Hyperion

New features

- Image and SED groups now have a `set_stokes` option that allows users to specify whether to save Stokes componenets other than I. Prior to this version, all Stokes components were always saved, but this resulted in an unecessarily high memory usage in many cases, so the default is now set to `False`, and users have to explicitly set `set_stokes(True)` in order to save all Stokes components. [61]
- It is now possible to turn off the warnings that occur when photons are killed due to too many interactions, using the `warn=True/False` option for the :meth:`~hyperion.model.Model.set_max_interactions` method (and other similar methods). [68]

Bug fixes

- Fix Fortran dependency installer for gfortran 4.5 and earlier
- Fixed a bug that caused models using the monochromatic radiative transfer settings to not be read in correctly by :meth:`~hyperion.model.Model.read`. [78]

API Changes

- When using the monochromatic radiative transfer mode, users should now use the :meth:`~hyperion.conf.PeeledImageConf.set_wavelength_index_range` method instead of :meth:`~hyperion.conf.PeeledImageConf.set_wavelength_range`. [78]

New features

- For models that require many point sources with a common spectrum, a new source type (point source collection) is now available. To add a point source collection, use `source = m.add_point_source_collection()`. The `source.luminosity` attribute should be set to an array with as many elements as sources, and the `source.position` attribute should be set to a 2-d array where the first dimension matches `source.luminosity`, and with 3 elements in the second dimension (x, y, and z).
- Sources can now be given names as strings, which can then be used as an argument to `source_id` in :meth:`~hyperion.model.ModelOutput.get_sed` and :meth:`~hyperion.model.ModelOutput.get_image` (when using photon tracking).
- Improved documentation to explain better in which cases dust and total densities should be used. This is summarized in :doc:`important/important`.
- Added an option to specify the minimum (relative) radial cell spacing for the :class:`~hyperion.model.AnalyticalYSOModel` class.
- Fixed bug that prevented users from setting the grid manually with the :class:`~hyperion.model.AnalyticalYSOModel` class.
- It is now possible to include multiple ambient mediums with different dust properties (this was limited to a single ambient medium property previously).
- The :meth:`~hyperion.model.Model.add_density_grid` method can now be called with a grid view for all grid types (previously this was only possible for AMR grids).
- Added dust classes to the API documentation.
- Fixed a typo in the equation for the :class:`~hyperion.densities.AlphaDisk` class, and added definitions of the scaleheight for :class:`~hyperion.densities.AlphaDisk` and :class:`~hyperion.densities.FlaredDisk`.
- Improve the reliability of the configure script.

New Features

- :meth:`~hyperion.model.ModelOutput.get_sed` and :meth:`~hyperion.model.ModelOutput.get_image` now return SED and Image objects that contain meta-data in addition to the data itself. For example, images contain information about the field of view (in physical/angular units, where appropriate), and information about the units is also included. The old syntax of `wav, nufnu = m.get_sed(...)` will still work, but the meta-data will not be accessible in those cases.
- New library of dust models, accessible in :doc:`dust/dust`
- It is now possible to read in previous models completely, including the density structure, geometry, sources, dust, and configuration, using the :meth:`~hyperion.model.Model.read` method. In addition, new methods individual methods :meth:`~hyperion.model.Model.use_sources`, :meth:`~hyperion.model.Model.use_image_config`, :meth:`~hyperion.model.Model.use_run_config`, and :meth:`~hyperion.model.Model.use_output_config` allow more detailed control over reading in parameters from previous models.
- It is now possible to force overwrite Hyperion output from the command-line using the `-f` option: `hyperion -f input output`
- or when using the individual fortran binaries: `mpirun -n 8 hyperion_car_mpi -f input output`. This will likely be useful for users of computer clusters who don't want a job to fail just because the output file already exists.
- Regular Cartesian grids can now also be exported for viewing in `yt <http://yt-project.org/>`_ (as was previously possible for AMR and Octree grids).
- A new function, :func:`~hyperion.model.helpers.run_with_vertical_hseq`, is available to help with the calculation of vertical Hydrostatic equilibrium in disks. Note that this feature is still experimental and should be used with care.
- A new function, :func:`~hyperion.model.helpers.tau_to_radius`, is available to compute, for spherical polar grids, the optical depth from infinity to a given radius.

Improvements

- PyFITS, PyWCS, and ATpy are no longer required for Hyperion. Instead, the `Astropy <http://www.astropy.org>`_ package is now required as a dependency.
- Updated download link for MPICH2
- The `rho_0` attribute for disks is now a property, not a method, and can be set by the user instead of the disk mass.
- The documentation has been improved and fixed in places thanks to user feedback.
- AnalyticalYSOModel instances are no longer 'static' once they have been written out (this means one can write out a model, change a parameter, and write out a new different model, which was not possible previously).
- The Fortran code now reads in dust models faster because it computes all cumulative distribution functions more efficiently.
- Statistics for killed photons are now kept for each iteration rather than just summing all of them.

Bug fixes

- Fix compatibility with Numpy 1.8.0.dev
- Fix coverage testing for Python 3
- Fixed an issue which caused temporary files to not be deleted after running tests.

API changes

- The `AnalyticalYSOModel.evaluate_optically_thin_radii()` method has been removed.

New Features

- Updated hyperion2fits to extract binned images
- Added wmax= option for AnalyticalYSOModel.set_cylindrical_grid_auto

Improvements

- Made deps/fortran/install.py script more robust to architecture, and to lack of zlib library.
- Ensure that spectrum always gets converted to floating-point values
- Give a more explicit error message if optical properties for dust are not set.

Bug fixes

- Fixed bug that prevented BipolarCavity from being used
- Ensure that get_quantities works even if no initial iterations were computed
- Fix scattering for cases where P2=0. The code could sometimes crash if a mix of isotropic and non-isotropic dust was used (reported by M. Wolff).
- Fix a bug that occurred when outputting multiple images with the depth option (reported and fixed by T. Bowers) [21, 22]

- Initial public release.