update documentation and fix autodocs

3 files changed, 53 insertions, 13 deletions

diff --git a/docs/cls_gensvm.rst b/docs/cls_gensvm.rst
index 4e67631..fc19bf4 100644
--- a/docs/cls_gensvm.rst
+++ b/docs/cls_gensvm.rst
@@ -26,16 +26,19 @@
                   'linear', 'poly', 'rbf', or 'sigmoid'.
    :type kernel: string, optional (default='linear')
    :param gamma: Kernel parameter for the rbf, poly, and sigmoid kernel. If gamma is
-                 'auto' then 1/n_features will be used.
+                 'auto' then 1/n_features will be used. See `Kernels in GenSVM
+                 <gensvm_kernels_>`_ for the exact implementation of the kernels.
    :type gamma: float, optional (default='auto')
-   :param coef: Kernel parameter for the poly and sigmoid kernel
+   :param coef: Kernel parameter for the poly and sigmoid kernel. See `Kernels in
+                GenSVM <gensvm_kernels_>`_ for the exact implementation of the kernels.
    :type coef: float, optional (default=0.0)
-   :param degree: Kernel parameter for the poly kernel
+   :param degree: Kernel parameter for the poly kernel. See `Kernels in GenSVM
+                  <gensvm_kernels_>`_ for the exact implementation of the kernels.
    :type degree: float, optional (default=2.0)
-   :param kernel_eigen_cutoff: Cutoff point for the reduced eigendecomposition used with
-                               kernel-GenSVM. Eigenvectors for which the ratio between their
-                               corresponding eigenvalue and the largest eigenvalue is smaller than the
-                               cutoff will be dropped.
+   :param kernel_eigen_cutoff: Cutoff point for the reduced eigendecomposition used with nonlinear
+                               GenSVM.  Eigenvectors for which the ratio between their corresponding
+                               eigenvalue and the largest eigenvalue is smaller than the cutoff will
+                               be dropped.
    :type kernel_eigen_cutoff: float, optional (default=1e-8)
    :param verbose: Enable verbose output
    :type verbose: int, (default=0)
@@ -67,6 +70,10 @@
       :class:`.GenSVMGridSearchCV`
           Helper class to run an efficient grid search for GenSVM.
    
+   .. _gensvm_kernels:
+       https://gensvm.readthedocs.io/en/latest/#kernels-in-gensvm
+   
+   
    
    .. py:method:: GenSVM.fit(X, y, seed_V=None)
       :noindex:
diff --git a/docs/generate_autodocs.py b/docs/generate_autodocs.py
index 6138287..b2c9fb6 100644
--- a/docs/generate_autodocs.py
+++ b/docs/generate_autodocs.py
@@ -15,7 +15,8 @@ import os
 
 from docutils.statemachine import StringList, ViewList
 
-from sphinx.ext.autodoc import AutoDirective, ClassDocumenter, Options
+from sphinx.ext.autodoc import (AutoDirective, ClassDocumenter, Options, 
+        FunctionDocumenter)
 from sphinx.application import Sphinx
 from sphinx.environment import BuildEnvironment
 
@@ -27,14 +28,20 @@ CLASSES = [
         'GenSVM'
         ]
 
+FUNCTIONS = [
+        'load_default_grid'
+        ]
+
 FULL_NAMES = {
         'GenSVM': 'gensvm.core.GenSVM',
-        'GenSVMGridSearchCV': 'gensvm.gridsearch.GenSVMGridSearchCV'
+        'GenSVMGridSearchCV': 'gensvm.gridsearch.GenSVMGridSearchCV',
+        'load_default_grid': 'gensvm.gridsearch.load_default_grid'
         }
 
 OUTPUT_FILES = {
         'GenSVMGridSearchCV': os.path.join(DOCDIR, 'cls_gridsearch.rst'),
-        'GenSVM': os.path.join(DOCDIR, 'cls_gensvm.rst')
+        'GenSVM': os.path.join(DOCDIR, 'cls_gensvm.rst'),
+        'load_default_grid': os.path.join(DOCDIR, 'auto_functions.rst')
         }
 
 
@@ -49,7 +56,7 @@ def load_app():
     return app
 
 
-def generate_autodoc(app, cls):
+def generate_class_autodoc(app, cls):
     ad = AutoDirective(name='autoclass', arguments=[FULL_NAMES[cls]], 
             options={'noindex': True}, content=StringList([], items=[]), 
             lineno=0, content_offset=1, block_text='', state=None, 
@@ -67,10 +74,36 @@ def generate_autodoc(app, cls):
         for line in ad.result:
             fid.write(line + '\n')
 
+
+def generate_func_autodoc(app, func):
+    ad = AutoDirective(name='autofunc', arguments=[FULL_NAMES[func]], 
+            options={'noindex': True}, content=StringList([], items=[]), 
+            lineno=0, content_offset=1, block_text='', state=None, 
+            state_machine=None)
+
+    ad.env = BuildEnvironment(app)
+    ad.genopt = Options(noindex=True)
+    ad.filename_set = set()
+    ad.result = ViewList()
+
+    documenter = FunctionDocumenter(ad, ad.arguments[0])
+    documenter.generate(all_members=True)
+
+    with open(OUTPUT_FILES[func], 'a') as fid:
+        for line in ad.result:
+            fid.write(line + '\n')
+
+
 def main():
+    for of in OUTPUT_FILES:
+        fname = OUTPUT_FILES[of]
+        os.unlink(fname)
     app = load_app()
     for cls in CLASSES:
-        generate_autodoc(app, cls)
+        generate_class_autodoc(app, cls)
+    for func in FUNCTIONS:
+        generate_func_autodoc(app, func)
+
 
 if __name__ == '__main__':
     main()
diff --git a/docs/index.rst b/docs/index.rst
index 6064b56..403dc8b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -23,7 +23,7 @@ GenSVMGridSearchCV
 Functions
 ---------
 
-.. autofunction:: gensvm.gridsearch.load_default_grid
+.. include:: ./auto_functions.rst
 
 .. include:: ./kernels.rst