From 652a89cc9f972e88a593c7beebaff64ba6387533 Mon Sep 17 00:00:00 2001
From: Garry O'Donnell <garry.o'donnell@diamond.ac.uk>
Date: Tue, 12 Jul 2022 14:50:05 +0000
Subject: [PATCH] Add api reference to docs

---
 docs/conf.py           |  17 ++++++-
 docs/reference/api.rst | 101 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 117 insertions(+), 1 deletion(-)

diff --git a/docs/conf.py b/docs/conf.py
index 71ce2b23..18b94f38 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -3,11 +3,17 @@
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
 # https://www.sphinx-doc.org/en/main/usage/configuration.html
+from sphinx.domains.python import PythonDomain
 
 import adcorr
 
 # -- General configuration ------------------------------------------------
 
+# Workaround for NewType as autodata, to be removed when issue is resolved
+# see: https://github.com/sphinx-doc/sphinx/issues/9560
+assert PythonDomain.object_types["data"].roles == ("data", "obj")
+PythonDomain.object_types["data"].roles = ("data", "class", "obj")
+
 # General information about the project.
 project = "adcorr"
 
@@ -42,7 +48,16 @@
 # generating warnings in "nitpicky mode". Note that type should include the
 # domain name if present. Example entries would be ('py:func', 'int') or
 # ('envvar', 'LD_LIBRARY_PATH').
-nitpick_ignore = [("py:func", "int")]
+nitpick_ignore: list[tuple[str, str]] = [
+    ("py:class", "dtype"),
+    ("py:class", "floating"),
+    ("py:class", "ndarray"),
+    ("py:class", "numpy.bool_"),
+    ("py:class", "numpy.dtype"),
+    ("py:class", "numpy.floating"),
+    ("py:class", "numpy.ndarray"),
+    ("py:class", "numpy.ma.core.MaskedArray"),
+]
 
 # Both the class’ and the __init__ method’s docstring are concatenated and
 # inserted into the main body of the autoclass directive
diff --git a/docs/reference/api.rst b/docs/reference/api.rst
index 2093681e..c42adf08 100644
--- a/docs/reference/api.rst
+++ b/docs/reference/api.rst
@@ -6,6 +6,107 @@ API
     ``adcorr``
     ----------
 
+    .. automodule:: adcorr.utils
+        
+        ``adcorr.utils``
+        ----------------
+
+        .. automodule:: adcorr.utils.geometry
+            :members:
+
+            ``adcorr.utils.geometry``
+            -------------------------
+
+        .. automodule:: adcorr.utils.typing
+            :members:
+
+            ``adcorr.utils.typing``
+            -----------------------
+
+    .. automodule:: adcorr.angular_efficiency
+        :members:
+        
+        ``adcorr.angular_efficiency``
+        -----------------------------
+
+    .. automodule:: adcorr.background_subtraction
+        :members:
+
+        ``adcorr.background_subtraction``
+        ---------------------------------
+
+    .. automodule:: adcorr.dark_current
+        :members:
+
+        ``adcorr.dark_current``
+        -----------------------
+
+    .. automodule:: adcorr.deadtime
+        :members:
+
+        ``adcorr.deadtime``
+        -------------------
+
+    .. automodule:: adcorr.displaced_volume
+        :members:
+
+        ``adcorr.displaced_volume``
+        ---------------------------
+
+    .. automodule:: adcorr.flatfield
+        :members:
+
+        ``adcorr.flatfield``
+        --------------------
+
+    .. automodule:: adcorr.flux_and_transmission
+        :members:
+
+        ``adcorr.flux_and_transmission``
+        --------------------------------
+
+    .. automodule:: adcorr.frame_average
+        :members:
+
+        ``adcorr.frame_average``
+        ------------------------
+
+    .. automodule:: adcorr.frame_time
+        :members:
+
+        ``adcorr.frame_time``
+        ---------------------
+
+    .. automodule:: adcorr.masking
+        :members:
+
+        ``adcorr.masking``
+        ------------------
+
+    .. automodule:: adcorr.polarization
+        :members:
+
+        ``adcorr.polarization``
+        -----------------------
+
+    .. automodule:: adcorr.self_absorption
+        :members:
+
+        ``adcorr.self_absorption``
+        --------------------------
+
+    .. automodule:: adcorr.solid_angle
+        :members:
+
+        ``adcorr.solid_angle``
+        ----------------------
+
+    .. automodule:: adcorr.thickness
+        :members:
+
+        ``adcorr.thickness``
+        --------------------
+
 .. data:: adcorr.__version__
     :type: str