From e8d3455d6084cc4b2f39e5097836e3d7ff1eef1f Mon Sep 17 00:00:00 2001 From: zjzace Date: Wed, 14 Dec 2022 18:22:05 +0800 Subject: [PATCH] Update dependencies version and switch to python3.11 --- README.md | 4 ++-- requirements.txt | 16 +++++++++------- settings.ini | 6 +++--- 3 files changed, 14 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index de8e02f..bdaa8c2 100644 --- a/README.md +++ b/README.md @@ -15,13 +15,13 @@ Prerequisites * [Minimap2](https://github.com/lh3/minimap2) * [nanopolish](https://github.com/jts/nanopolish) * [samtools](http://www.htslib.org) -* Python 3.8/3.9 +* Python 3.11 Installation ------------ To avoid potential conflicts, we recommend running LAFITE in a conda environment. ``` -conda create -n LAFITE_env -c bioconda python=3.8 bedtools +conda create -n LAFITE_env -c conda-forge python=3.11 conda activate LAFITE_env # stable release diff --git a/requirements.txt b/requirements.txt index 5d573dd..acc989b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,9 @@ -biopython == 1.78 -interlap == 0.2.7 -numpy == 1.21.5 -pandas == 1.1.3 -pysam == 0.16.0.1 -scikit-learn == 0.24.2 -tqdm == 4.56.0 +biopython >= 1.80 +interlap >= 0.2.7 +joblib >= 1.2.0 +numpy >= 1.23.5 +pandas >= 1.5.2 +pysam >= 0.20.0 +scikit-learn >= 1.2.0 +tqdm >= 4.64.1 + diff --git a/settings.ini b/settings.ini index be4584e..6e9b3b7 100644 --- a/settings.ini +++ b/settings.ini @@ -13,8 +13,8 @@ author = Jizhou ZHANG author_email = zjzace@ourlook.com copyright = Jizhou ZHANG branch = main -version = 1.0.1 -min_python = 3.7 +version = 1.0.2 +min_python = 3.11 audience = Developers language = English # Set to True if you want to create a more fancy sidebar.json than the default @@ -25,7 +25,7 @@ license = apache2 status = 2 # Optional. Same format as setuptools requirements -requirements = biopython==1.78 interlap==0.2.7 joblib==1.1.0 numpy==1.21.5 pandas==1.1.3 pysam==0.16.0.1 python-dateutil==2.8.2 pytz==2022.1 scikit-learn==0.24.2 scipy==1.8.1 six==1.16.0 threadpoolctl==3.1.0 tqdm==4.56.0 +requirements = biopython>=1.80 interlap>=0.2.7 joblib>=1.2.0 numpy>=1.23.5 pandas>=1.5.2 pysam>=0.20.0 scikit-learn>=1.2.0 tqdm==4.64.1 # Optional. Same format as setuptools console_scripts console_scripts = lafite=LAFITE.lafite_wrapper:main # Optional. Same format as setuptools dependency-links