Merge pull request #54 from lukashergt/docs_autodoc

make full use of autodoc such that cross referencing can find all targets

docs/Makefile

@@ -3,9 +3,9 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SOURCEDIR     = source
 BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".

docs/source/conf.py

@@ -48,6 +48,7 @@ def get_version(short=False):
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
@@ -63,12 +64,16 @@ def get_version(short=False):
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 source_suffix = '.rst'
-master_doc='index'
+master_doc = 'index'
 
 # 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 = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = []
+
+autosummary_generate = True
+
+numpydoc_class_members_toctree = False
 
 
 # -- Options for HTML output -------------------------------------------------

docs/source/functions.rst

@@ -4,27 +4,18 @@
 margarine Functions
 --------------------
 
-margarine.maf.MAF()
-~~~~~~~~~~~~~~~~~~~~
+.. automodule:: margarine.maf
+    :members:
+    :special-members: __call__
 
-.. automodule:: margarine.maf.MAF()
-    :members: gen_mades, train, _train_step, _test_step, _training, __call__, sample, log_prob, log_like, save, load
+.. automodule:: margarine.kde
+    :members:
+    :special-members: __call__
 
-margarine.kde.KDE()
-~~~~~~~~~~~~~~~~~~~~
+.. automodule:: margarine.clustered
+    :members:
+    :special-members: __call__
 
-.. automodule:: margarine.kde.KDE()
-    :members: generate_kde, __call__, sample, log_prob, log_like, save, load
-
-margarine.clustered.clusterMAF()
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. automodule:: margarine.clustered.clusterMAF()
-    :members: train, __call__, sample, log_prob, log_like, save, load
-
-margarine.marginal_stats.calculate()
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-.. automodule:: margarine.marginal_stats.calculate
-    :members: statistics
+.. automodule:: margarine.marginal_stats
+    :members:
 

margarine/kde.py

@@ -45,6 +45,7 @@ class KDE(object):
             | A list of the relevant parameters to train on. Only needed
                 if theta is an anestehetic samples object. If not provided,
                 all parameters will be used.
+
     **Attributes:**
 
     A list of some key attributes accessible to the user.

margarine/marginal_stats.py

@@ -212,8 +212,8 @@ def integrate(
                   The definition of zero for the loglikelihood function.
 
         returns:
-        stats: **dict**
-            | Dictionary containing useful statistics
+            stats: **dict**
+                | Dictionary containing useful statistics
 
         """
         xs = np.empty((sample_size, self.de.theta.shape[-1]))