fixup for how-to

doc/lsst.synpipe/index.rst

@@ -16,7 +16,7 @@ Using lsst.synpipe
 .. toctree::
    :maxdepth: 1
 
-   Synpipe_QuickStart.rst
+   quick-start.rst
 
 Python API reference
 ====================

doc/lsst.synpipe/Synpipe_QuickStart.rst → doc/lsst.synpipe/quick-start.rst

@@ -2,8 +2,8 @@
 Synpipe Quick Start Guide
 #########################
 
-Synpipe is a tool in the LSST software stack that is used to insert fake objects
-into data that is to be processed with the sofware stack. Though Synpipe is not
+Synpipe is a tool in the LSST Science Pipelines that is used to insert fake objects
+into data that is to be processed. Though Synpipe is not
 the only way to insert fake objects into the stack, anyone can create a custom
 fake object tasks, it provides a quick and convenient method for the most common
 use cases. This document aims to make a user able to start using Synpipe in the
@@ -14,11 +14,11 @@ An important note is that this tool was initially created for the HSC survey,
 and although the LSST stack supports many different cameras, at this point Synpipe
 is currently limited to working with HSC data repositories.
 
-This guide will assume processing will be done though the pipe_drivers scripts.
+This guide will assume processing will be done though the ``pipe_drivers`` scripts.
 All the information is generally applicable, but configuration paths will change
 relative to what task is run in place of pipe_driver tasks.
 
-Generating A Catlaog
+Generating A Catalog
 ====================
 
 For many of the fake object insertion tasks it is necessary to pre-generate a
@@ -28,11 +28,11 @@ sky such that they are inserted in the same place consistently in each input
 frame.
 
 Generating an input catalog for both stars and galaxies are done with the
-`makeSourceList.py` command, but differ on some of the inputs. For either type
-of fake object `makeSourceList.py` takes an input repository as its first
-positional argument and the switch `--id` which is used to specify the data from
+``makeSourceList.py`` command, but differ on some of the inputs. For either type
+of fake object ``makeSourceList.py`` takes an input repository as its first
+positional argument and the switch ``--id`` which is used to specify the data from
 which spatial (in ra, dec) coordinates will be generated. All of the coordinates
-generated will lie inside the bonding box defined by `--id`, and thus it is most
+generated will lie inside the bonding box defined by ``--id``, and thus it is most
 common to use the tract of a coaddition as the id argument. If fake objects are
 to be inserted and measured such that single frame processing is the last step,
 a single frame id may be used, but a different input catalog will need to be
@@ -43,32 +43,32 @@ numbers of objects to ensure the desired density.
 
 Additional configuration for this script is done using the standard LSST
 configuration procedure. Configurations can either be specified on the
-command-line using `-c` or with a config file. The nuances of this system are
+command-line using ``-c`` or with a config file. The nuances of this system are
 left to another LSST guide on configurations. This guide will assume everything
-is to be entered on the command line behind a `-c` switch for each configuration.
+is to be entered on the command line behind a ``-c`` switch for each configuration.
 There are many configurations available to control the scripts behavior, but
 this guide will highlight the most commonly used.  A full list along with
 descriptions can be found within the script.
 Listed below are all the configurations that may be set:
 
-- rhoFakes : Number of fakes per patch in the specified tract. Defaults to 500
+- rhoFakes : Number of fakes per patch in the specified tract. Defaults to 500.
 - inputCatalog : Catalog from which to draw input magnitudes, see below for appropriate settings for stars vs. galaxies
 - outDir : Specify the file-system path that the output will be saved in
 
 This script will not create the outDir if it does not already exist, the user
 must create the output directory prior to running this script.
 
 As this script is based on the LSST command line task, there is currently a quirk
-where and output must be specified with either `--output` or `--rerun`, but this
+where and output must be specified with either ``--output`` or ``--rerun``, but this
 directory is not really used for anything. This may change in a future version
 but for now the output must be specified, but can safely be removed after.
 
-A final caveat for using this command is that a valid `skymap` must already exist in the
-input repo. This is different to the normal usage of `pipe_drivers` where the `skymap`
+A final caveat for using this command is that a valid ``skymap`` must already exist in the
+input repo. This is different to the normal usage of ``pipe_drivers`` where the ``skymap``
 is created just prior to making coadds. It should not be a problem to use the 
-`makeSkyMap.py` command prior to building the fake object catalog. Using the
-`makeDiscreteSkyMap.py` may be problematic if the input ids are not know. The reason a
-`skymap` is needed in the input is due to the way synpipe looks up the ranges of RA and
+``makeSkyMap.py`` command prior to building the fake object catalog. Using the
+``makeDiscreteSkyMap.py`` may be problematic if the input ids are not know. The reason a
+``skymap`` is needed in the input is due to the way synpipe looks up the ranges of RA and
 Dec which form a tract and patch. These ranges are used when selecting the positions 
 where fake objects should be inserted.
 
@@ -187,10 +187,10 @@ The runMatchFakes.py script can be used to extract fake sources from a
 measurement catalog, and place them into their own catalog. This script takes
 the input data repository where the measurement catalog resides as its
 first positional argument, and the visit or tract number as the second. If a
-tract number is specified, the `-f` switch **must** be used to specify the desired
+tract number is specified, the ``-f`` switch **must** be used to specify the desired
 filter. To complete a repository dataid, the --ccd options is used to specify
 the ccd number or patch id. The location the output will be written to is given
-by the `-o` switch. The catalog of fakes to match against is specified with the
+by the ``-o`` switch. The catalog of fakes to match against is specified with the
 -c switch. These are the most commonly used options in extracting fake objects,
 but there are other switches available which control additional parameters of
 the matching which can be found within the runMatchFakes script. An example