From 7e23f7cf25feb36a8c3aea0069759d6f46864c7d Mon Sep 17 00:00:00 2001 From: Qiyun Zhu Date: Mon, 7 Oct 2024 12:34:13 -0700 Subject: [PATCH] upgrading to 0.1.7 --- CHANGELOG.md | 2 +- doc/install.md | 17 +++-------------- doc/perform.md | 3 +-- woltka/__init__.py | 2 +- 4 files changed, 6 insertions(+), 18 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6e8a770..66c65bf 100644 --- a/CHANGELOG.md +++ b/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)). diff --git a/doc/install.md b/doc/install.md index e5b833a..8d845b3 100644 --- a/doc/install.md +++ b/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 diff --git a/doc/perform.md b/doc/perform.md index be5c620..348f2fa 100644 --- a/doc/perform.md +++ b/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 diff --git a/woltka/__init__.py b/woltka/__init__.py index 577926e..b4d6aa0 100644 --- a/woltka/__init__.py +++ b/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'