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Merged in MatthewTurk/yt-doc (pull request #74)

Changelog update

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File source/api/api.rst

    ~yt.visualization.plot_window.SlicePlot
    ~yt.visualization.plot_window.OffAxisSlicePlot
    ~yt.visualization.plot_window.ProjectionPlot
-   ~yt.visualization.plot_window.PlotWindow
-   ~yt.visualization.plot_window.PWViewer
-   ~yt.visualization.plot_window.PWViewerMPL
-   ~yt.visualization.plot_window.PWViewerExtJS
+   ~yt.visualization.plot_window.OffAxisProjectionPlot
 
 PlotCollection
 ^^^^^^^^^^^^^^
 
    ~yt.visualization.plot_collection.PlotCollection
    ~yt.visualization.plot_collection.PlotCollectionInteractive
-   ~yt.visualization.plot_types.PCSlicePlot
-   ~yt.visualization.plot_types.PCProjectionPlot
-   ~yt.visualization.plot_types.PhasePlot
-   ~yt.visualization.plot_types.Profile1DPlot
    ~yt.visualization.fixed_resolution.FixedResolutionBuffer
    ~yt.visualization.fixed_resolution.ObliqueFixedResolutionBuffer
-   ~yt.visualization.profile_plotter.PhasePlotter
    ~yt.visualization.plot_collection.get_multi_plot
 
 Data Sources
 .. autosummary::
    :toctree: generated/
 
-   ~yt.data_objects.data_containers.AMRData
-   ~yt.data_objects.data_containers.AMR1DData
-   ~yt.data_objects.data_containers.AMR2DData
-   ~yt.data_objects.data_containers.AMR3DData
    ~yt.data_objects.data_containers.AMRCoveringGridBase
    ~yt.data_objects.data_containers.AMRCuttingPlaneBase
    ~yt.data_objects.data_containers.AMRCylinderBase
    ~yt.data_objects.data_containers.AMRSliceBase
    ~yt.data_objects.data_containers.AMRSmoothedCoveringGridBase
    ~yt.data_objects.data_containers.AMRSphereBase
+   ~yt.data_objects.data_containers.AMRSurfaceBase
 
 Time Series Objects
 ^^^^^^^^^^^^^^^^^^^
 Halo Finding and Particle Functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Halo finding can be executed using these types.
+Halo finding can be executed using these types.  Here we list the main halo
+finders as well as a few other supplemental objects.
 
+.. rubric:: Halo Finders
 
 .. autosummary::
    :toctree: generated/
 
    ~yt.analysis_modules.halo_finding.halo_objects.FOFHaloFinder
    ~yt.analysis_modules.halo_finding.halo_objects.HOPHaloFinder
+   ~yt.analysis_modules.halo_finding.halo_objects.parallelHF
+   ~yt.analysis_modules.halo_finding.rockstar.api.RockstarHaloFinder
+
+You can also operate on the Halo and HAloList objects themselves:
+
+.. autosummary::
+   :toctree: generated/
+
    ~yt.analysis_modules.halo_finding.halo_objects.Halo
    ~yt.analysis_modules.halo_finding.halo_objects.HaloList
+   ~yt.analysis_modules.halo_finding.halo_objects.HOPHalo
+   ~yt.analysis_modules.halo_finding.halo_objects.RockstarHalo
+   ~yt.analysis_modules.halo_finding.halo_objects.parallelHOPHalo
+   ~yt.analysis_modules.halo_finding.halo_objects.FOFHalo
+   ~yt.analysis_modules.halo_finding.halo_objects.LoadedHalo
+   ~yt.analysis_modules.halo_finding.halo_objects.TextHalo
+   ~yt.analysis_modules.halo_finding.halo_objects.RockstarHaloList
+   ~yt.analysis_modules.halo_finding.halo_objects.HOPHaloList
+   ~yt.analysis_modules.halo_finding.halo_objects.FOFHaloList
+   ~yt.analysis_modules.halo_finding.halo_objects.LoadedHaloList
+   ~yt.analysis_modules.halo_finding.halo_objects.TextHaloList
+   ~yt.analysis_modules.halo_finding.halo_objects.parallelHOPHaloList
+
+There are also functions for loading halos from disk:
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.halo_finding.halo_objects.LoadHaloes
+   ~yt.analysis_modules.halo_finding.halo_objects.LoadTextHaloes
+   ~yt.analysis_modules.halo_finding.halo_objects.LoadRockstarHalos
+
+We have several methods that work to create merger trees:
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.halo_merger_tree.merger_tree.MergerTree
+   ~yt.analysis_modules.halo_merger_tree.merger_tree.MergerTreeConnect
+   ~yt.analysis_modules.halo_merger_tree.merger_tree.MergerTreeDotOutput
+   ~yt.analysis_modules.halo_merger_tree.merger_tree.MergerTreeTextOutput
+
+You can use Halo catalogs generatedl externally as well:
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.halo_merger_tree.enzofof_merger_tree.HaloCatalog
+   ~yt.analysis_modules.halo_merger_tree.enzofof_merger_tree.EnzoFOFMergerTree
+   ~yt.analysis_modules.halo_merger_tree.enzofof_merger_tree.plot_halo_evolution
+
+Halo Profiling
+^^^^^^^^^^^^^^
+
+yt provides a comprehensive halo profiler that can filter, center, and analyze
+halos en masse.
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.halo_profiler.multi_halo_profiler.HaloProfiler
+   ~yt.analysis_modules.halo_profiler.multi_halo_profiler.VirialFilter
+
 
 Two Point Functions
 ^^^^^^^^^^^^^^^^^^^
    ~yt.analysis_modules.coordinate_transformation.transforms.arbitrary_regrid
    ~yt.analysis_modules.coordinate_transformation.transforms.spherical_regrid
 
-Cosmology and Star Particle Analysis
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Cosmology, Star Particle Analysis, and Simulated Observations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 For the generation of stellar SEDs.  (See also :ref:`star_analysis`.)
 
    :toctree: generated/
 
    ~yt.analysis_modules.cosmological_observation.light_cone.light_cone.LightCone
+   ~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay
+
+Absorption and X-ray spectra and spectral lines:
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum
+   ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.SpectralFrequencyIntegrator
+   ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.create_table_from_textfiles
+   ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.EmissivityIntegrator
+   ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.add_xray_emissivity_field
+   ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.add_xray_luminosity_field
+   ~yt.analysis_modules.spectral_integrator.spectral_frequency_integrator.add_xray_photon_emissivity_field
+
+Sunrise exporting:
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.sunrise_export.sunrise_exporter.export_to_sunrise
+   ~yt.analysis_modules.sunrise_export.sunrise_exporter.export_to_sunrise_from_halolist
+
+Radial Column Density
+^^^^^^^^^^^^^^^^^^^^^
+
+If you'd like to calculate the column density out to a given point, from a
+specified center, yt can provide that information.
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.analysis_modules.radial_column_density.radial_column_density.RadialColumnDensity
 
 Volume Rendering
 ^^^^^^^^^^^^^^^^
 
 See also :ref:`volume_rendering`.
 
+Here are the primary entry points:
 
 .. autosummary::
    :toctree: generated/
 
    ~yt.visualization.volume_rendering.camera.Camera
    ~yt.visualization.volume_rendering.camera.off_axis_projection
+   ~yt.visualization.volume_rendering.camera.allsky_projection
+
+These objects set up the way the image looks:
+
+.. autosummary::
+   :toctree: generated/
+
    ~yt.visualization.volume_rendering.transfer_functions.ColorTransferFunction
-   ~yt.visualization.volume_rendering.grid_partitioner.HomogenizedVolume
    ~yt.visualization.volume_rendering.transfer_functions.MultiVariateTransferFunction
-   ~yt.utilities.lib.PartitionedGrid
-   ~yt.utilities.amr_kdtree.amr_kdtree.AMRKDTree
-   ~yt.visualization.volume_rendering.camera.PerspectiveCamera
    ~yt.visualization.volume_rendering.transfer_functions.PlanckTransferFunction
    ~yt.visualization.volume_rendering.transfer_functions.ProjectionTransferFunction
-   ~yt.visualization.volume_rendering.camera.StereoPairCamera
    ~yt.visualization.volume_rendering.transfer_functions.TransferFunction
 
-.. _image_writer:
+There are also advanced objects for particular use cases:
+
+.. autosummary::
+   :toctree: generated/
+
+   ~yt.visualization.volume_rendering.camera.MosaicFisheyeCamera
+   ~yt.visualization.volume_rendering.camera.FisheyeCamera
+   ~yt.visualization.volume_rendering.camera.MosaicCamera
+   ~yt.visualization.volume_rendering.camera.plot_allsky_healpix
+   ~yt.visualization.volume_rendering.camera.PerspectiveCamera
+   ~yt.utilities.amr_kdtree.amr_kdtree.AMRKDTree
+   ~yt.visualization.volume_rendering.camera.StereoPairCamera
 
 Streamlining
 ^^^^^^^^^^^^
 
 .. _image-panner-api:
 
-Image Panning and Scanning
-^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. autosummary::
-   :toctree: generated/
-
-   ~yt.visualization.image_panner.vm_panner.VariableMeshPanner
-   ~yt.visualization.image_panner.vm_panner.WindowedVariableMeshPanner
-   ~yt.visualization.image_panner.vm_panner.MultipleWindowVariableMeshPanner
-   ~yt.visualization.image_panner.vm_panner.ImageSaver
-
 Derived Quantities
 ------------------
 

File source/changelog.rst

 
  * Tom Abel
  * David Collins
+ * Brian Crosby
  * Andrew Cunningham
  * Nathan Goldbaum
+ * Markus Haider
  * Cameron Hummels
+ * Christian Karch
  * Ji-hoon Kim
  * Steffen Klemer
  * Kacper Kowalik
  * Michael Kuhlen
  * Eve Lee
+ * Yuan Li
  * Chris Malone
+ * Josh Moloney
  * Chris Moody
  * Andrew Myers
  * Jeff Oishi
  * Jean-Claude Passy
+ * Mark Richardson
  * Thomass Robitaille
  * Anna Rosen
  * Anthony Scopatz
  * Sam Skillman
  * Stephen Skory
  * Britton Smith
- * Georey So
+ * Geoffrey So
  * Casey Stark
  * Elizabeth Tasker
+ * Stephanie Tonnesen
  * Matthew Turk
  * Rick Wagner
  * John Wise
  * John ZuHone
 
+Version 2.5
+-----------
+
+Many below-the-surface changes happened in yt 2.5 to improve reliability,
+fidelity of the answers, and streamlined user interface.  The major change in
+this release has been the immense expansion in testing of yt.  We now have over
+2000 unit tests (run on every commit, thanks to both Kacper Kowalik and Shining
+Panda) as well as answer testing for FLASH, Enzo, Chombo and Orion data.
+
+The Stream frontend, which can construct datasets in memory, has been improved
+considerably.  It's now easier than ever to load data from disk.  If you know
+how to get volumetric data into Python, you can use either the
+``load_uniform_grid`` function or the ``load_amr_grid`` function to create an
+in-memory parameter file that yt can analyze.
+
+yt now supports the Athena code.
+
+yt is now focusing on providing first class support for the IPython notebook.
+In this release, plots can be displayed inline.  The Reason HTML5 GUI will be
+merged with the IPython notebook in a future release.
+
+Install Script Changes:
+~~~~~~~~~~~~~~~~~~~~~~~
+
+ * SciPy can now be installed
+ * Rockstar can now be installed
+ * Dependencies can be updated with "yt update --all"
+ * Cython has been upgraded to 0.17.1
+ * Python has been upgraded to 2.7.3
+ * h5py has been upgraded to 2.1.0
+ * hdf5 has been upgraded to 1.8.9
+ * matplotlib has been upgraded to 1.2.0
+ * IPython has been upgraded to 0.13.1
+ * Forthon has been upgraded to 0.8.10
+ * nose has been added
+ * sympy has been added
+ * python-hglib has been added
+
+We've also improved support for installing on OSX, Ubuntu and OpenSUSE.
+
+Most Visible Improvements
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ * Nearly 200 pull requests and over 1000 changesets have been merged since yt
+   2.4 was release on August 2nd, 2012.
+ * numpy is now imported as np, not na.  na will continue to work for the
+   foreseeable future.
+ * You can now get a `yt cheat sheet <http://yt-project.org/docs/2.5/cheatsheet.pdf>`!
+ * yt can now load simulation data created by Athena.
+ * The Rockstar halo finder can now be installed by the install script
+ * SciPy can now be installed by the install script
+ * Data can now be written out in two ways:
+
+   * Sidecar files containing expensive derived fields can be written and
+     implicitly loaded from.
+   * GDF files, which are portable yt-specific representations of full
+     simulations, can be created from any parameter file.  Work is underway on
+     a pure C library that can be linked against to load these files into
+     simulations.
+
+ * The "Stream" frontend, for loading raw data in memory, has been greatly
+   expanded and now includes initial conditions generation functionality,
+   particle fields, and simple loading of AMR grids with ``load_amr_grids``.
+ * Spherical and Cylindrical fields have been sped up and made to have a
+   uniform interface.  These fields can be the building blocks of more advanced
+   fields.
+ * Coordinate transformations have been sped up and streamlined. It is now
+   possible to convert any scalar or vector field to a new cartesian, spherical,
+   or cylindrical coordinate system with an arbitrary orientation. This makes it
+   possible to do novel analyses like profiling the toroidal and poloidal
+   velocity as a function of radius in an inclined disk.
+ * Many improvements to the EnzoSimulation class, which can now find many
+   different types of data.
+ * Image data is now encapsulated in an ImageArray class, which carries with it
+   provenance information about its trajectory through yt.
+ * Streamlines now query at every step along the streamline, not just at every
+   cell.
+ * Surfaces can now be extracted and examined, as well as uploaded to
+   Sketchfab.com for interactive visualization in a web browser.
+ * allsky_projection can now accept a datasource, making it easier to cut out
+   regions to examine.
+ * Many, many improvements to PlotWindow.  If you're still using
+   PlotCollection, check out ``ProjectionPlot``, ``SlicePlot``,
+   ``OffAxisProjectionPlot`` and ``OffAxisSlicePlot``.
+ * PlotWindow can now accept a timeseries instead of a parameter file.
+ * Many fixes for 1D and 2D data, especially in FLASH datasets.
+ * Vast improvements to the particle file handling for FLASH datasets.
+ * Particles can now be created ex nihilo with CICSample_3.
+ * Rockstar halo finding is now a targeted goal.  Support for using Rockstar
+   has improved dramatically.
+ * The command ``yt notebook`` has been added to spawn an IPython notebook
+   server, and the ``yt.imods`` module can replace ``yt.mods`` in the IPython
+   Notebook to enable better integration.
+ * Metallicity-dependent X-ray fields have now been added.
+ * Grid lines can now be added to volume renderings.
+ * Volume renderings now have alpha blending
+ * Periodicity, or alternately non-periodicity, is now a part of radius
+   calculations.
+ * AMRKDTree has been rewritten to allow for sub-region selection.
+
 Version 2.4
 -----------
 

File source/index.rst

 
 yt provides full support for several simulation codes in the current release:
 
- * `Enzo <http://enzo-project.org/>`_ Orion, 
+ * `Enzo <http://enzo-project.org/>`_ 
  * Orion
  * `Nyx <https://ccse.lbl.gov/Research/NYX/index.html>`_
  * `FLASH <http://flash.uchicago.edu/website/home/>`_
        </td>
      </tr>
  
+     <tr valign="top">
+       <td width="25%">
+         <p>
+           <a href="cheatsheet.pdf">Cheat Sheet</a>
+         </p>
+       </td>
+       <td width="75%">
+         <p class="linkdescr">A cheat sheet for yt you can print out</p>
+       </td>
+     </tr>
+ 
    </table>
  
    <h2>User Guide</h2>