Merge pull request #260 from ihmeuw/develop

Release candidate 0.10.17

.github/workflows/build.yml

@@ -53,3 +53,8 @@ jobs:
       - name: Doctest
         run: |
           make doctest -C docs/
+      - name: Lint
+        run: |
+          pip install black==22.1.0 isort
+          black . --check --diff
+          isort . --check --verbose --only-modified --diff

CHANGELOG.rst

@@ -1,3 +1,8 @@
+**0.10.17 - 02/15/22**
+
+ - Autoformat code with black and isort.
+ - Add black and isort checks to CI.
+
 **0.10.16 - 02/13/22**
 
  - Update CI

docs/source/conf.py

@@ -10,28 +10,29 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+import sys
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 from pathlib import Path
-import sys
 
 from docutils.nodes import Text
 from sphinx.ext.intersphinx import missing_reference
 
-
 import vivarium_public_health
+
 base_dir = Path(vivarium_public_health.__file__).parent
 
 about = {}
 with (base_dir / "__about__.py").open() as f:
     exec(f.read(), about)
 
-sys.path.insert(0, str(Path('..').resolve()))
+sys.path.insert(0, str(Path("..").resolve()))
 
 # -- Project information -----------------------------------------------------
 
-project = about['__title__']
+project = about["__title__"]
 copyright = f'2021, {about["__author__"]}'
 author = about["__author__"]
 
@@ -45,35 +46,35 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 
-needs_sphinx = '4.0'
+needs_sphinx = "4.0"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.doctest',
-    'sphinx.ext.todo',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
-    'sphinx_click.ext',
-    'matplotlib.sphinxext.plot_directive',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.doctest",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx_click.ext",
+    "matplotlib.sphinxext.plot_directive",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
 
@@ -91,7 +92,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
@@ -102,8 +103,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
-html_theme_path = ['_theme']
-html_theme = 'sphinx_rtd_theme'
+html_theme_path = ["_theme"]
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -114,17 +115,17 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'globaltoc.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
+    "**": [
+        "globaltoc.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
     ]
 }
 
@@ -141,15 +142,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -159,8 +157,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, f'{about["__title__"]}.tex', f'{about["__title__"]} Documentation',
-     about["__author__"], 'manual'),
+    (
+        master_doc,
+        f'{about["__title__"]}.tex',
+        f'{about["__title__"]} Documentation',
+        about["__author__"],
+        "manual",
+    ),
 ]
 
 
@@ -169,8 +172,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, f'{about["__title__"]}', f'{about["__title__"]} Documentation',
-     [author], 1)
+    (master_doc, f'{about["__title__"]}', f'{about["__title__"]} Documentation', [author], 1)
 ]
 
 
@@ -180,36 +182,44 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, f'{about["__title__"]}', f'{about["__title__"]} Documentation',
-     author, f'{about["__title__"]}', about["__summary__"],
-     'Miscellaneous'),
+    (
+        master_doc,
+        f'{about["__title__"]}',
+        f'{about["__title__"]} Documentation',
+        author,
+        f'{about["__title__"]}',
+        about["__summary__"],
+        "Miscellaneous",
+    ),
 ]
 
 # Other docs we can link to
-intersphinx_mapping = {'python': ('https://docs.python.org/3.8', None),
-                       'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
-                       'tables': ('https://www.pytables.org/', None),
-                       'numpy': ('https://numpy.org/doc/stable/', None),
-                       'vivarium': ('https://vivarium.readthedocs.io/en/latest/', None)}
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3.8", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "tables": ("https://www.pytables.org/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "vivarium": ("https://vivarium.readthedocs.io/en/latest/", None),
+}
 
 
 # -- Autodoc configuration ------------------------------------------------
 
 autodoc_default_options = {
     # Automatically document members (e.g. classes in a module,
     # methods in a class, etc.)
-    'members': True,
+    "members": True,
     # Order of items documented is determined by the order
     # of appearance in the source code
-    'member-order': 'bysource',
+    "member-order": "bysource",
     # Generate docs even if an item has no docstring.
-    'undoc-members': True,
+    "undoc-members": True,
     # Don't document things with a leading underscore.
-    'private-members': False,
+    "private-members": False,
 }
 
 # Display type hints in the description instead of the signature.
-autodoc_typehints = 'description'
+autodoc_typehints = "description"
 
 
 # -- nitpicky mode --------------------------------------------------------
@@ -218,7 +228,7 @@
 nitpicky = True
 nitpick_ignore = []
 
-for line in open('../nitpick-exceptions'):
+for line in open("../nitpick-exceptions"):
     if line.strip() == "" or line.startswith("#"):
         continue
     dtype, target = line.split(None, 1)

pyproject.toml

@@ -0,0 +1,13 @@
+[tool.black]
+line_length = 94
+exclude = '''
+/(
+   vivarium
+)/
+
+'''
+
+[tool.isort]
+profile = "black"
+skip = ["vivarium"]
+known_third_party = ["vivarium"]

setup.py

@@ -1,8 +1,7 @@
 #!/usr/bin/env python
 import os
 
-from setuptools import setup, find_packages
-
+from setuptools import find_packages, setup
 
 if __name__ == "__main__":
 
@@ -17,40 +16,37 @@
         long_description = f.read()
 
     install_requirements = [
-        'vivarium>=0.10.1',
-        'numpy',
-        'pandas',
-        'scipy',
-        'tables',
-        'risk_distributions>=2.0.6',
+        "vivarium>=0.10.1",
+        "numpy",
+        "pandas",
+        "scipy",
+        "tables",
+        "risk_distributions>=2.0.6",
     ]
 
     test_requirements = [
-        'pytest',
-        'pytest-mock',
-        'hypothesis',
+        "pytest",
+        "pytest-mock",
+        "hypothesis",
     ]
 
     doc_requirements = [
-        'sphinx>=4.0',
-        'sphinx-rtd-theme',
-        'sphinx-click',
-        'IPython',
-        'matplotlib'
+        "sphinx>=4.0",
+        "sphinx-rtd-theme",
+        "sphinx-click",
+        "IPython",
+        "matplotlib",
     ]
 
     setup(
-        name=about['__title__'],
-        version=about['__version__'],
-
-        description=about['__summary__'],
+        name=about["__title__"],
+        version=about["__version__"],
+        description=about["__summary__"],
         long_description=long_description,
-        license=about['__license__'],
+        license=about["__license__"],
         url=about["__uri__"],
-
         author=about["__author__"],
         author_email=about["__email__"],
-
         classifiers=[
             "Intended Audience :: Developers",
             "Intended Audience :: Education",
@@ -73,18 +69,15 @@
             "Topic :: Scientific/Engineering :: Physics",
             "Topic :: Software Development :: Libraries",
         ],
-
-        package_dir={'': 'src'},
-        packages=find_packages(where='src'),
+        package_dir={"": "src"},
+        packages=find_packages(where="src"),
         include_package_data=True,
-
         install_requires=install_requirements,
         tests_require=test_requirements,
         extras_require={
-            'docs': doc_requirements,
-            'test': test_requirements,
-            'dev': doc_requirements + test_requirements,
+            "docs": doc_requirements,
+            "test": test_requirements,
+            "dev": doc_requirements + test_requirements,
         },
-
         zip_safe=False,
     )

src/vivarium_public_health/__about__.py

@@ -1,13 +1,19 @@
 __all__ = [
-    "__title__", "__summary__", "__uri__", "__version__", "__author__",
-    "__email__", "__license__", "__copyright__",
+    "__title__",
+    "__summary__",
+    "__uri__",
+    "__version__",
+    "__author__",
+    "__email__",
+    "__license__",
+    "__copyright__",
 ]
 
 __title__ = "vivarium_public_health"
 __summary__ = "Components for modelling diseases, risks, and interventions with ``vivarium``"
 __uri__ = "https://github.com/ihmeuw/vivarium_public_health"
 
-__version__ = "0.10.16"
+__version__ = "0.10.17"
 
 __author__ = "The vivarium_public_health developers"
 __email__ = "[email protected]"