Update API reference listings (#105)

* Update API reference listings
* improve api page+some fixes
* update to pymc theme
* add pymc theme to requirements
* fix indent in docstring
---------

Co-authored-by: Oriol (ZBook) <[email protected]>

Author: ricardoV94

docs/_templates/autosummary/base.rst

@@ -0,0 +1,5 @@
+{{ objname | escape | underline }}
+
+.. currentmodule:: {{ module }}
+
+.. auto{{ objtype }}:: {{ objname }}

docs/_templates/autosummary/class.rst

@@ -0,0 +1,29 @@
+{{ objname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/api_reference.rst

@@ -4,23 +4,50 @@ API Reference
 This reference provides detailed documentation for all modules, classes, and
 methods in the current release of PyMC experimental.
 
+.. currentmodule:: pymc_experimental
+.. autosummary::
+   :toctree: generated/
 
-.. toctree::
-  :maxdepth: 2
+   marginal_model.MarginalModel
+   model_builder.ModelBuilder
 
+Inference
+=========
 
-:mod:`pymc_experimental.distributions`
-=============================
+.. currentmodule:: pymc_experimental.inference
+.. autosummary::
+   :toctree: generated/
 
-.. automodule:: pymc_experimental.distributions.histogram_utils
-   :members: histogram_approximation
+   fit
 
 
-:mod:`pymc_experimental.utils`
-=============================
+Distributions
+=============
 
-.. automodule:: pymc_experimental.utils.spline
-   :members: bspline_interpolation
+.. currentmodule:: pymc_experimental.distributions
+.. autosummary::
+   :toctree: generated/
 
-.. automodule:: pymc_experimental.utils.prior
-   :members: prior_from_idata
+   GenExtreme
+   histogram_utils.histogram_approximation
+
+
+Gaussian Processess
+===================
+
+.. currentmodule:: pymc_experimental.gp
+.. autosummary::
+   :toctree: generated/
+
+   latent_approx.HSGP
+
+
+Utils
+=====
+
+.. currentmodule:: pymc_experimental.utils
+.. autosummary::
+   :toctree: generated/
+
+   spline.bspline_interpolation
+   prior.prior_from_idata

docs/conf.py

@@ -56,16 +56,18 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     "sphinx.ext.mathjax",
     "nbsphinx",
+    "matplotlib.sphinxext.plot_directive",
 ]
 
 nbsphinx_execute = "never"
 
 # Add any paths that contain templates here, relative to this directory.
-# templates_path = ["_templates"]
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -81,7 +83,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+# language = None
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -97,7 +99,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "pydata_sphinx_theme"
+html_theme = "pymc_sphinx_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -110,14 +112,17 @@
     "show_toc_level": 2,
     "navigation_depth": 4,
     "search_bar_text": "Search the docs...",
-    "icon_links": [
-        {
-            "name": "GitHub",
-            "url": "https://github.com/pymc-devs/pymc-experimental",
-            "icon": "fab fa-github-square",
-        },
-    ],
+    "use_search_override": False,
+    "logo": {"text": project},
 }
+html_context = {
+    "github_user": "pymc-devs",
+    "github_repo": "pymc-experimental",
+    "github_version": "main",
+    "doc_path": "docs",
+    "default_mode": "light",
+}
+
 
 # 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,

docs/index.rst

@@ -38,16 +38,7 @@ Contributors
 ============
 See the `GitHub contributor page <https://github.com/pymc-devs/pymc-experimental/graphs/contributors>`_.
 
-Contents
-========
-
 .. toctree::
-   :maxdepth: 4
+   :hidden:
 
    api_reference
-
-Indices
-=======
-
-* :ref:`genindex`
-* :ref:`modindex`

pymc_experimental/distributions/continuous.py

@@ -60,7 +60,7 @@ def rng_fn(
 
 class GenExtreme(Continuous):
     r"""
-        Univariate Generalized Extreme Value log-likelihood
+    Univariate Generalized Extreme Value log-likelihood
 
     The cdf of this distribution is
 
@@ -119,13 +119,13 @@ class GenExtreme(Continuous):
 
     Parameters
     ----------
-    mu: float
+    mu : float
         Location parameter.
-    sigma: float
+    sigma : float
         Scale parameter (sigma > 0).
-    xi: float
+    xi : float
         Shape parameter
-    scipy: bool
+    scipy : bool
         Whether or not to use the Scipy interpretation of the shape parameter
         (defaults to `False`).
 

pymc_experimental/marginal_model.py

@@ -54,6 +54,7 @@ class MarginalModel(Model):
     Marginalize over a single variable
 
     .. code-block:: python
+
         import pymc as pm
         from pymc_experimental import MarginalModel
 

requirements-docs.txt

@@ -1,3 +1,4 @@
 nbsphinx>=0.4.2
 pydata-sphinx-theme>=0.6.3
 sphinx>=4
+git+https://github.com/pymc-devs/pymc-sphinx-theme