown/run_dbcan/blob/master/LICENSE)
-[![Platform](https://anaconda.org/bioconda/dbcan/badges/platforms.svg)](https://anaconda.org/bioconda/dbcan/badges/platforms.svg)
-[![GitHub downloads](https://anaconda.org/bioconda/dbcan/badges/downloads.svg)](https://anaconda.org/bioconda/dbcan)
-[![GitHub versions](https://img.shields.io/pypi/pyversions/dbcan.svg)](https://anaconda.org/bioconda/dbcan)
-
-# run_dbcan - Standalone Tool of [dbCAN3](http://bcb.unl.edu/dbCAN2/)
+<h3 align="center">
+  <img src="https://raw.githubusercontent.com/linnabrown/run_dbcan/master/docs/_static/img/dbCAN3_logo.png" width="400" alt="dbCAN-logo"/><br/>
+  <img src="https://raw.githubusercontent.com/linnabrown/run_dbcan/master/docs/_static/img/transparment.png"
+    height="30" width="0px"/>
+  run_dbcan - Standalone Tool of <a href="http://bcb.unl.edu/dbCAN2/">dbCAN3</a>
+  <img src="https://raw.githubusercontent.com/linnabrown/run_dbcan/master/docs/_static/img/transparment.png"
+    height="30" width="0px"/>
+</h3>
+
+<p align="center">
+  <a href="https://github.com/linnabrown/run_dbcan/stargazers"><img alt="GitHub Repo stars" src="https://img.shields.io/github/stars/linnabrown/run_dbcan?style=for-the-badge&logo=starship&labelColor=363a4f&color=b7bdf8"></a>
+  <a href="https://pypi.org/p/dbcan/"><img alt="PyPI - Version" src="https://img.shields.io/pypi/v/dbcan?style=for-the-badge&logo=pypi&color=74c7ec"></a>
+  <a href="https://anaconda.org/bioconda/dbcan"><img alt="Conda Downloads" src="https://img.shields.io/conda/dn/bioconda/dbcan?style=for-the-badge&logo=anaconda&labelColor=363a4f&color=a6da95"></a>
+  <a href="https://dbcan.readthedocs.io/en/latest/"><img alt="Read the Docs" src="https://img.shields.io/readthedocs/dbcan?style=for-the-badge&logo=Read%20the%20Docs&labelColor=363a4f&color=cba6f7"></a>
+  <a href="https://github.com/linnabrown/run_dbcan/issues"><img alt="GitHub Issues or Pull Requests" src="https://img.shields.io/github/issues/linnabrown/run_dbcan?style=for-the-badge&logo=data%3Aimage%2Fsvg%2Bxml%3Bbase64%2CPHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCAyNTYgMjU2Ij4KPHBhdGggZD0iTTIxNiwzMlYxOTJhOCw4LDAsMCwxLTgsOEg3MmExNiwxNiwwLDAsMC0xNiwxNkgxOTJhOCw4LDAsMCwxLDAsMTZINDhhOCw4LDAsMCwxLTgtOFY1NkEzMiwzMiwwLDAsMSw3MiwyNEgyMDhBOCw4LDAsMCwxLDIxNiwzMloiIHN0eWxlPSJmaWxsOiAjQ0FEM0Y1OyIvPgo8L3N2Zz4%3D&labelColor=363a4f&color=f5a97f"></a>
+  <br/>
+  <a href="#"><img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/dbcan?style=for-the-badge&logo=python&labelColor=363a4f&color=99d1db"></a>
+  <a href="https://github.com/linnabrown/run_dbcan/releases/latest"><img alt="GitHub Release" src="https://img.shields.io/github/v/release/linnabrown/run_dbcan?style=for-the-badge&logo=github&labelColor=363a4f&color=89dceb"></a>
+  <a href="https://github.com/linnabrown/run_dbcan/blob/master/LICENSE"><img alt="GitHub License" src="https://img.shields.io/github/license/linnabrown/run_dbcan?style=for-the-badge&labelColor=363a4f&color=eba0ac"></a>
+  <a href="https://github.com/linnabrown/run_dbcan/actions/workflows/build.yaml"><img alt="GitHub Actions Workflow Status" src="https://img.shields.io/github/actions/workflow/status/linnabrown/run_dbcan/build.yaml?branch=master&style=for-the-badge&logo=github&labelColor=363a4f&color=f2cdcd"></a>
+  <a href="https://github.com/linnabrown/run_dbcan/actions/workflows/test.yaml"><img alt="GitHub Actions Workflow Status" src="https://img.shields.io/github/actions/workflow/status/linnabrown/run_dbcan/test.yaml?branch=master&style=for-the-badge&logo=github&label=Test&labelColor=363a4f&color=a6d189"></a>
+</p>
+
+## Introduction
 
 **run_dbcan** is the standalone version of the [dbCAN3](http://bcb.unl.edu/dbCAN2/) annotation tool for automated CAZyme annotation. This tool, known as `run_dbcan`, incorporates HMMER, Diamond, and dbCAN_sub for annotating CAZyme families, and integrates Cazyme Gene Clusters (CGCs) and substrate predictions.
 

conda-recipe/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "dbcan" %}
-{% set version = "4.1.4" %}
+{% set version = "4.2.0" %}
 
 package:
   name: "{{ name|lower }}"

docs/change-logs/4.2.0.rst

@@ -0,0 +1,16 @@
+4.2.0
+~~~~~
+
+.. rubric:: Features
+
+#. Add unit testing in ``tests/test_dbcan.py`` to test `run_dbcan` using different configurations.
+#. Make the docker images hosted via github packages instead of docker hub for CI/CD experience.
+#. Add more github workflows in github actions.
+
+.. rubric:: BugFix
+
+- Please split your files if your input contains > 1 million proteins.
+
+.. rubric:: Regular Updates
+
+- All the databases are updated.