Merge remote-tracking branch 'origin/main' into transfer

.github/workflows/python-pytest.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
 
     steps:
       - name: Checkout base repo

pyproject.toml

@@ -1,25 +1,53 @@
 [build-system]
-requires = [
-    "setuptools>=45",
-    "wheel",
-    "setuptools_scm>=6.2"
-]
+requires = ["setuptools>=69.0.3", "setuptools_scm>=8.0.4"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "baskerville"
+description = "baskerville"
 authors = [
-    {name = "Calico f(DNA)", email = "[email protected]"}
+    {name = "Calico f(DNA)", email = "[email protected]"},
 ]
 readme = "README.md"
-requires-python = ">=3.8, <3.11"
-classifiers = ["License :: OSI Approved :: Apache License"]
-dynamic = ["version", "description", "dependencies"]
+classifiers = ["License :: OSI Approved :: MIT License"]
+dynamic = ["version"]
+
+requires-python = ">=3.9"
+dependencies = [
+    "h5py~=3.10.0",
+    "intervaltree~=3.1.0",
+    "joblib~=1.1.1",
+    "matplotlib~=3.7.1",
+    "google-cloud-storage~=2.0.0",
+    "natsort~=7.1.1",
+    "networkx~=2.8.4",
+    "numpy~=1.24.3",
+    "pandas~=1.5.3",
+    "pybigwig~=0.3.18",
+    "pybedtools~=0.10.0",
+    "pysam~=0.22.0",
+    "qnorm~=0.8.1",
+    "seaborn~=0.12.2",
+    "scikit-learn~=1.2.2",
+    "scipy~=1.9.1",
+    "statsmodels~=0.13.5",
+    "tabulate~=0.8.10",
+    "tensorflow~=2.15.0",
+    "tqdm~=4.65.0",
+]
 
 [project.optional-dependencies]
 dev = [
-    "black==22.3.0",
-    "pytest==7.1.2"
+    "black~=23.12.1",
+    "pytest~=7.4.4",
+    "ruff~=0.1.11",
 ]
 
-[tool.setuptools_scm]
+gpu = [
+    "tensorrt==8.6.1"
+]
+
+[project.urls]
+Homepage = "https://github.com/calico/baskerville"
+
+[tool.setuptools_scm]