John Wise avatar John Wise committed 64215a9

Fixing some sphinx warnings

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doc/manual/source/developer_guide/DebuggingWithGDB.rst

 order, one command per line); let's call this file ``gdb.in``.  Then
 when you start ``mpirun``, you can specify this script to the GDB
 processes::
+
   18:16:32 [dreynolds@zeno ~]$  mpirun -np 4 xterm -e gdb -x gdb.in ./enzo.exe
 
 
 :ref:`MakeOptions`).
 
 Run Enzo
--------
+--------
 
 Now you're ready to run a test simulation.  This method works best when using
 only a few processors, so don't start a simulation with hundreds of processors

doc/manual/source/parameters/radiation.rst

+.. _radiation_backgrounds:
+
 Background Radiation Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

doc/manual/source/parameters/starform.rst

+.. _starparticleparameters:
+
 Star Formation and Feedback Parameters
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

doc/manual/source/parameters/streaming.rst

+.. _streaming_param:
+
 Streaming Data Format
 ~~~~~~~~~~~~~~~~~~~~~
 

doc/manual/source/tutorials/DataAnalysisBasics.rst

 Data Analysis Basics
 ====================
 
-Data analysis in Enzo can be complicated. There are excellent premade packages
-available for doing Enzo data analysis (see :ref:`SupportingCodes`.). However,
-it is likely that your data analysis needs will grow beyond these tools.
+Data analysis in Enzo can be complicated. There are excellent premade
+packages available for doing Enzo data analysis.  However, it is likely
+that your data analysis needs will grow beyond these tools.
 
 HDF5 Tools
 ----------

doc/manual/source/tutorials/WritingParameterFiles.rst

 Putting together a parameter file for Enzo is possibly the most
 critical step when setting up a simulation, and is certainly the step
 which is most fraught with peril. There are over 200 parameters that
-one can set - see :doc:`../parameters/index.rst` for a complete
+one can set - see :ref:`parameters` for a complete
 listing. For the most part, defaults are set to be sane values for
 cosmological simulations, and most physics packages are turned off by
 default, so that you have to explicitly turn on modules. All physics
 files for their first simulation and therefore is not intended to be
 an exhaustive list of parameters nor a complete description of each
 parameter mentioned. It would be wise to refer to the Enzo user
-guide's :doc:`../parameters/index.rst` for a more-or-less complete list of
+guide's :ref:`parameters` for a more-or-less complete list of
 AMR parameters, some of which may be extremely useful for your
 specific application.
 

doc/manual/source/user_guide/EnzoOutputFormat.rst

     This ascii file contains a complete listing of all the parameter
     settings, both those specified in the initial parameter file, as
     well as all those for which default values were assumed. The
-    parameters (see :doc:`../parameters/index.rst`) are in the same format
+    parameters (see :ref:`parameters`) are in the same format
     as that used in the input file: parameter_name = value. This file
     is modifiable if you would like to restart from a certain point
     with different parameter values.

doc/manual/source/user_guide/RunningEnzo.rst

 ascii, and can be edited.
 It consists of a series of lines (and optional comments) each of
 which specifies the value of one parameter. The parameters are
-discussed in more detail in :doc:`../parameters/index.rst`.
+discussed in more detail in :ref:`parameters`.
 
 If you just type ``enzo`` without any arguments, or if the number of
 arguments is incorrect, the program should respond with a summary

doc/manual/source/user_guide/index.rst

 and the various analysis tools bundled with Enzo. The instructions on
 actually running the code are not comprehensive in that they are not
 machine or platform-specific.  Arguably the most useful and important
-piece of this guide is :doc:`../parameters/index.rst`, which contains
+piece of this guide is :ref:`parameters`, which contains
 descriptions of all of the roughly 300 possible input parameters (as
 of September 2008). For more detailed information on the Enzo
 algorithms and on running Enzo on different platforms, you should
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