Add initial documentation and docstrings

VERSION

@@ -1 +1 @@
-0.0.1dev2
+0.0.1dev3

aakr/_aakr.py

@@ -1,4 +1,4 @@
-"""Module for models."""
+"""Module for Auto Associative Kernel Regression models."""
 
 
 import numpy as np
@@ -9,15 +9,19 @@
 
 
 class AAKR(TransformerMixin, BaseEstimator):
-    """A template estimator to be used as a reference implementation.
+    """Auto Associative Kernel Regressor.
 
-    For more information regarding how to build your own estimator, read more
-    in the :ref:`User Guide <user_guide>`.
+    Please see the :ref:`Getting started <readme.rst>` documentation for more
+        information.
 
     Parameters
     ----------
-    demo_param : str, default='demo_param'
-        A parameter used for demonstation of how to pass and store paramters.
+    metric : str, default='euclidean'
+        Metric for calculating kernel distances.
+    bw : float, default=1.0
+        Kernel bandwith parameter.
+    n_jobs : int, default=-1
+        The number of jobs to run in parallel.
 
     Examples
     --------
@@ -26,43 +30,74 @@ class AAKR(TransformerMixin, BaseEstimator):
     >>> X = np.arange(100).reshape(50, 2)
     >>> aakr = AAKR()
     >>> aakr.fit(X)
-    AAKR(metric='euclidean', bw=1, n_jobs=None)
+    AAKR(metric='euclidean', bw=1, n_jobs=-1)
     """
-    def __init__(self, metric='euclidean', bw=1, n_jobs=None):
+    def __init__(self, metric='euclidean', bw=1, n_jobs=-1):
         self.metric = metric
         self.bw = bw
         self.n_jobs = n_jobs
 
     def fit(self, X, y=None):
-        """A reference implementation of a fitting function for a transformer.
+        """Fit normal condition examples.
 
         Parameters
         ----------
-        X : array-like, shape (n_samples, n_features)
+        X : array-like of shape (n_samples, n_features)
             Training examples from normal conditions.
         y : None
-            Not needed, exists for compability purposes.
+            Not required, exists only for compability purposes.
 
         Returns
         -------
         self : object
             Returns self.
         """
+        # Validation
         X = check_array(X)
+
+        # Save history
         self.X_ = X
+
+        return self
+
+    def partial_fit(self, X, y=None):
+        """Fit more normal condition examples.
+
+        Parameters
+        ----------
+        X : array-like of shape (n_samples, n_features)
+            Training examples from normal conditions.
+        y : None
+            Not required, exists only for compability purposes.
+
+        Returns
+        -------
+        self : object
+            Returns self.
+        """
+        # Validation
+        X = check_array(X)
+
+        if self.X_.shape[1] != X.shape[1]:
+            raise ValueError('Shape of input is different from what was seen'
+                             'in `fit`')
+
+        # Add new examples
+        self.X_ = np.vstack((self.X_, X))
+
         return self
 
-    def predict(self, X, **kwargs):
-        """ A reference implementation of a prediction for a classifier.
+    def transform(self, X, **kwargs):
+        """Transform given array into expected values in normal conditions.
 
         Parameters
         ----------
-        X : array-like, shape (n_samples, n_features)
+        X : array-like of shape (n_samples, n_features)
             The input samples.
 
         Returns
         -------
-        X_nc : ndarray, shape (n_samples, n_features)
+        X_nc : ndarray of shape (n_samples, n_features)
             Expected values in normal conditions for each sample and feature.
         """
         # Validation

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/source/aakr.rst

@@ -0,0 +1,10 @@
+aakr package
+============
+
+Module contents
+---------------
+
+.. automodule:: aakr
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/conf.py

@@ -41,13 +41,14 @@ def add_source_parser(_old_add_source_parser, self, *args, **kwargs):
 
 # -- Project information -----------------------------------------------------
 
-project = 'finscraper'
+project = 'aakr'
 copyright = '2020, Jesse Myrberg'
 author = 'Jesse Myrberg'
 
 # The full version, including alpha/beta/rc tags
 with open('../../VERSION', 'r') as f:
-    release = f.read().strip()
+    version = f.read().strip()
+    release = version
 
 
 # -- General configuration ---------------------------------------------------
@@ -56,10 +57,15 @@ def add_source_parser(_old_add_source_parser, self, *args, **kwargs):
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'm2r',
+    'm2r2',
     'sphinxcontrib.napoleon',
-    'sphinx.ext.autodoc',
     'sphinx_rtd_theme',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.viewcode',
+    'numpydoc'
 ]
 
 # Autodoc settings
@@ -102,13 +108,13 @@ def add_source_parser(_old_add_source_parser, self, *args, **kwargs):
 
 html_theme_options = {
     'canonical_url': '',
-    #'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard
+    # 'analytics_id': 'UA-XXXXXXX-1',  #  Provided by Google in your dashboard
     'logo_only': False,
     'display_version': True,
     'prev_next_buttons_location': 'bottom',
     'style_external_links': False,
-    #'vcs_pageview_mode': '',
-    #'style_nav_header_background': 'white',
+    # 'vcs_pageview_mode': '',
+    # 'style_nav_header_background': 'white',
     # Toc options
     'collapse_navigation': True,
     'sticky_navigation': True,
@@ -120,4 +126,4 @@ def add_source_parser(_old_add_source_parser, self, *args, **kwargs):
 # 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']

docs/source/index.rst

@@ -0,0 +1,13 @@
+.. include:: readme.rst
+
+.. toctree::
+   :caption: Documentation
+   :maxdepth: 2
+
+   Getting started <readme.rst>
+
+.. toctree::
+   :caption: API
+   :maxdepth: 4
+
+   aakr

docs/source/readme.rst

@@ -0,0 +1 @@
+.. mdinclude:: ../../README.md

requirements-dev.txt

@@ -1,2 +1,8 @@
 pytest==5.4.2
-twine==3.2.0
+pytest-cov==2.10.1
+twine==3.2.0
+sphinx==3.3.1
+sphinx_rtd_theme==0.5.0
+numpydoc==1.1.0
+m2r2==0.2.7
+sphinxcontrib-napoleon==0.7

scripts/build-documentation.sh

@@ -1,8 +1,8 @@
 #!/bin/sh
 
-conda activate finscraper && \
+conda activate aakr && \
 rm -rf docs/build && \
-sphinx-apidoc -f -o docs/source finscraper && \
+sphinx-apidoc -f -o docs/source aakr && \
 rm -rf docs/source/modules.rst && \
 sphinx-build -b html docs/source docs/build
-open -a /Applications/Safari.app file://~/Documents/Personal/finscraper/docs/build/index.html
+open -a /Applications/Safari.app file:///Users/e103089/Documents/Personal/aakr/docs/build/index.html

setup.py

@@ -17,7 +17,8 @@
     author='Jesse Myrberg',
     author_email='[email protected]',
     url='https://github.com/jmyrberg/aakr',
-    keywords=['aakr', 'auto', 'associative', 'kernel', 'regression', 'anomaly', 'detection'],
+    keywords=['aakr', 'auto', 'associative', 'kernel', 'regression', 'anomaly',
+              'detection'],
     install_requires=[
         'numpy>=1.19.4',
         'pandas>=1.1.5',
@@ -45,10 +46,10 @@
             'pytest-cov'],
         'docs': [
             'sphinx',
-            'sphinx-gallery',
             'sphinx_rtd_theme',
             'numpydoc',
-            'matplotlib'
+            'm2r2',
+            'sphinxcontrib-napoleon'
         ]
     }
 )