DOC: Documentation updates

doc/build-docs.bat

@@ -1,6 +1,6 @@
 @echo off
 rmdir /s /q build
-% del source\pphelper.rst
-% del source\modules.rst
-% sphinx-apidoc -f -o source ..\pphelper ..\pphelper\version.py ..\pphelper\tests
+REM del source\pphelper.rst
+REM del source\modules.rst
+REM sphinx-apidoc --no-toc -f -o source ..\pphelper ..\pphelper\version.py ..\pphelper\tests
 make html

doc/build-docs.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env sh
 
-rm -rf build source/pphelper.rst source/modules.rst
-# sphinx-apidoc -o source ../pphelper ../pphelper/version.py ../pphelper/tests
+# rm -rf build source/pphelper.rst source/modules.rst
+# sphinx-apidoc --no-toc -f -o source ../pphelper ../pphelper/version.py ../pphelper/tests
 make html

doc/source/about.rst

@@ -2,6 +2,7 @@ About pphelper
 ==============
 
 .. automodule:: pphelper
-    :members:
-    :undoc-members:
-    :inherited-members:
+    :no-members:
+    :no-undoc-members:
+    :no-inherited-members:
+    :no-show-inheritance:

doc/source/conf.py

@@ -63,13 +63,25 @@ def __getattr__(cls, name):
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
     # 'sphinx.ext.doctest',
     # 'sphinx.ext.todo',
     'sphinx.ext.viewcode',
     # 'numpydoc',
     'sphinxcontrib.napoleon',
 ]
 
+autodoc_default_flags = [
+    'members',
+    'undoc-members',
+    'inherited-members',
+    'show-inheritance'
+]
+
+# Also document __init__() methods.
+autoclass_content = 'both'
+autodoc_member_order = 'source'
+
 # Napoleon settings
 napoleon_include_special_with_doc = False
 
@@ -94,7 +106,7 @@ def __getattr__(cls, name):
 # built documents.
 #
 
-import pphelper
+# import pphelper
 # Ger version info.
 # This basically imports __version__ from version.py.
 exec(open('../../pphelper/version.py').read())

doc/source/hardware.rst

@@ -1,9 +1,23 @@
 The ``hardware`` Module
 =======================
+.. currentmodule:: pphelper.hardware
+.. autosummary::
+   :nosignatures:
 
-.. toctree::
-   :maxdepth: 1
+   Olfactometer
+   Gustometer
+   AnalogInput
 
-   olfactometer
-   analoginput
-   gustometer
+.. automodule:: pphelper.hardware
+
+Olfactometer
+------------
+.. autoclass:: pphelper.hardware.Olfactometer
+
+Gustometer
+----------
+.. autoclass:: pphelper.hardware.Gustometer
+
+AnalogInput
+-----------
+.. autoclass:: pphelper.hardware.AnalogInput

doc/source/image.rst

@@ -1,7 +1,11 @@
 The ``image`` Module
 ====================
 
+.. currentmodule:: pphelper.image
+.. autosummary::
+   :nosignatures:
+
+   fft_image
+   lowpass_filter_image
+
 .. automodule:: pphelper.image
-    :members:
-    :undoc-members:
-    :inherited-members:

doc/source/index.rst

@@ -6,12 +6,13 @@
 Welcome to pphelper's documentation!
 ====================================
 .. Contents:
+
 .. toctree::
    :maxdepth: 1
 
    about
+   hardware
    racemodel
    sdt
-   hardware
    image
    utils

doc/source/racemodel.rst

@@ -1,7 +1,14 @@
 The ``racemodel`` Module
 ========================
 
+.. currentmodule:: pphelper.racemodel
+.. autosummary::
+   :nosignatures:
+
+   gen_cdf
+   gen_cdfs_from_list
+   gen_percentiles
+   get_percentiles_from_cdf
+   gen_step_fun
+
 .. automodule:: pphelper.racemodel
-    :members:
-    :undoc-members:
-    :inherited-members:

doc/source/sdt.rst

@@ -1,7 +1,12 @@
-The ``utils`` Module
-====================
+The ``sdt`` Module
+==================
+
+.. currentmodule:: pphelper.sdt
+.. autosummary::
+   :nosignatures:
+
+   d_prime
+   a_prime
+   criterion
 
 .. automodule:: pphelper.sdt
-    :members:
-    :undoc-members:
-    :inherited-members:

doc/source/utils.rst

@@ -1,7 +1,10 @@
 The ``utils`` Module
 ====================
+.. currentmodule:: pphelper.utils
+.. autosummary::
+   :nosignatures:
+
+   add_zero_padding
+   get_max_from_list
 
 .. automodule:: pphelper.utils
-    :members:
-    :undoc-members:
-    :inherited-members:

pphelper/__init__.py

@@ -15,4 +15,4 @@
     print('Problem importing the hardware module, skipping.\n'
           'Please check if PyLibNIDAQmx is installed.')
 
-__all__ = ['racemodel', 'sdt', 'hardware', 'utils', 'image']
+__all__ = ['racemodel', 'hardware', 'image', 'sdt', 'utils']

pphelper/image.py

@@ -1,14 +1,7 @@
 # -*- coding: utf-8 -*-
 
 """
-pphelper.image
-==================
-
-Provides
---------
- - ``fft_image`` : Perform an FFT on the supplied image array.
- - ``lowpass_filter_image`` : Load an image from a file, and low-pass
-                              filter via a Gaussian kernel.
+Some basic image processing routines.
 
 """
 

pphelper/racemodel.py

@@ -6,14 +6,6 @@
 and computer programs', published in Behavior Research Methods 39 (2),
 pp. 291-302.
 
-Provides
---------
- - ``gen_cdf`` : Estimate the cumulative distribution function from response time data.
- - ``gen_cdfs_from_list`` : Convenience function: Applys ``gen_cdf`` to a list of data sets.
- - ``gen_percentiles`` : Calculate equally spaced percentiles values.
- - ``get_percentiles_from_cdf`` : Get the values (response times) of a cumulative distribution function at the specified percentiles.
- - ``gen_step_fun`` : Generate a step function from a set of observed response times.
-
 """
 
 from __future__ import division, unicode_literals

pphelper/sdt.py

@@ -1,13 +1,8 @@
 # -*- coding: utf-8 -*-
 
 """
-Some functions that come in handy when working with psychophysics
-datasets.
+Signal detection theory calculations.
 
-Provides
---------
- - ``d_prime`` : Calculate the sensitivity index d' ("d-prime").
- - ``criterion`` : Calculate the decision criterion C.
 """
 
 from __future__ import division, unicode_literals
@@ -17,7 +12,7 @@
 
 def d_prime(hits, false_alarms, n, nafc=1):
     """
-    Calculate the sensitivity index d' ("d-prime").
+    Calculate the sensitivity index d'.
 
     Parameters
     ----------

pphelper/utils.py

@@ -4,10 +4,6 @@
 Some functions that come in handy when working with psychophysics
 datasets.
 
-Provides
---------
- - ``add_zero_padding`` : Convert numbers (typically participant IDs) to strings of specific length, with leading zeros where necessary.
- - ``get_max_from_list`` : Return the maximum value from a list or a list of lists.
 """
 
 from __future__ import division, unicode_literals