Merge pull request #3 from TF-Chan-Lab/dev_github

Switch to python 3.11

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

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
+

settings.ini

@@ -13,8 +13,8 @@ author = Jizhou ZHANG
 author_email = [email protected]
 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

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']