DOC: implement ReadTheDocs documentation (#58)

.gitignore

@@ -1,3 +1,5 @@
+docs/source/generated
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.readthedocs.yaml

@@ -0,0 +1,9 @@
+build:
+  image: latest
+python:
+  version: 3.8
+  pip_install: true
+  install:
+    - requirements: docs/requirements.txt
+  extra_requirements:
+    - docs

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,2 @@
+# Pins sphinx version, probably won't need updating for a while
+sphinx>=3.2.1

docs/source/_templates/class.rst

@@ -0,0 +1,11 @@
+:mod:`{{module}}`.{{objname}}
+{{ underline }}==============
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+
+.. raw:: html
+
+    <div class="clearer"></div>

docs/source/api.rst

@@ -0,0 +1,9 @@
+API
+===
+
+.. autosummary::
+   :template: class.rst
+   :toctree: generated/
+
+   scikeras.wrappers.KerasClassifier
+   scikeras.wrappers.KerasRegressor

docs/source/conf.py

@@ -0,0 +1,189 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# 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.
+#
+import os
+import sys
+
+
+sys.path.insert(0, os.path.abspath(".."))
+
+# -- Project information -----------------------------------------------------
+
+from scikeras import __version__
+
+
+project = "SciKeras"
+copyright = "2020, SciKeras Developers"
+author = "SciKeras Developers"
+release = __version__
+
+
+# -- General configuration ---------------------------------------------------
+
+#  on_rtd is whether we are on readthedocs.org, this line of code grabbed
+#  from docs.readthedocs.org
+on_rtd = os.environ.get("READTHEDOCS", None) == "True"
+
+# 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.napoleon",
+    "sphinx.ext.linkcode",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.intersphinx",
+]
+autosummary_generate = True
+autodoc_default_options = {
+    "members": True,
+    "member-order": "alphabetical",
+    "special-members": "__init__",
+    "undoc-members": True,
+    "exclude-members": "__weakref__",
+    "inherited-members": True,
+}
+intersphinx_mapping = {
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "python": ("https://docs.python.org/3", None),
+}
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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 = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "default"
+
+# 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_context = {
+    "display_github": True,
+    "github_user": "adriangb",
+    "github_repo": "scikeras",
+    "github_version": "master",
+    "conf_py_path": "/source/",
+}
+
+if not on_rtd:  # only import and set the theme if we're building docs locally
+    import sphinx_rtd_theme
+
+    html_theme = "sphinx_rtd_theme"
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# -- GitHub source code link ----------------------------------------------
+
+# Functionality to build github source URI, taken from sklearn.
+
+import inspect
+import subprocess
+
+from functools import partial
+from operator import attrgetter
+
+
+REVISION_CMD = "git rev-parse --short HEAD"
+
+
+def _get_git_revision():
+    try:
+        revision = subprocess.check_output(REVISION_CMD.split()).strip()
+    except (subprocess.CalledProcessError, OSError):
+        print("Failed to execute git to get revision")
+        return None
+    return revision.decode("utf-8")
+
+
+def _linkcode_resolve(domain, info, package, url_fmt, revision):
+    """Determine a link to online source for a class/method/function
+    This is called by sphinx.ext.linkcode
+    An example with a long-untouched module that everyone has
+    >>> _linkcode_resolve('py', {'module': 'tty',
+    ...                          'fullname': 'setraw'},
+    ...                   package='tty',
+    ...                   url_fmt='http://hg.python.org/cpython/file/'
+    ...                           '{revision}/Lib/{package}/{path}#L{lineno}',
+    ...                   revision='xxxx')
+    'http://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
+    """
+
+    if revision is None:
+        return
+    if domain not in ("py", "pyx"):
+        return
+    if not info.get("module") or not info.get("fullname"):
+        return
+
+    class_name = info["fullname"].split(".")[0]
+    if type(class_name) != str:
+        # Python 2 only
+        class_name = class_name.encode("utf-8")
+    module = __import__(info["module"], fromlist=[class_name])
+    obj = attrgetter(info["fullname"])(module)
+
+    try:
+        fn = inspect.getsourcefile(obj)
+    except Exception:
+        fn = None
+    if not fn:
+        try:
+            fn = inspect.getsourcefile(sys.modules[obj.__module__])
+        except Exception:
+            fn = None
+    if not fn:
+        return
+
+    fn = os.path.relpath(
+        fn, start=os.path.dirname(__import__(package).__file__)
+    )
+    try:
+        lineno = inspect.getsourcelines(obj)[1]
+    except Exception:
+        lineno = ""
+    return url_fmt.format(
+        revision=revision, package=package, path=fn, lineno=lineno
+    )
+
+
+def project_linkcode_resolve(domain, info):
+    global _linkcode_git_revision
+    return _linkcode_resolve(
+        domain,
+        info,
+        package="scikeras",
+        revision=_linkcode_git_revision,
+        url_fmt="https://github.com/adriangb/scikeras/"
+        "blob/{revision}/"
+        "{package}/{path}#L{lineno}",
+    )
+
+
+_linkcode_git_revision = _get_git_revision()
+
+# The following is used by sphinx.ext.linkcode to provide links to github
+linkcode_resolve = project_linkcode_resolve

docs/source/index.rst

@@ -0,0 +1,23 @@
+.. SciKeras documentation master file, created by
+   sphinx-quickstart on Sat Aug 15 16:47:22 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SciKeras's documentation!
+====================================
+
+SciKeras provides a Scikit-Learn style API for Keras.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   api
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

pyproject.toml

@@ -38,6 +38,13 @@ pytest-cov = "*"
 pre-commit = "*"
 pytest-xdist = "*"
 
+# docs
+sphinx = { version=">=3.2.1", optional = true }
+sphinx_rtd_theme = { version=">=0.5.0", optional = true }
+
+[tool.poetry.extras]
+docs = ["sphinx", "sphinx_rtd_theme"]
+
 [tool.isort]
 line_length = 79
 force_single_line = true
@@ -67,4 +74,3 @@ show_missing = true
 [build-system]
 requires = ["poetry>=1.0.10"]
 build-backend = "poetry.masonry.api"
-

scikeras/wrappers.py

@@ -354,8 +354,6 @@ def preprocess_y(y):
         Returns:
             y : numpy array of shape (n_samples, n_ouputs)
             extra_args : dictionary of output attributes, ex: n_outputs_
-                    These parameters are added to `self` by `fit` and
-                    consumed (but not reset) by `score`.
         """
 
         extra_args = dict()
@@ -377,8 +375,7 @@ def postprocess_y(y):
         Returns:
             y : 2D numpy array with singular dimensions stripped
                 or 1D numpy array
-            extra_args : attributes of output `y` such as probabilites.
-                Currently unused by KerasRegressor but kept for flexibility.
+            extra_args : attributes of output `y`.
         """
         y = np.column_stack(y)
 
@@ -397,9 +394,7 @@ def preprocess_X(X):
 
         Returns:
             X : unchanged 2D numpy array
-            extra_args : attributes of output `y` such as probabilites.
-                    Currently unused by KerasRegressor but kept for
-                    flexibility.
+            extra_args : attributes of output `y`.
         """
         extra_args = dict()
         return X, extra_args
@@ -573,7 +568,7 @@ def score(self, X, y, sample_weight=None, **kwargs):
             sample_weight : array-like of shape (n_samples,), default=None
                 Sample weights. The Keras Model must support this.
             **kwargs: dictionary arguments
-                Legal arguments are those of self.model_.evaluate.
+                Legal arguments are those of `self.model_.evaluate`.
 
         Returns:
             score: float
@@ -667,16 +662,14 @@ class KerasClassifier(BaseWrapper):
     def preprocess_y(y):
         """Handles manipulation of y inputs to fit or score.
 
-             For KerasClassifier, this handles interpreting classes from `y`.
+        For KerasClassifier, this handles interpreting classes from `y`.
 
         Arguments:
             y : 1D or 2D numpy array
 
         Returns:
             y : modified 2D numpy array with 0 indexed integer class labels.
-            classes_ : list of original class labels.
-            n_classes_ : number of classes.
-            one_hot_encoded : True if input y was one-hot-encoded.
+            extra_args : dictionary of output attributes, ex `n_outputs_`
         """
         y, _ = super(KerasClassifier, KerasClassifier).preprocess_y(y)