Merge pull request #225 from bashtage/add-more-r2

ENH: Add system R2 measures

.coveragerc

@@ -5,6 +5,7 @@ branch = True
 omit =
     */results/*
     */_version.py
+    */conftest.py
 
 [report]
 # Regexes for lines to exclude from consideration

doc/source/changes.rst

@@ -1,13 +1,15 @@
 Change Log
 ----------
 
-Since 4.14
-==========
-* Removed support for Python 3.5 inline with NEP-29 (:issue:`222`)
+Version 4.15
+============
+* Blackened the code.
+* Added McElroy's and Berndt's measures of system fit (:issue:`215`).
+* Removed support for Python 3.5 inline with NEP-29 (:issue:`222`).
 
 Version 4.14
 ============
-* Fixed issue where datasets were not installed with wheels (:issue:`217`)
+* Fixed issue where datasets were not installed with wheels (:issue:`217`).
 * Switched to property-cached to inherit cached property from property (:issue:`211`).
 * Removed all use of :class:`pandas.Panel` (:issue:`211`).
 

doc/source/conf.py

@@ -21,6 +21,9 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+import glob
+import os
+import hashlib
 from distutils.version import LooseVersion
 
 import linearmodels
@@ -38,54 +41,78 @@
 # 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.autosummary',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.todo',
-              'sphinx.ext.coverage',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.ifconfig',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.githubpages',
-              'numpydoc',
-              'sphinx_autodoc_typehints',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.extlinks',
-              'sphinx.ext.doctest',
-              'IPython.sphinxext.ipython_console_highlighting',
-              'IPython.sphinxext.ipython_directive',
-              'nbsphinx',
-              'sphinx_material'
-              ]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "numpydoc",
+    "sphinx_autodoc_typehints",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.doctest",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "IPython.sphinxext.ipython_directive",
+    "nbsphinx",
+    "sphinx_material",
+]
 
 try:
     import sphinxcontrib.spelling  # noqa: F401
 except ImportError as err:  # noqa: F841
     pass
 else:
-    extensions.append('sphinxcontrib.spelling')
+    extensions.append("sphinxcontrib.spelling")
 
-spelling_word_list_filename = ['spelling_wordlist.txt', 'names_wordlist.txt']
+spelling_word_list_filename = ["spelling_wordlist.txt", "names_wordlist.txt"]
 spelling_ignore_pypi_package_names = True
 
 add_module_names = False
 
+# Copy over notebooks from examples to docs for build
+files = glob.glob("../../examples/*.ipynb") + glob.glob("../../examples/*.png")
+for file_to_copy in files:
+    full_name = os.path.split(file_to_copy)[-1]
+    folder, file_name = full_name.split("_")
+    if not file_name.endswith("ipynb"):
+        file_name = "_".join((folder, file_name))
+    out_dir = os.path.join(folder, "examples")
+    if not os.path.exists(out_dir):
+        os.makedirs(out_dir, exist_ok=True)
+    out_file = os.path.join(out_dir, file_name)
+    existing_hash = ""
+    with open(file_to_copy, "rb") as example:
+        example_file = example.read()
+        example_hash = hashlib.md5(example_file).hexdigest()
+    if os.path.exists(out_file):
+        with open(out_file, "rb") as existing:
+            existing_hash = hashlib.md5(existing.read()).hexdigest()
+    if existing_hash != example_hash:
+        print(f"Copying {file_to_copy} to {out_file}")
+        with open(out_file, "wb") as out:
+            out.write(example_file)
+
 # 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.
-project = 'linearmodels'
-copyright = '2017, Kevin Sheppard'
-author = 'Kevin Sheppard'
+project = "linearmodels"
+copyright = "2017, Kevin Sheppard"
+author = "Kevin Sheppard"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -94,14 +121,14 @@
 # The short X.Y version.
 # The short X.Y version.
 version = LooseVersion(linearmodels.__version__)
-if '+' in version.version:
+if "+" in version.version:
     version = linearmodels.__version__
-    version = version.replace('.dirty', '')
-    version = version.split('+')
-    commits, tag = version[1].split('.')
+    version = version.replace(".dirty", "")
+    version = version.split("+")
+    commits, tag = version[1].split(".")
     version = version[0]
-    short_tag = ' (+{0})'.format(commits)
-    tag = ' (+' + commits + ', ' + tag + ')'
+    short_tag = " (+{0})".format(commits)
+    tag = " (+" + commits + ", " + tag + ")"
     short_version = version + short_tag
     version = version + tag
 else:
@@ -137,40 +164,40 @@
 
 html_theme_path = sphinx_material.html_theme_path()
 html_context = sphinx_material.get_html_context()
-html_theme = 'sphinx_material'
+html_theme = "sphinx_material"
 # Adds an HTML table visitor to apply Bootstrap table classes
 
 # sphinx_material theme options (see theme.conf for more information)
 html_theme_options = {
-    'base_url': 'http://bashtage.github.io/linearmodels/',
-    'repo_url': 'https://github.com/bashtage/linearmodels/',
-    'repo_name': 'linearmodels',
+    "base_url": "http://bashtage.github.io/linearmodels/",
+    "repo_url": "https://github.com/bashtage/linearmodels/",
+    "repo_name": "linearmodels",
     # Set the name of the project to appear in the sidebar
     "nav_title": project + " " + short_version,
-    'globaltoc_depth': 2,
-    'globaltoc_collapse': True,
-    'globaltoc_includehidden': True,
-    'theme_color': '#2196f3',
-    'color_primary': 'blue',
-    'color_accent': 'orange',
-    'html_minify': True,
-    'css_minify': True,
-    'master_doc': False,
-    'heroes': {
-        'index': 'Models for panel data, system regression, instrumental \
-        variables and asset pricing.'
-    }
+    "globaltoc_depth": 2,
+    "globaltoc_collapse": True,
+    "globaltoc_includehidden": True,
+    "theme_color": "#2196f3",
+    "color_primary": "blue",
+    "color_accent": "orange",
+    "html_minify": True,
+    "css_minify": True,
+    "master_doc": False,
+    "heroes": {
+        "index": "Models for panel data, system regression, instrumental \
+        variables and asset pricing."
+    },
 }
 
-html_favicon = 'images/favicon.ico'
-html_logo = 'images/bw-logo.svg'
+html_favicon = "images/favicon.ico"
+html_logo = "images/bw-logo.svg"
 
 #  Register the theme as an extension to generate a sitemap.xml
 
 # 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_sidebars = {
     "**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]
@@ -183,15 +210,12 @@
     # 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',
@@ -201,42 +225,50 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'linearmodels.tex', 'linearmodels Documentation',
-     'Kevin Sheppard', 'manual'),
+    (
+        master_doc,
+        "linearmodels.tex",
+        "linearmodels Documentation",
+        "Kevin Sheppard",
+        "manual",
+    ),
 ]
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'linearmodels', 'linearmodels Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "linearmodels", "linearmodels Documentation", [author], 1)]
 
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'linearmodels', 'linearmodels Documentation',
-     author, 'linearmodels', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "linearmodels",
+        "linearmodels Documentation",
+        author,
+        "linearmodels",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    'statsmodels': ('https://www.statsmodels.org/dev/', None),
-    'matplotlib': ('https://matplotlib.org/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
-    'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://docs.scipy.org/doc/numpy', None),
-    'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
-    'xarray': ('https://xarray.pydata.org/en/stable/', None)
+    "statsmodels": ("https://www.statsmodels.org/dev/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "xarray": ("https://xarray.pydata.org/en/stable/", None),
 }
 
-extlinks = {'issue': ('https://github.com/bashtage/linearmodels/issues/%s', 'GH')}
+extlinks = {"issue": ("https://github.com/bashtage/linearmodels/issues/%s", "GH")}
 
 
 doctest_global_setup = """
@@ -256,4 +288,54 @@
 napoleon_use_admonition_for_references = True
 
 autosummary_generate = True
-autoclass_content = 'class'
+autoclass_content = "class"
+
+# Create xrefs
+numpydoc_use_autodoc_signature = True
+numpydoc_xref_param_type = True
+numpydoc_class_members_toctree = False
+numpydoc_xref_aliases = {
+    "Figure": "matplotlib.figure.Figure",
+    "Axes": "matplotlib.axes.Axes",
+    "AxesSubplot": "matplotlib.axes.Axes",
+    "DataFrame": "pandas.DataFrame",
+    "Series": "pandas.Series",
+    "BetweenOLS": "linearmodels.panel.model.BetweenOLS",
+    "FamaMacBeth": "linearmodels.panel.model.FamaMacBeth",
+    "FirstDifferenceOLS": "linearmodels.panel.model.FirstDifferenceOLS",
+    "IV2SLS": "linearmodels.iv.model.IV2SLS",
+    "IV3SLS": "linearmodels.system.model.IV3SLS",
+    "IVGMM": "linearmodels.iv.model.IVGMM",
+    "IVGMMCUE": "linearmodels.iv.model.IVGMMCUE",
+    "IVLIML": "linearmodels.iv.model.IVLIML",
+    "IVSystemGMM": "linearmodels.system.model.IVSystemGMM",
+    "LinearFactorModel": "linearmodels.asset_pricing.model.LinearFactorModel",
+    "LinearFactorModelGMM": "linearmodels.asset_pricing.model.LinearFactorModelGMM",
+    "OLS": "linearmodels.iv.model.OLS",
+    "PanelOLS": "linearmodels.panel.model.PanelOLS",
+    "PooledOLS": "linearmodels.panel.model.PooledOLS",
+    "RandomEffects": "linearmodels.panel.model.RandomEffects",
+    "SUR": "linearmodels.system.model.SUR",
+    "TradedFactorModel": "linearmodels.asset_pricing.model.TradedFactorModel",
+    "AbsorbingLSResults": "linearmodels.iv.absorbing.AbsorbingLSResults",
+    "FirstStageResults": "linearmodels.iv.results.FirstStageResults",
+    "IVGMMResults": "linearmodels.iv.results.IVGMMResults",
+    "IVModelComparison": "linearmodels.iv.results.IVModelComparison",
+    "IVResults": "linearmodels.iv.results.IVResults",
+    "InvalidTestStatistic": "linearmodels.utility.InvalidTestStatistic",
+    "OLSResults": "linearmodels.iv.results.OLSResults",
+    "WaldTestStatistic": "linearmodels.utility.WaldTestStatistic",
+    "PanelEffectsResults": "linearmodels.panel.results.PanelEffectsResults",
+    "PanelModelComparison": "linearmodels.panel.results.PanelModelComparison",
+    "PanelResults": "linearmodels.panel.results.PanelResults",
+    "RandomEffectsResults": "linearmodels.panel.results.RandomEffectsResults",
+    "GMMSystemResults": "linearmodels.system.results.GMMSystemResults",
+    "Summary": "linearmodels.compat.statsmodels.Summary",
+    "SystemEquationResult": "linearmodels.system.results.SystemEquationResult",
+    "SystemResults": "linearmodels.system.results.SystemResults",
+    "GMMFactorModelResults": "linearmodels.asset_pricing.results.GMMFactorModelResults",
+    "LinearFactorModelResults": "linearmodels.asset_pricing.results.LinearFactorModelResults",
+    "PanelData": "linearmodels.panel.data.PanelData",
+    "IVData": "linearmodels.iv.data.IVData",
+    "AttrDict": "linearmodels.utility.AttrDict",
+}