From fa600b6753362c62e277af9cf6016709a8f488f3 Mon Sep 17 00:00:00 2001
From: Alex Rogozhnikov <iamfullofspam@gmail.com>
Date: Tue, 27 Feb 2024 18:47:45 -0800
Subject: [PATCH] move to pyproject and use hatch

---
 pyproject.toml | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++
 setup.py       | 24 -----------------
 2 files changed, 73 insertions(+), 24 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..dc1838b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,73 @@
+[build-system]
+requires = ["hatchling>=1.21.0"]
+build-backend = "hatchling.build"
+
+[project]
+name = "demuxalot"
+
+description = "Scalable and reliable demulitplexing for single-cell RNA sequencing."
+readme = "README.md"
+requires-python = ">=3.8"
+
+keywords = [
+    "genotype learning",
+    "single cell RNA sequencing",
+    "demultiplexing",
+    "bayesian modelling",
+]
+
+license = { text = "MIT" }
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+]
+
+dependencies = [
+    "pysam", # reads BAM files (alignment)
+    "scipy",
+    "numpy",
+    "joblib", # multiprocessing in separate processes
+    "pandas",
+    "pyarrow", # required to read and write parquet files
+]
+dynamic = ["version"]
+authors = [{ name = "Alex Rogozhnikov, System1 Biosciences" }]
+
+[project.urls]
+Homepage = "https://github.com/arogozhnikov/demuxalot"
+
+[tool.setuptools]
+packages = ["demuxalot"]
+
+[tool.hatch.version]
+path = "demuxalot/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+    "/.github",
+    "/.idea",
+    "/.pytest_cache",
+    "/build",
+    "/dist",
+    "/tests",
+    "/examples",
+]
+
+[tool.hatch.build.targets.wheel]
+# should use packages from main section
+
+
+[tool.hatch.envs.pypi.scripts]
+# hatch run pypi:deploy_test
+deploy_test = "hatch build --clean && hatch publish -r test"
+deploy = "hatch build --clean && hatch publish"
+
+
+[tool.hatch.envs.testing.scripts]
+# hatch run testing:test
+test = "pytest tests"
+
+
+[tool.ruff]
+line-length = 120
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 00cc6ef..0000000
--- a/setup.py
+++ /dev/null
@@ -1,24 +0,0 @@
-from setuptools import setup
-
-setup(
-    name="demuxalot",
-    version='0.4.0',
-    description="Scalable and reliable demultiplexing for single-cell RNA sequencing that refines genotypes",
-    long_description=open('README.md', encoding='utf-8').read(),
-    long_description_content_type='text/markdown',
-    author='Alex Rogozhnikov',
-    packages=['demuxalot'],
-    classifiers=[
-        'Intended Audience :: Science/Research',
-        'Programming Language :: Python :: 3 ',
-    ],
-    keywords='genotype learning, single cell RNA sequencing, demultiplexing, bayesian modelling',
-    install_requires=[
-        'pysam',  # reads BAM files (alignment)
-        'scipy',
-        'numpy',
-        'joblib',  # multiprocessing in separate processes
-        'pandas',
-        'pyarrow',  # required to read and write parquet files
-    ],
-)
\ No newline at end of file