From 30f3f96bdc51c2254d722c52e2e8c0e9a6796075 Mon Sep 17 00:00:00 2001
From: Israel Martinez <imc@umd.edu>
Date: Tue, 23 Jan 2024 11:07:15 -0500
Subject: [PATCH] Add mode module to docs API. Move COSILike init decription to
 the top so it can be find by sphinx

---
 cosipy/threeml/COSILike.py       | 51 ++++++++++++++++----------------
 docs/api/data_io.rst             | 11 +++++++
 docs/api/image_deconvolution.rst |  7 +++++
 docs/api/index.rst               |  3 ++
 docs/api/threeml.rst             | 10 +++++++
 5 files changed, 56 insertions(+), 26 deletions(-)
 create mode 100644 docs/api/data_io.rst
 create mode 100644 docs/api/image_deconvolution.rst
 create mode 100644 docs/api/threeml.rst

diff --git a/cosipy/threeml/COSILike.py b/cosipy/threeml/COSILike.py
index 7dd76541..4bc072e9 100644
--- a/cosipy/threeml/COSILike.py
+++ b/cosipy/threeml/COSILike.py
@@ -27,32 +27,31 @@
 logger = logging.getLogger(__name__)
 
 class COSILike(PluginPrototype):
-    
-    def __init__(self, name, dr, data, bkg, sc_orientation, nuisance_param=None, coordsys=None, **kwargs):
-        
-        """
-        COSI 3ML plugin
-        
-        Parameters
-        ----------
-        name : str
-            Plugin name e.g. "cosi". Needs to have a distinct name with respect to other plugins in the same analysis
-        dr : Path
-            Path to full detector response
-        data: histpy.Histogram
-            Binned data. Note: Eventually this should be a cosipy data class
-        bkg: histpy.Histogram
-            Binned background model. Note: Eventually this should be a cosipy data class
-        sc_orientation: cosipy.spacecraftfile.SpacecraftFile
-            Contains the information of the orientation: timestamps (astropy.Time) and attitudes (scoord.Attitude) that describe
-            the spacecraft for the duration of the data included in the analysis
-        nuisance_param: astromodels.core.parameter.Parameter
-            Background parameter (optional)
-        coordsys: str
-            Coordinate system ('galactic' or 'spacecraftframe') to perform fit in, which should match coordinate system of data 
-            and background. This only needs to be specified if the binned data and background do not have a coordinate system 
-            attached to them
-        """
+    """
+    COSI 3ML plugin
+
+    Parameters
+    ----------
+    name : str
+        Plugin name e.g. "cosi". Needs to have a distinct name with respect to other plugins in the same analysis
+    dr : Path
+        Path to full detector response
+    data: histpy.Histogram
+        Binned data. Note: Eventually this should be a cosipy data class
+    bkg: histpy.Histogram
+        Binned background model. Note: Eventually this should be a cosipy data class
+    sc_orientation: cosipy.spacecraftfile.SpacecraftFile
+        Contains the information of the orientation: timestamps (astropy.Time) and attitudes (scoord.Attitude) that describe
+        the spacecraft for the duration of the data included in the analysis
+    nuisance_param: astromodels.core.parameter.Parameter
+        Background parameter (optional)
+    coordsys: str
+        Coordinate system ('galactic' or 'spacecraftframe') to perform fit in, which should match coordinate system of data 
+        and background. This only needs to be specified if the binned data and background do not have a coordinate system 
+        attached to them
+    """
+
+    def __init__(self, name, dr, data, bkg, sc_orientation, nuisance_param=None, coordsys=None, **kwargs):        
         
         # create the hash for the nuisance parameters. We have none for now.
         self._nuisance_parameters = collections.OrderedDict()
diff --git a/docs/api/data_io.rst b/docs/api/data_io.rst
new file mode 100644
index 00000000..f613a242
--- /dev/null
+++ b/docs/api/data_io.rst
@@ -0,0 +1,11 @@
+Data IO
+=======
+
+Module
+------
+
+.. automodule:: cosipy.data_io
+   :imported-members:
+   :members:
+   :undoc-members:
+      
diff --git a/docs/api/image_deconvolution.rst b/docs/api/image_deconvolution.rst
new file mode 100644
index 00000000..b2c43491
--- /dev/null
+++ b/docs/api/image_deconvolution.rst
@@ -0,0 +1,7 @@
+Image deconvolution
+===================
+
+.. automodule:: cosipy.image_deconvolution
+   :imported-members:
+   :members:
+   :undoc-members:
diff --git a/docs/api/index.rst b/docs/api/index.rst
index bde41e45..a9d026e8 100644
--- a/docs/api/index.rst
+++ b/docs/api/index.rst
@@ -7,3 +7,6 @@ API
 
    response
    coordinates
+   data_io
+   threeml
+   image_deconvolution
diff --git a/docs/api/threeml.rst b/docs/api/threeml.rst
new file mode 100644
index 00000000..a2406af8
--- /dev/null
+++ b/docs/api/threeml.rst
@@ -0,0 +1,10 @@
+COSILike
+========
+
+ThreeML plugin
+
+.. automodule:: cosipy.threeml
+   :imported-members:
+   :members:
+   :undoc-members:
+