Merge pull request #155 from ketch/clean_up_toctrees

Clean up toctrees

doc/amrclaw.rst

@@ -31,4 +31,14 @@ Python plotting tools for 3d are still under development.  For now, the
 Matlab tools from Clawpack 4.3 can still be used, see
 :ref:`matlabplots`.
 
+.. toctree::
+   :maxdepth: 2
+
+   amrclaw1d
+   setrun_amrclaw
+   setrun_amrclaw_sample
+   amr_algorithm
+   refinement
+   gauges
+
 

doc/b4step_defaults.rst

@@ -1,3 +1,4 @@
+:orphan:
 
 .. _b4step_defaults:
 

doc/changes_to_master.rst

@@ -1,3 +1,4 @@
+:orphan:
 
 .. _changes_to_master:
 

doc/claw4x.rst

@@ -1,3 +1,4 @@
+:orphan:
 
 .. _claw4x:
 

doc/clawpack5.rst

@@ -1,3 +1,5 @@
+:orphan:
+
 .. _clawpack5:
 
 

doc/contents.rst

@@ -11,7 +11,7 @@ Overview and Getting Started
 ============================
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    about
    changes
@@ -22,6 +22,7 @@ Overview and Getting Started
    setenv
    first_run
    clawpack_components
+   wp_algorithms
    trouble
 
 .. toctree::
@@ -32,19 +33,15 @@ Overview and Getting Started
    aws
 
 
-
 Examples and Applications
 ============================
 
 .. toctree::
    :maxdepth: 1
 
-
    galleries
    apps
    fvmbook
-   newapp
-   sharing
    contribute_apps
    testing
    sphinxdoc
@@ -54,9 +51,12 @@ Classic, AMRClaw, and GeoClaw
 
 Using the Fortran codes
 -------------------------
+General information that applies to Classic, AMRClaw, and GeoClaw.
+
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
+   first_run_fortran
    fortran
    fortran_compilers
    f77_vs_f90
@@ -74,6 +74,8 @@ Using the Fortran codes
    output_styles
    mapc2p
    restart
+   newapp
+   sharing
 
 AMRClaw: adaptive mesh refinement
 ---------------------------------
@@ -82,11 +84,6 @@ AMRClaw: adaptive mesh refinement
    :maxdepth: 2
 
    amrclaw
-   setrun_amrclaw
-   setrun_amrclaw_sample
-   amr_algorithm
-   refinement
-   gauges
 
 GeoClaw: geophysical flows
 --------------------------
@@ -95,21 +92,6 @@ GeoClaw: geophysical flows
    :maxdepth: 2
 
    geoclaw
-   geohints
-   topo
-   topotools
-   setrun_geoclaw
-   plotting_geoclaw
-   googleearth_plotting
-   quick_tsunami
-   okada
-   sealevel
-   manning
-   fgout
-   fgmax
-   tsunamidata
-
-
 
 PyClaw
 ======
@@ -120,6 +102,14 @@ PyClaw
    pyclaw/index
 
 
+Riemann
+=======
+All Clawpack packages make use of the same collection of Riemann solvers.
+
+.. toctree::
+   :maxdepth: 2
+
+   riemann
 
 VisClaw: Plotting and Visualization Tools
 =========================================
@@ -128,16 +118,18 @@ VisClaw: Plotting and Visualization Tools
    :maxdepth: 2
 
    plotting
-   plotting_python
-   setplot
-   current_data
-   plotexamples
-   plotting_faq
-   geoplot
-   matlab_plotting
-   visit_plotting
 
 
+Migrating applications from older versions of Clawpack
+======================================================
+If you are looking to run an application that was written
+for Clawpack 4.x, this may be helpful.
+
+.. toctree::
+   :maxdepth: 2
+
+   claw43to46
+   claw46to50
 
 
 Developers' resources
@@ -151,6 +143,7 @@ Developers' resources
    howto_doc
    regression
    git_versions
+   photos
 
 See also :ref:`setup_dev`
 

doc/first_run_pyclaw.rst

@@ -15,19 +15,34 @@ This should return 'OK'.
 Running an example
 ------------------
 
-Many examples of Clawpack simulations can be seen in the :ref:`galleries`.
+Many examples of PyClaw simulations can be seen in the :ref:`galleries`
+and :ref:`notebooks`.
+
+You might also want to download the :ref:`apps`, which contains additional
+examples.
+
+From the Jupyter notebook
+*************************
+
+Try any of the notebooks listed under PyClaw in the :ref:`notebooks`.
+
+From the IPython interpreter
+****************************
+Launch an IPython session and then::
+
+    from clawpack.pyclaw import examples
+    claw = examples.shock_bubble_interaction.setup()
+    claw.run()
+    claw.plot()
+
+From the command line
+*********************
 
 To run an example and plot the results using PyClaw, simply do the following
 (starting from your `clawpack` directory)::
 
     cd pyclaw/examples/euler_2d
     python shock_bubble_interaction.py iplot=1
 
-That's it.  For next steps with PyClaw, see :ref:`basics`.
-
-More examples
--------------
-
-You might also want to download the :ref:`apps`, which contains additional
-examples.
 
+That's it.  For next steps with PyClaw, see :ref:`basics`.