Move to setup.cfg

.github/workflows/test.yml

@@ -25,7 +25,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install -r requirements_dev.txt
+        run: pip install .[testing]
       - name: pre-commit validation
         run: pre-commit run --files catenets/*
       - name: Security checks
@@ -53,8 +53,7 @@ jobs:
         if: ${{ matrix.os == 'macos-latest' }}
       - name: Install dependencies
         run: |
-            pip install -r requirements_dev.txt
-            pip install .
+            pip install .[testing]
       - name: Test with pytest Unix
         run: pytest -vvvsx -m "not slow"
         if: ${{ matrix.os != 'windows-latest' }}

catenets/version.py

@@ -1 +1 @@
-__version__ = "0.2.2"
+__version__ = "0.2.3"

pyproject.toml

@@ -0,0 +1,4 @@
+[build-system]
+# AVOID CHANGING REQUIRES: IT WILL BE UPDATED BY PYSCAFFOLD!
+requires = ["setuptools>=46.1.0", "wheel"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,106 @@
+[metadata]
+name = catenets
+author = Alicia Curth
+author_email = [email protected]
+description = Conditional Average Treatment Effect Estimation Using Neural Networks
+license = BSD-3-Clause
+license_files = LICENSE
+long_description = file: README.md
+long_description_content_type = text/markdown; charset=UTF-8
+# Add here related links, for example:
+# Change if running only on Windows, Mac or Linux (comma-separated)
+platforms = any
+
+# Add here all kinds of additional classifiers as defined under
+# https://pypi.org/classifiers/
+classifiers =
+    Programming Language :: Python :: 3
+    Topic :: Scientific/Engineering :: Artificial Intelligence
+    Intended Audience :: Science/Research
+    Operating System :: OS Independent
+
+[options]
+zip_safe = False
+packages = find_namespace:
+include_package_data = True
+package_dir =
+    =.
+
+python_requires = >=3.7
+
+install_requires =
+    gdown
+    jax>=0.3.16
+    jaxlib>=0.3.14; sys_platform != 'win32'
+    loguru>=0.5.3
+    numpy>=1.20
+    pandas>=1.3
+    pytest>=6.2.4
+    requests
+    scikit_learn>=0.24.2
+    scipy>=1.2
+    torch>=1.9
+    importlib-metadata; python_version<"3.8"
+
+
+[options.packages.find]
+where = .
+exclude =
+    tests
+
+[options.extras_require]
+# Add here test requirements (semicolon/line-separated)
+testing =
+    bandit
+    black
+    catboost
+    flake8
+    pre-commit
+    pytest
+    sklearn
+    xgboost
+    setuptools
+    pytest
+    pytest-cov
+    jupyter
+    notebook
+    py # pytest 7.2.0 bug https://github.com/pytest-dev/pytest-xprocess/issues/110
+
+[tool:pytest]
+addopts =
+    --verbose
+norecursedirs =
+    dist
+    build
+    .tox
+testpaths = tests
+# Use pytest markers to select/deselect specific tests
+markers =
+     slow: mark tests as slow (deselect with '-m "not slow"')
+
+[devpi:upload]
+# Options for the devpi: PyPI server and packaging tool
+# VCS export must be deactivated since we are using setuptools-scm
+no_vcs = 1
+formats = bdist_wheel
+
+[flake8]
+# Some sane defaults for the code style checker flake8
+max_line_length = 88
+extend_ignore = E203, W503
+# ^  Black-compatible
+#    E203 and W503 have edge cases handled by black
+exclude =
+    .tox
+    build
+    dist
+    .eggs
+    docs/conf.py
+
+[pyscaffold]
+# PyScaffold's parameters when the project was created.
+# This will be used when updating. Do not change!
+version = 4.1.1
+package = catenets
+extensions =
+    pre_commit

setup.py

@@ -1,15 +1,19 @@
+# stdlib
 import os
 import re
 
-import setuptools
+# third party
+from setuptools import setup
+
+PKG_DIR = os.path.dirname(os.path.abspath(__file__))
 
 
 def read(fname: str) -> str:
     return open(os.path.join(os.path.dirname(__file__), fname)).read()
 
 
 def find_version() -> str:
-    version_file = read("catenets/version.py")
+    version_file = read("catenets/version.py").split("\n")[0]
     version_re = r"__version__ = \"(?P<version>.+)\""
     version_raw = re.match(version_re, version_file)
 
@@ -20,30 +24,16 @@ def find_version() -> str:
     return version
 
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-with open("requirements.txt") as fp:
-    install_requires = fp.read()
-
-
-setuptools.setup(
-    name="catenets",
-    version=find_version(),
-    author="Alicia Curth",
-    author_email="[email protected]",
-    description="Conditional Average Treatment Effect Estimation Using Neural Networks",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/vanderschaarlab/mlforhealthlabpub/tree/main/alg/CATENets",
-    license="BSD-3-Clause",
-    packages=setuptools.find_packages(),
-    classifiers=[
-        "Programming Language :: Python :: 3",
-        "Topic :: Scientific/Engineering :: Artificial Intelligence",
-        "Intended Audience :: Healthcare Industry",
-        "License :: OSI Approved :: BSD License",
-        "Operating System :: OS Independent",
-    ],
-    install_requires=install_requires,
-)
+if __name__ == "__main__":
+    try:
+        setup(
+            version=find_version(),
+        )
+    except:  # noqa
+        print(
+            "\n\nAn error occurred while building the project, "
+            "please ensure you have the most updated version of setuptools, "
+            "setuptools_scm and wheel with:\n"
+            "   pip install -U setuptools setuptools_scm wheel\n\n"
+        )
+        raise