Move from setup.py to pyproject.toml

MANIFEST.in

@@ -1,4 +1,7 @@
 include README.rst
 include LICENSE
 include requirements.txt
-include requirements-rtd.txt
+include requirements-rtd.txt
+include requirements-dev.txt
+include cellbender/VERSION.txt
+include cellbender/remove_background/report.ipynb

build_docker_release.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-tag=$(cat cellbender/__init__.py | sed -e 's?__version__ = ??' | sed "s/^'\(.*\)'$/\1/")
+tag=$(cat cellbender/VERSION.txt)
 release=v${tag}
 
 docker build \

cellbender/VERSION.txt

@@ -0,0 +1 @@
+0.3.0

cellbender/__init__.py

@@ -1 +1,3 @@
-__version__ = '0.3.0'
+from .base_cli import get_version
+
+__version__ = get_version()

cellbender/base_cli.py

@@ -23,12 +23,7 @@ def read(rel_path):
 
 
 def get_version() -> str:
-    for line in read('__init__.py').splitlines():
-        if line.startswith('__version__'):
-            delim = '"' if '"' in line else "'"
-            return line.split(delim)[1]
-    else:
-        raise RuntimeError("Unable to find version string.")
+    return read('VERSION.txt').splitlines()[0]
 
 
 class AbstractCLI(ABC):

pyproject.toml

@@ -0,0 +1,45 @@
+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cellbender"
+authors = [{name = "Stephen Fleming"}, {name = "Mehrtash Babadi"}]
+license = {text = "BSD (3-Clause)"}
+description = "A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data"
+keywords = ["scRNA-seq", "bioinformatics"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.7",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dynamic = ["version", "dependencies", "optional-dependencies"]
+
+[project.readme]
+file = "README.rst"
+content-type = "text/x-rst"
+
+[project.urls]
+Homepage = "http://github.com/broadinstitute/CellBender"
+Documentation = "http://cellbender.readthedocs.io"
+
+[project.scripts]
+cellbender = "cellbender.base_cli:main"
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.packages]
+find = {namespaces = false}
+
+[tool.setuptools.dynamic]
+version = {attr = "cellbender.__version__"}
+dependencies = {file = ["requirements.txt"]}
+optional-dependencies.dev = {file = ["requirements-dev.txt"]}
+optional-dependencies.docs = {file = ["requirements-rtd.txt"]}
+
+[tool.setuptools.package-data]
+"*" = ["cellbender.remove_background.report.ipynb", "cellbender.VERSION.txt"]

requirements-dev.txt

@@ -0,0 +1,2 @@
+pytest
+scikit-learn