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 diff --git a/setup.py b/setup.py index 2ec2c98..0ff5ec6 100644 --- a/setup.py +++ b/setup.py @@ -26,7 +26,7 @@ } statuses = [ '1 - Planning', '2 - Pre-Alpha', '3 - Alpha', '4 - Beta', '5 - Production/Stable', '6 - Mature', '7 - Inactive' ] -py_versions = '2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8'.split() +py_versions = '3.11'.split() lic = licenses.get(cfg['license'].lower(), (cfg['license'], None)) min_python = cfg['min_python']