Updated python version

.github/workflows/ci_push.yml

@@ -11,21 +11,20 @@ jobs:
   test_suite:
     runs-on: ubuntu-20.04
 
+    strategy:
+      matrix:
+        python-version: ["3.7.9", "3.8", "3.9"]
+
     steps:
     - name: Work around permissions issue
       run: git config --global --add safe.directory /__w/longbow/longbow
 
-    - uses: 'actions/checkout@v2'
-    - uses: actions/setup-python@v2
+    - uses: 'actions/checkout@v3'
+    - uses: actions/setup-python@v4
       with:
-        python-version: '3.7.9'
+        python-version: ${{ matrix.python-version }}
         architecture: 'x64'
 
-    # - name: wget
-    #   uses: wei/wget@v1
-    #   with:
-    #     args: -O /usr/local/bin/starcode https://github.com/gui11aume/starcode/releases/download/1.4/starcode-1.4
-
     - name: pytest
       run: |-
         wget -O /usr/local/bin/starcode https://github.com/gui11aume/starcode/releases/download/1.4/starcode-1.4

setup.py

@@ -33,7 +33,7 @@
         "symspellpy"
     ],
     tests_require=["coverage", "pytest"],
-    python_requires=">=3.6, <3.8",
+    python_requires=">3.6, <3.12",
     packages=find_packages("src"),
     package_dir={"": "src"},
     classifiers=[
@@ -42,9 +42,10 @@
         "License :: OSI Approved :: BSD License",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "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",
+        "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: Implementation :: CPython",
     ],
     entry_points={"console_scripts": ["longbow=longbow.__main__:main_entry"]},

test-requirements.txt

@@ -2,16 +2,3 @@ pytest
 pytest-cov
 pytest-skip-slow
 coverage >= 4.5
-click
-click_log
-tqdm
-ssw
-pysam
-construct
-numpy
-pandas
-git+https://github.com/jonn-smith/pomegranate.git@d80ec9304bba4c42ee3943c887754fd78885cd55#egg=pomegranate
-matplotlib
-polyleven
-ordered-set
-symspellpy

tox.ini

@@ -4,7 +4,8 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = lint,py36,py37,py38
+min_version = 4.0
+envlist = lint,py38,py39,py310,py311
 skip_missing_interpreters =
     true
 
@@ -40,9 +41,9 @@ commands =
 
 [testenv:lint]
 deps = 
-		pylint
-		black
-		flake8
+    pylint
+    black
+    flake8
 
 commands =
     black --check --diff --target-version py38 src tests setup.py
@@ -52,6 +53,7 @@ commands =
 
 [gh-actions]
 python =
-    3.6: lint,py36
-    3.7: py37
     3.8: py38
+    3.9: py39
+    3.10: py310
+    3.11: py311