upgrading to 0.1.7

CHANGELOG.md

@@ -1,6 +1,6 @@
 # Change Log
 
-## Version 0.1.7-dev
+## Version 0.1.7 (10/7/2024)
 
 ### Added
 - Formally adopted the NumPy + Numba solution in the ordinal mapper. This significantly accelerated the algorithm ([#209](https://github.com/qiyunzhu/woltka/pull/209)).

doc/install.md

@@ -51,17 +51,6 @@ python setup.py install
 
 Type `woltka` to check if installation is successful, in which case command-line help information will be displayed on the screen.
 
-## 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 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
-pip install git+https://github.com/qiyunzhu/woltka.git@numba
-```
-
-[**Note**] This feature only accelerates read-gene matching. It does not help with the analysis of microbiome structure.
-
 ## Upgrade
 
 If you installed Woltka using Conda, do:
@@ -101,10 +90,10 @@ 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=3.12.2
+conda create -n woltka python=3.12.7
 conda activate woltka
-conda install -c conda-forge biom-format=2.1.15
-conda install -c bioconda woltka=0.1.6
+conda install -c conda-forge numba=0.60.0 biom-format=2.1.16
+conda install -c bioconda woltka=0.1.7
 ```
 
 ## Test

doc/perform.md

@@ -52,8 +52,7 @@ _Functional analysis_
 Simple read-gene matching | 4:08:53 | 7.745 GB
 Simple read-gene matching, reporting RPK | 4:16:31 | 11.99 GB
 Functional profiling at UniRef entry, then GO process | 4:24:49 | 14.92 GB
-_Experimental_
-Simple read-gene matching, with Numba [acceleration](install.md#acceleration) | 1:55:40 | 5.066 GB
+Simple read-gene matching, with Numba acceleration (default since v0.1.7) | 1:55:40 | 5.066 GB
 
 
 ## Tips for efficient computing

woltka/__init__.py

@@ -10,7 +10,7 @@
 
 __name__ = 'woltka'
 __description__ = 'versatile meta-omic data classifier'
-__version__ = '0.1.6'
+__version__ = '0.1.7'
 __license__ = 'BSD-3-Clause'
 __author__ = 'Qiyun Zhu'
 __email__ = 'qiyunzhu@gmail.com'