added python workflow

.github/workflows/black_lint_test.yml

@@ -0,0 +1,29 @@
+name: Black, lint and test
+
+push:
+  branches:
+    - docs
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      # You can test your matrix by printing the current Python version
+      - name: Install spoc, black and pylint
+        run: pip install . && pip install black==23.9.1 && pip install pylint==2.15.5
+      - name: Run black
+        run: black --check --extend-exclude .
+      - name: Run pylint
+        run: pylint --fail-under=8 spoc/* tests/test_*.py
+      - name: Run tests
+        run: pytest tests

.github/workflows/build_pages.yml

@@ -4,7 +4,6 @@ on:
     branches:
       - master 
       - main
-      - docs
 permissions:
   contents: write
 jobs:

requirements_dev.txt

@@ -1,27 +1,17 @@
-pip==22.2.2
-bump2version==0.5.11
-wheel==0.33.6
-watchdog==0.9.0
-flake8==3.7.8
-tox==3.14.0
-coverage==4.5.4
-Sphinx==1.8.5
-twine==1.14.0
-Click==7.1.2
-pytest==6.2.4
-black==21.7b0
-pandas==1.2.4
-numpy==1.19.0
-pandera==0.11.0
+click>=7.0
+pandas==1.3.0
+numpy>=1.19.0
+pandera>=0.9.0
 pydantic==1.9.1
 pyarrow==8.0.0
 hypothesis==6.52.4
-dask==2022.7.1
-sorted_nearest==0.0.37
-pyranges==0.0.117
-cooler==0.8.11
+dask>=2023.3.0
+ipykernel
+matplotlib>=3.5.3
+seaborn>=0.11.2
 duckdb==0.3.4
-bioframe==0.3.3
 sparse==0.13.0
-pytest-mock==3.10.0
-multiprocess>=0.70.13
+numba>=0.57.0
+pytest==6.2.4
+black==23.9.1
+pylint==2.15.5

setup.py

@@ -4,11 +4,6 @@
 
 from setuptools import setup, find_packages
 
-with open("readme.md") as readme_file:
-    readme = readme_file.read()
-
-with open("HISTORY.rst") as history_file:
-    history = history_file.read()
 
 requirements = [
     "Click>=7.0",
@@ -23,9 +18,7 @@
     "matplotlib>=3.5.3",
     "seaborn>=0.11.2",
     "duckdb==0.3.4",
-    "bioframe==0.3.3",
     "sparse==0.13.0",
-    "multiprocess>=0.70.13",
     "numba>=0.57.0",
 ]
 
@@ -55,7 +48,6 @@
     },
     install_requires=requirements,
     license="MIT license",
-    long_description=readme + "\n\n" + history,
     include_package_data=True,
     keywords="spoc",
     name="spoc",