DM-15872: Incorporate AP documentation into pipelines.lsst.io

doc/index.rst

@@ -9,5 +9,4 @@ ap_association documentation preview
 .. toctree::
    :maxdepth: 1
 
-   ap_association/index
    lsst.ap.association/index

doc/lsst.ap.association/index.rst

@@ -1,15 +1,38 @@
+.. py:currentmodule:: lsst.ap.association
+
 .. _lsst.ap.association:
 
 ###################
 lsst.ap.association
 ###################
 
-.. Paragraph that describes what this Python module does and links to related modules and frameworks.
+The ``ap_association`` package provides tools for associating DIAObjects to DIASources, persisting this association, and computing DIAObject summary statistics.
+
+.. .. _lsst.ap.association-using:
+
+.. Using lsst.ap.association
+.. =========================
+
+.. toctree linking to topics related to using the module's APIs.
+
+.. .. toctree::
+..    :maxdepth: 1
+
+.. _lsst.ap.association-contributing:
+
+Contributing
+============
+
+``lsst.ap.association`` is developed at https://github.com/lsst/ap_association.
+You can find Jira issues for this module under the `ap_association <https://jira.lsstcorp.org/issues/?jql=project%20%3D%20DM%20AND%20component%20%3D%20ap_association>`_ component.
+
+.. If there are topics related to developing this module (rather than using it), link to this from a toctree placed here.
 
-.. Add subsections with toctree to individual topic pages.
+.. _lsst.ap.association-pyapi:
 
 Python API reference
 ====================
 
-.. automodapi:: lsst.ap.association.association
-.. automodapi:: lsst.ap.association.dia_object
+.. automodapi:: lsst.ap.association
+   :no-main-docstr:
+   :no-inheritance-diagram:

doc/manifest.yaml

@@ -1,15 +1,12 @@
 # Documentation manifest.
 
-# Name of this package
-# Also the name of the package documentation subdirectory.
-package: "ap_association"
-
 # List of names of Python modules in this package.
 # For each module there is a corresponding module doc subdirectory.
 modules:
   - "lsst.ap.association"
 
 # Name of the static content directories (subdirectories of `_static`).
 # Static content directories are usually named after the package.
-statics:
-  - "_static/ap_association"
+# Most packages do not need a static content directory (leave commented out).
+# statics:
+#   - "_static/ap_association"

python/lsst/ap/association/afwUtils.py

@@ -43,11 +43,11 @@ def make_minimal_dia_object_schema(filter_names=None):
 
     Parameters
     ----------
-    filter_names : `list` of `str`s
+    filter_names : `list` of `str`
         Names of the filters expect and compute means for.
 
-    Return
-    ------
+    Returns
+    -------
     schema : `lsst.afw.table.Schema`
         Minimal schema for DIAObjects.
     """
@@ -79,8 +79,8 @@ def make_minimal_dia_object_schema(filter_names=None):
 def make_minimal_dia_source_schema():
     """ Define and create the minimal schema required for a DIASource.
 
-    Return
-    ------
+    Returns
+    -------
     schema : `lsst.afw.table.Schema`
         Minimal schema for DIAObjects.
     """
@@ -111,9 +111,9 @@ def make_minimal_dia_source_schema():
 def getCcdVisitSchemaSql():
     """Define the schema for the CcdVisit table.
 
-    Return
-    ------
-    ccdVisitNames: `collections.OrderedDict`
+    Returns
+    -------
+    ccdVisitNames : `collections.OrderedDict`
        Names of columns in the ccdVisit table.
     """
     return oDict([("ccdVisitId", "INTEGER PRIMARY KEY"),
@@ -132,8 +132,8 @@ def get_ccd_visit_info_from_exposure(exposure):
     """
     Extract info on the ccd and visit from the exposure.
 
-    Paramters
-    ---------
+    Parameters
+    ----------
     exposure : `lsst.afw.image.Exposure`
         Exposure to store information from.
 
@@ -205,7 +205,7 @@ def convert_dia_source_to_asssoc_schema(dia_sources,
     ----------
     dia_sources : `lsst.afw.table.SourceCatalog`
         Input source catalog to alias and overwrite values of.
-    obj_ids:  array-like of `int`
+    obj_ids :  array-like of `int`
         DIAObject ids to associate with the input DIASources. Overwrites
         the current value in diaObjectId column. If None the obj_id no action
         is taken. The array should be the same length as dia_sources.

python/lsst/ap/association/assoc_db_sqlite.py

@@ -299,7 +299,7 @@ def load_dia_sources(self, dia_obj_ids):
 
         Parameters
         ----------
-        dia_obj_ids : array-like of `int`s
+        dia_obj_ids : array-like of `int`
             Id of the DIAObject that is associated with the DIASources
             of interest.
 
@@ -375,7 +375,7 @@ def store_dia_sources(self,
         ----------
         dia_sources : `lsst.afw.table.SourceCatalog`
             Catalog of DIASources to store.
-        associated_ids : array-like of `int`s (optional)
+        associated_ids : array-like of `int` (optional)
             DIAObject ids that have been associated with these DIASources
         exposure : `lsst.afw.image.Exposure`
             Exposure object the DIASources were detected in.
@@ -388,8 +388,8 @@ def store_dia_sources(self,
     def store_ccd_visit_info(self, exposure):
         """Store information describing the exposure for this ccd, visit.
 
-        Paramters
-        ---------
+        Parameters
+        ----------
         exposure : `lsst.afw.image.Exposure`
             Exposure to store information from.
         """
@@ -410,7 +410,7 @@ def _get_dia_object_catalog(self, indexer_indices, bbox, wcs):
 
         Parameters
         ----------
-        indexer_indices : array-like of `int`s
+        indexer_indices : array-like of `int`
             Pixelized indexer indices from which to load.
         bbox : `lsst.geom.Box2D`
             Bounding box of exposure.
@@ -442,7 +442,7 @@ def _query_dia_objects(self, indexer_indices):
 
         Parameters
         ----------
-        indexer_indices : array-like of `int`s
+        indexer_indices : array-like of `int`
             Spatial indices in the indexer specifying the area on the sky
             to load DIAObjects for.
 
@@ -500,7 +500,7 @@ def _query_dia_sources(self, dia_object_ids):
 
         Parameters
         ----------
-        dia_object_ids : array-like of `int`s
+        dia_object_ids : array-like of `int`
             Spatial indices in the indexer specifying the area on the sky
             to load DIAObjects for.
 
@@ -541,7 +541,7 @@ def _store_catalog(self, source_catalog, converter, obj_ids=None, exposure=None)
         converter : `lsst.ap.association.SqliteDBConverter`
             A converter object specifying the correct database table to write
             into.
-        obj_id : array-like of `int`s (optional)
+        obj_id : array-like of `int` (optional)
             Ids of the DIAObjects these objects are associated with. Use only
             when storing DIASources.
         exposure : `lsst.afw.image.Exposure` (optional)

python/lsst/ap/association/association.py

@@ -161,7 +161,7 @@ def associate_sources(self, dia_objects, dia_sources):
 
         Returns
         -------
-        updated_ids: array-like of `int`s
+        updated_ids : array-like of `int`
             Ids of the DIAObjects that the DIASources associated to including
             the ids of newly created DIAObjects.
         """
@@ -185,7 +185,7 @@ def update_dia_objects(self, dia_objects, updated_obj_ids, exposure):
         dia_objects : `lsst.afw.table.SourceCatalog`
             Pre-existing/loaded DIAObjects to copy values that are not updated
             from.
-        updated_obj_ids : array-like of `int`s
+        updated_obj_ids : array-like of `int`
             Ids of the dia_objects that should be updated.
         exposure : `lsst.afw.image.Exposure`
             Input exposure representing the region of the sky the dia_sources
@@ -254,11 +254,12 @@ def score(self, dia_objects, dia_sources, max_dist):
             Results struct with components:
 
             - ``scores``: array of floats of match quality updated DIAObjects
-                (array-like of `float`s).
+                (array-like of `float`).
             - ``obj_idxs``: indexes of the matched DIAObjects in the catalog.
-                (array-like of `int`s)
+                (array-like of `int`)
             - ``obj_ids``: array of floats of match quality updated DIAObjects
-                (array-like of `int`s).
+                (array-like of `int`).
+
             Default values for these arrays are
             INF, -1, and -1 respectively for unassociated sources.
         """
@@ -328,11 +329,12 @@ def match(self, dia_objects, dia_sources, score_struct):
             Results struct with components:
 
             - ``scores``: array of floats of match quality
-                updated DIAObjects (array-like of `float`s).
+                updated DIAObjects (array-like of `float`).
             - ``obj_ids``: array of floats of match quality
-                updated DIAObjects (array-like of `ints`s).
+                updated DIAObjects (array-like of `int`).
             - ``obj_idxs``: indexes of the matched DIAObjects in the catalog.
-                (array-like of `int`s)
+                (array-like of `int`)
+
             Default values for these arrays are
             INF, -1 and -1 respectively for unassociated sources.
 
@@ -342,7 +344,7 @@ def match(self, dia_objects, dia_sources, score_struct):
             Results struct with components:
 
             - ``updated_and_new_dia_object_ids`` : ids of new and updated
-              dia_objects as the result of association. (`list` of `int`s).
+              dia_objects as the result of association. (`list` of `int`).
             - ``n_updated_dia_objects`` : Number of previously know dia_objects
               with newly associated DIASources. (`int`).
             - ``n_new_dia_objects`` : Number of newly created DIAObjects from
@@ -406,7 +408,7 @@ def _add_association_meta_data(self, match_result):
             Results struct with components:
 
             - ``updated_and_new_dia_object_ids`` : ids new and updated
-              dia_objects in the collection (`list` of `int`s).
+              dia_objects in the collection (`list` of `int`).
             - ``n_updated_dia_objects`` : Number of previously know dia_objects
               with newly associated DIASources. (`int`).
             - ``n_new_dia_objects`` : Number of newly created DIAObjects from

python/lsst/ap/association/l1dbproto.py

@@ -188,7 +188,7 @@ def load_dia_sources(self, dia_obj_ids):
 
         Parameters
         ----------
-        dia_obj_ids : array-like of `int`s
+        dia_obj_ids : array-like of `int`
             Id of the DIAObject that is associated with the DIASources
             of interest.
 
@@ -215,7 +215,7 @@ def store_dia_objects(self,
         compute_spatial_index : `bool`
             If True, compute the spatial search indices using the
             indexer specified at class instantiation.
-        exposure: `lsst.afw.image.Exposure` (optional)
+        exposure : `lsst.afw.image.Exposure` (optional)
             CcdExposure associated with these DIAObjects being inserted.
             Inserts the CcdVisitInfo for this exposure in the CcdVisitTable.
         """
@@ -254,7 +254,7 @@ def store_dia_sources(self,
         ----------
         dia_sources : `lsst.afw.table.SourceCatalog`
             Catalog of DIASources to store.
-        associated_ids : array-like of `int`s (optional)
+        associated_ids : array-like of `int` (optional)
             DIAObject ids that have been associated with these DIASources
         exposure : `lsst.afw.image.Exposure`
             Exposure object the DIASources were detected in.