Merge pull request #199 from qiyunzhu/0.1.6

Upgrading to v0.1.6

.github/workflows/main.yml

@@ -2,9 +2,9 @@ name: main CI
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:

README.md

@@ -2,7 +2,7 @@
 
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![CI Status](https://github.com/qiyunzhu/woltka/actions/workflows/main.yml/badge.svg)](https://github.com/qiyunzhu/woltka/actions)
-[![Coverage Status](https://coveralls.io/repos/github/qiyunzhu/woltka/badge.svg?branch=master)](https://coveralls.io/github/qiyunzhu/woltka?branch=master)
+[![Coverage Status](https://coveralls.io/repos/github/qiyunzhu/woltka/badge.svg?branch=main)](https://coveralls.io/github/qiyunzhu/woltka?branch=main)
 ![PyPI](https://img.shields.io/pypi/v/woltka)
 ![Conda (channel only)](https://img.shields.io/conda/vn/bioconda/woltka)
 
@@ -70,7 +70,7 @@ See more details about [installation](doc/install.md).
 
 ## Example usage
 
-Woltka provides several small test datasets under [woltka/tests/data](woltka/tests/data). To access them, [download](https://github.com/qiyunzhu/woltka/archive/master.zip) this GitHub repo, unzip, and navigate to this directory.
+Woltka provides several small test datasets under [woltka/tests/data](woltka/tests/data). To access them, [download](https://github.com/qiyunzhu/woltka/archive/main.zip) this GitHub repo, unzip, and navigate to this directory.
 
 One can execute the following commands to make sure that Woltka functions correctly, and to get an impression of the basic usage of Woltka.
 
@@ -173,4 +173,4 @@ Note: This paper focuses on the [OGU analysis](doc/ogu.md). Although it does not
 
 ## Contact
 
-Please forward any questions to the project leader: Dr. Qiyun Zhu (qiyunzhu@gmail.com) or the senior PI: Dr. Rob Knight (robknight@ucsd.edu).
+Please forward any questions to the project leader: **Dr. Qiyun Zhu** (qiyunzhu@gmail.com).

doc/install.md

@@ -43,7 +43,7 @@ pip install git+https://github.com/qiyunzhu/woltka.git
 
 Option 4: Install from a local copy:
 
-Download this [repository](https://github.com/qiyunzhu/woltka/archive/master.zip) or any of the previous [releases](https://github.com/qiyunzhu/woltka/releases). Unzip and navigate to the package directory. Then execute:
+Download this [repository](https://github.com/qiyunzhu/woltka/archive/main.zip) or any of the previous [releases](https://github.com/qiyunzhu/woltka/releases). Unzip and navigate to the package directory. Then execute:
 
 ```bash
 python setup.py install
@@ -53,7 +53,7 @@ Type `woltka` to check if installation is successful, in which case command-line
 
 ## Acceleration
 
-Woltka has a [Numba](https://numba.pydata.org/)-accelerated version (the [numba](https://github.com/qiyunzhu/woltka/tree/numba) branch) in parallel to the master branch. In this version, the "coord-match" algorithm for functional analysis (see [details](ordinal.md)) is significantly faster and consumes less memory. To use this feature, install Woltka using the following commands instead:
+Woltka has a [Numba](https://numba.pydata.org/)-accelerated version (the [numba](https://github.com/qiyunzhu/woltka/tree/numba) branch) in parallel to the main branch. In this version, the "coord-match" algorithm for functional analysis (see [details](ordinal.md)) is significantly faster and consumes less memory. To use this feature, install Woltka using the following commands instead:
 
 ```bash
 conda install -c conda-forge numba biom-format
@@ -101,10 +101,10 @@ conda env remove -n woltka
 If in the future some dependencies have changes that are not compatible with the current release of Woltka, the following "safe" commands can be used to install the current versions of dependencies.
 
 ```bash
-conda create -n woltka python=3.10.8
+conda create -n woltka python=3.12.2
 conda activate woltka
-conda install -c conda-forge biom-format=2.1.13
-conda install -c bioconda woltka=0.1.5
+conda install -c conda-forge biom-format=2.1.15
+conda install -c bioconda woltka=0.1.6
 ```
 
 ## Test

woltka/__init__.py

@@ -10,7 +10,7 @@
 
 __name__ = 'woltka'
 __description__ = 'versatile meta-omic data classifier'
-__version__ = '0.1.5'
+__version__ = '0.1.6'
 __license__ = 'BSD-3-Clause'
 __author__ = 'Qiyun Zhu'
 __email__ = 'qiyunzhu@gmail.com'

woltka/q2/README.md

@@ -39,7 +39,7 @@ qiime woltka
 
 ## Example usage
 
-Multiple small test files can be found under [tests/data](tests/data). To access them, [download](https://github.com/qiyunzhu/woltka/archive/master.zip) this GitHub repo, unzip, and navigate to this directory.
+Multiple small test files can be found under [tests/data](tests/data). To access them, [download](https://github.com/qiyunzhu/woltka/archive/main.zip) this GitHub repo, unzip, and navigate to this directory.
 
 [**Note**] These files are QIIME 2 artifacts (*.qza). They are containers of actual data files. See [below](#data-importing) for how to generate these files.