Refactor formatting

docs/source/conf.py

@@ -12,58 +12,59 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 
-from pathlib import Path
 import sys
+from pathlib import Path
 
 import mrtool
+
 base_dir = Path(mrtool.__file__).parent
 
 about = {}
-with (base_dir / '__about__.py').open() as f:
+with (base_dir / "__about__.py").open() as f:
     exec(f.read(), about)
 
-sys.path.insert(0, Path('..').resolve())
+sys.path.insert(0, Path("..").resolve())
 
 
 # -- Project information -----------------------------------------------------
 
-project = about['__title__']
+project = about["__title__"]
 copyright = f"2020, {about['__author__']}"
-author = about['__author__']
+author = about["__author__"]
 
 # The short X.Y version.
-version = about['__version__']
+version = about["__version__"]
 # The full version, including alpha/beta/rc tags.
-release = about['__version__']
+release = about["__version__"]
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 
-needs_sphinx = '1.5'
+needs_sphinx = "1.5"
 
 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_autodoc_typehints',
-    '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_autodoc_typehints",
+    "matplotlib.sphinxext.plot_directive",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
-source_suffix = '.rst'
-master_doc = 'index'
+source_suffix = ".rst"
+master_doc = "index"
 
-# List of patterns, relative to source directory, that match files and
+# list of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
@@ -74,14 +75,14 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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"]
 html_css_files = [
-    'css/custom.css',
+    "css/custom.css",
 ]
 
 add_module_names = False

pyproject.toml

@@ -12,7 +12,7 @@ license = { file = "LICENSE" }
 authors = [
     { name = "IHME Math Sciences", email = "[email protected]" },
 ]
-dependencies = ["numpy", "pandas", "scipy", "xspline<0.1.0", "xarray", "limetr<0.1.0"]
+dependencies = ["numpy", "pandas", "scipy", "xspline<0.1.0", "xarray", "limetr<0.1.0", "matplotlib"]
 
 [project.optional-dependencies]
 dev = ["pytest", "pytest-mock"]

ruff.toml

@@ -0,0 +1,8 @@
+line-length = 80
+src = ["src"]
+
+[format]
+docstring-code-format = true
+
+[lint.pydocstyle]
+convention = "numpy"

src/mrtool/__init__.py

@@ -1,12 +1,24 @@
 # -*- coding: utf-8 -*-
 """
-    mrtool
-    ~~~~~~
+mrtool
+~~~~~~
 
-    `mrtool` package.
+`mrtool` package.
 """
-from .core.data import MRData
+
+from .core import utils
 from .core.cov_model import CovModel, LinearCovModel, LogCovModel
+from .core.data import MRData
 from .core.model import MRBRT, MRBeRT
-from .core import utils
 from .cov_selection.covfinder import CovFinder
+
+__all__ = [
+    "MRData",
+    "CovModel",
+    "LinearCovModel",
+    "LogCovModel",
+    "MRBRT",
+    "MRBeRT",
+    "utils",
+    "CovFinder",
+]