Switch to setup.cfg (#74)

* MAINT: switch to setup.cfg

* Fix cupy numpy switching (#73)

* DEV: improve backend settings

* TEST: make tests run on cupy if available

* TYPO: typo fixes

* MAINT: Some more packaging updates

* DOCS: some docs updates

* MAINT: make subpackages work again

.github/workflows/python-package.yml

@@ -40,12 +40,9 @@ jobs:
         conda-channels: anaconda, conda-forge
     - name: Install dependencies
       run: |
-        conda install flake8 pytest-cov
-        conda install --file requirements.txt
-        conda install pre-commit codespell
-        conda install jupyter
         conda install pip setuptools
-        conda update nbconvert
+        conda install --file requirements.txt
+        conda install --file test_requirements.txt
         pre-commit install
     - name: Install gwpopulation
       run: |
@@ -57,7 +54,6 @@ jobs:
       run: |
         pre-commit run --all-files --verbose --show-diff-on-failure
         jupyter nbconvert --clear-output --inplace examples/*.ipynb
-        codespell examples/*.ipynb -L "hist"
         git reset --hard
     - name: Test with pytest
       run: |

.gitignore

@@ -12,3 +12,4 @@ venv/
 .idea/
 **/.version
 **/_version.py
+.vscode

MANIFEST.in

@@ -1,3 +1,5 @@
 include README.md
 include LICENSE.md
 include requirements.txt
+include pages_requirements.txt
+include test_requirements.txt

docs/conf.py

@@ -74,7 +74,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

docs/index.rst

@@ -16,8 +16,8 @@ API:
    :recursive:
 
    models
+   backend
    conversions
-   cupy_utils
    hyperpe
    utils
    vt

gwpopulation/__init__.py

@@ -19,11 +19,11 @@
 from .hyperpe import RateLikelihood
 
 try:
-    from ._version import version as __version__
+    from ._version import __version__
 except ModuleNotFoundError:  # development mode
     __version__ = "unknown"
 
 try:
     set_backend("cupy")
-except ModuleNotFoundError:
+except ImportError:
     set_backend("numpy")

priors/bbh_population.prior

@@ -8,12 +8,12 @@ alpha_chi_2 = Uniform(minimum=1, maximum=5, name='alpha_2', latex_label='$\\alph
 beta_chi_1 = Uniform(minimum=1, maximum=5, name='beta_1', latex_label='$\\beta_1$')
 beta_chi_2 = Uniform(minimum=1, maximum=5, name='beta_2', latex_label='$\\beta_2$')
 alpha = Uniform(minimum=-4, maximum=12, name='alpha', latex_label='$\\alpha$')
-mmin = Uniform(minimum=3, maximum=10, name='mmin', latex_label='$m_{\min}$')
-mmax = Uniform(minimum=30, maximum=65, name='mmax', latex_label='$m_{\max}$')
-lam = Uniform(minimum=0, maximum=1, name='lam', latex_label='$\lambda$')
-mpp = Uniform(minimum=20, maximum=60, name='mpp', latex_label='$\mu_{pp}$')
+mmin = Uniform(minimum=3, maximum=10, name='mmin', latex_label='$m_{\\min}$')
+mmax = Uniform(minimum=30, maximum=65, name='mmax', latex_label='$m_{\\max}$')
+lam = Uniform(minimum=0, maximum=1, name='lam', latex_label='$\\lambda$')
+mpp = Uniform(minimum=20, maximum=60, name='mpp', latex_label='$\\mu_{pp}$')
 sigpp = Uniform(minimum=5e-1, maximum=1e1, name='sigpp', latex_label='$\\sigma_{pp}$')
 beta = Uniform(minimum=-4, maximum=12, name='beta', latex_label='$\\beta$')
-delta_m = Uniform(minimum=0, maximum=10, name='delta_m', latex_label='$\delta m$')
+delta_m = Uniform(minimum=0, maximum=10, name='delta_m', latex_label='$\\delta m$')
 lamb = Uniform(minimum=-5, maximum=10, name="lamb", latex_label="$\\lambda_{z}$")
 rate = LogUniform(minimum=1e-1, maximum=1e3, name='rate', latex_label='$R$')

priors/mass_rates.prior

@@ -10,8 +10,8 @@ beta_2 = 1
 alpha = Uniform(minimum=-4, maximum=6, name='alpha', latex_label='$\\alpha$')
 mmin = Uniform(minimum=2, maximum=10, name='mmin', latex_label='$m_{\\min}$')
 mmax = Uniform(minimum=20, maximum=65, name='mmax', latex_label='$m_{\\max}$')
-lam = Uniform(minimum=0, maximum=1, name='lam', latex_label='$\lambda$')
-mpp = Uniform(minimum=20, maximum=60, name='mpp', latex_label='$\mu_{pp}$')
+lam = Uniform(minimum=0, maximum=1, name='lam', latex_label='$\\lambda$')
+mpp = Uniform(minimum=20, maximum=60, name='mpp', latex_label='$\\mu_{pp}$')
 sigpp = Uniform(minimum=5e-1, maximum=1e1, name='sigpp', latex_label='$\\sigma_{pp}$')
 beta = Uniform(minimum=-4, maximum=6, name='beta', latex_label='$\\beta$')
 delta_m = Uniform(minimum=0, maximum=10, name='delta_m', latex_label='$\\delta m$')

setup.cfg

@@ -1,3 +1,35 @@
+[metadata]
+name = gwpopulation
+description = Unified population inference
+url = https://github.com/ColmTalbot/gwpopulation
+author = Colm Talbot
+author_email = [email protected]
+license_file = LICENSE.md
+long_description = file: README.md
+long_description_content_type = text/markdown
+classifiers =
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    License :: OSI Approved :: MIT License
+    Operating System :: OS Independent
+python_requires = ">=3.8"
+
+[options]
+packages = find:
+install_requires = file: requirements.txt
+
+[options.extras_require]
+cupy = cupy
+pages = file: pages_requirements.txt
+test = file: test_requirements.txt
+
+[options.packages.find]
+exclude =
+    test
+    venv
+    priors
+
 [flake8]
 exclude = .git,build,dist,docs,test,*__init__.py
 max-line-length = 120

setup.py

@@ -1,47 +1,5 @@
 #!/usr/bin/env python
 
-import os
+from setuptools import setup
 
-from setuptools import find_packages, setup
-
-
-def get_long_description():
-    """Finds the README and reads in the description"""
-    here = os.path.abspath(os.path.dirname(__file__))
-    with open(os.path.join(here, "README.md")) as f:
-        long_description = f.read()
-    return long_description
-
-
-# get version info from __init__.py
-def readfile(filename):
-    with open(filename) as fp:
-        filecontents = fp.read()
-    return filecontents
-
-
-long_description = get_long_description()
-
-with open("requirements.txt", "r") as ff:
-    requirements = ff.readlines()
-setup(
-    name="gwpopulation",
-    description="Unified population inference",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    url="https://github.com/ColmTalbot/gwpopulation",
-    author="Colm Talbot",
-    author_email="[email protected]",
-    license="MIT",
-    packages=find_packages(exclude=["test", "venv", "priors"]),
-    package_dir={"gwpopulation": "gwpopulation"},
-    install_requires=requirements,
-    classifiers=[
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],
-    python_requires=">=3.8",
-)
+setup()

test_requirements.txt

@@ -0,0 +1,4 @@
+pytest-cov
+pre-commit
+jupyter
+nbconvert