testing updated versions for python and biopython

.github/workflows/ci.yml

@@ -5,7 +5,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: ["3.9", "3.10"]
     steps:
     - uses: actions/checkout@master
     - name: Set up Python ${{ matrix.python-version }}
@@ -30,13 +30,13 @@ jobs:
   test-full:
     runs-on: macos-latest
     env:
-      PYTHON: '3.9'
+      PYTHON: "3.10"
     steps:
     - uses: actions/checkout@master
     - name: Setup Python
       uses: actions/setup-python@master
       with:
-        python-version: 3.9
+        python-version: "3.10"
     - name: Install dependencies
       run: |
         pip install -r requirements.txt
@@ -94,4 +94,4 @@ jobs:
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           BRANCH: gh-pages
-          FOLDER: docs/_build/html
+          FOLDER: docs/_build/html

README.md

@@ -33,11 +33,9 @@
         <a href="https://pypi.org/project/orthofisher/" alt="PyPI - Python Version">
             <img src="https://img.shields.io/pypi/pyversions/orthofisher">
         </a>
-        <br />
         <a href="https://academic.oup.com/g3journal/article/11/9/jkab250/6321954">
           <img src="https://zenodo.org/badge/DOI/10.1093/g3journal/jkab250.svg">
         </a>
-        <a href="https://patreon.com/jlsteenwyk"><img src="https://img.shields.io/endpoint.svg?url=https%3A%2F%2Fshieldsio-patreon.vercel.app%2Fapi%3Fusername%3Djlsteenwyk%26type%3Dpatrons&style=flat" alt="Support me on Patreon" /></a>
     </p>
 </p>
 

requirements.txt

@@ -1,4 +1,14 @@
-biopython>=1.79
-numpy>=1.19.5
-tqdm>=4.56.0
-cython
+biopython==1.81
+coverage==7.3.2
+Cython==3.0.4
+exceptiongroup==1.1.3
+iniconfig==2.0.0
+mock==5.1.0
+numpy==1.24.0
+packaging==23.2
+pluggy==1.3.0
+pytest==7.4.2
+pytest-cov==4.1.0
+pytest-mock==3.0.0
+tomli==2.0.1
+tqdm==4.66.1

setup.py

@@ -12,14 +12,12 @@
     'Operating System :: OS Independent',
     'Intended Audience :: Science/Research',
     'Programming Language :: Python',
-    'Programming Language :: Python :: 3.6',
-    'Programming Language :: Python :: 3.7',
-    'Programming Language :: Python :: 3.8',
     'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
     'Topic :: Scientific/Engineering',
 ]
 
-REQUIRES = ["biopython>=1.79", "numpy>=1.19.5", "tqdm>=4.56.0", "cython"]
+REQUIRES = ["biopython>=1.81", "numpy>=1.24.0", "tqdm>=4.66.1", "cython"]
 
 setup(
     name="orthofisher",
@@ -40,4 +38,4 @@
 ## push new version to pypi
 # rm -rf dist
 # python3 setup.py sdist bdist_wheel --universal
-# twine upload dist/* -r pypi
+# twine upload dist/* -r pypi