updated documentation for 1.0.0 release

rishi-kulkarni · Jun 5, 2021 · 7380088 · 7380088
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diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 ## A Hierarchical Resampling Package for Python
 
-Version 0.4
+Version 1.0
 
 hierarch is a package for hierarchical resampling (bootstrapping, permutation) of datasets in Python. Because for loops are ultimately intrinsic to cluster-aware resampling, hierarch uses Numba to accelerate many of its key functions.
 

diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst
@@ -0,0 +1,33 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+   :special-members: __call__, __add__, __mul__
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      {%- if not item.startswith('_') %}
+      ~{{ name }}.{{ item }}
+      {%- endif -%}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
diff --git a/docs/_templates/custom-module-template.rst b/docs/_templates/custom-module-template.rst
@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}
diff --git a/docs/conf.py b/docs/conf.py
@@ -33,7 +33,15 @@
 # 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_rtd_theme", "numpydoc", "sphinx.ext.autodoc"]
+extensions = [
+    "sphinx_rtd_theme",
+    "numpydoc",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+]
+
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
+numpydoc_show_class_members = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

diff --git a/docs/reference/_autosummary/hierarch.power.DataSimulator.rst b/docs/reference/_autosummary/hierarch.power.DataSimulator.rst
@@ -0,0 +1,25 @@
+hierarch.power.DataSimulator
+============================
+
+.. currentmodule:: hierarch.power
+
+.. autoclass:: DataSimulator
+   :members:
+   :show-inheritance:
+   :inherited-members:
+   :special-members: __call__, __add__, __mul__
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~DataSimulator.fit
+      ~DataSimulator.generate
+
+
+
+
+
+
diff --git a/docs/reference/_autosummary/hierarch.power.rst b/docs/reference/_autosummary/hierarch.power.rst
@@ -0,0 +1,32 @@
+hierarch.power
+==============
+
+.. automodule:: hierarch.power
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+
+      DataSimulator
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/_autosummary/hierarch.resampling.Bootstrapper.rst b/docs/reference/_autosummary/hierarch.resampling.Bootstrapper.rst
@@ -0,0 +1,25 @@
+hierarch.resampling.Bootstrapper
+================================
+
+.. currentmodule:: hierarch.resampling
+
+.. autoclass:: Bootstrapper
+   :members:
+   :show-inheritance:
+   :inherited-members:
+   :special-members: __call__, __add__, __mul__
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~Bootstrapper.fit
+      ~Bootstrapper.transform
+
+
+
+
+
+
diff --git a/docs/reference/_autosummary/hierarch.resampling.Permuter.rst b/docs/reference/_autosummary/hierarch.resampling.Permuter.rst
@@ -0,0 +1,25 @@
+hierarch.resampling.Permuter
+============================
+
+.. currentmodule:: hierarch.resampling
+
+.. autoclass:: Permuter
+   :members:
+   :show-inheritance:
+   :inherited-members:
+   :special-members: __call__, __add__, __mul__
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~Permuter.fit
+      ~Permuter.transform
+
+
+
+
+
+
diff --git a/docs/reference/_autosummary/hierarch.resampling.rst b/docs/reference/_autosummary/hierarch.resampling.rst
@@ -0,0 +1,33 @@
+hierarch.resampling
+===================
+
+.. automodule:: hierarch.resampling
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+      :nosignatures:
+
+      Bootstrapper
+      Permuter
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/_autosummary/hierarch.stats.confidence_interval.rst b/docs/reference/_autosummary/hierarch.stats.confidence_interval.rst
@@ -0,0 +1,6 @@
+hierarch.stats.confidence\_interval
+===================================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: confidence_interval
diff --git a/docs/reference/_autosummary/hierarch.stats.linear_regression_test.rst b/docs/reference/_autosummary/hierarch.stats.linear_regression_test.rst
@@ -0,0 +1,6 @@
+hierarch.stats.linear\_regression\_test
+=======================================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: linear_regression_test
diff --git a/docs/reference/_autosummary/hierarch.stats.multi_sample_test.rst b/docs/reference/_autosummary/hierarch.stats.multi_sample_test.rst
@@ -0,0 +1,6 @@
+hierarch.stats.multi\_sample\_test
+==================================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: multi_sample_test
diff --git a/docs/reference/_autosummary/hierarch.stats.preprocess_data.rst b/docs/reference/_autosummary/hierarch.stats.preprocess_data.rst
@@ -0,0 +1,6 @@
+hierarch.stats.preprocess\_data
+===============================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: preprocess_data
diff --git a/docs/reference/_autosummary/hierarch.stats.rst b/docs/reference/_autosummary/hierarch.stats.rst
@@ -0,0 +1,37 @@
+hierarch.stats
+==============
+
+.. automodule:: hierarch.stats
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+      :toctree:
+      :nosignatures:
+
+      confidence_interval
+      linear_regression_test
+      multi_sample_test
+      preprocess_data
+      studentized_covariance
+      two_sample_test
+      welch_statistic
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/_autosummary/hierarch.stats.studentized_covariance.rst b/docs/reference/_autosummary/hierarch.stats.studentized_covariance.rst
@@ -0,0 +1,6 @@
+hierarch.stats.studentized\_covariance
+======================================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: studentized_covariance
diff --git a/docs/reference/_autosummary/hierarch.stats.two_sample_test.rst b/docs/reference/_autosummary/hierarch.stats.two_sample_test.rst
@@ -0,0 +1,6 @@
+hierarch.stats.two\_sample\_test
+================================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: two_sample_test
diff --git a/docs/reference/_autosummary/hierarch.stats.welch_statistic.rst b/docs/reference/_autosummary/hierarch.stats.welch_statistic.rst
@@ -0,0 +1,6 @@
+hierarch.stats.welch\_statistic
+===============================
+
+.. currentmodule:: hierarch.stats
+
+.. autofunction:: welch_statistic
diff --git a/docs/reference/index.rst b/docs/reference/index.rst
@@ -1,8 +1,11 @@
 Reference 
 =========
 
-.. toctree::
-
-    stats.rst
-    power.rst
-    resampling.rst
+.. autosummary::
+    :toctree: _autosummary
+    :template: custom-module-template.rst
+    :recursive:
+
+    hierarch.stats
+    hierarch.power
+    hierarch.resampling
diff --git a/docs/reference/power.rst b/docs/reference/power.rst