Fermipy

-------------------

* Bug fix related to restoring analysis state for phased analysis
(scaled exposure).
* Many improvements and feature additions to senstivity tools (see e.g. `148
<https://github.com/fermiPy/fermipy/pull/148>`_, `#149
<https://github.com/fermiPy/fermipy/pull/149>`_, and `#152
<https://github.com/fermiPy/fermipy/pull/152>`_).
* Various updates to support DM pipeline package (`146
<https://github.com/fermiPy/fermipy/pull/146>`_).
* Improve robustness of algorithms for extracting peak and
uncertainty ellipse from 2D likelihood surface.
* Added `~fermipy.gtanalysis.GTAnalysis.curvature` method for testing a
source for spectral curvature.
* Added ``fix_shape`` option to
`~fermipy.gtanalysis.GTAnalysis.extension` and
`~fermipy.gtanalysis.GTAnalysis.localize` to fix spectral shape
parameters. Spectral shape parameters of the source of interest are
now free by default when localizing or fitting extension.

-------------------
* Refactoring and improvements in
`~fermipy.gtanalysis.GTAnalysis.localize` and
`~fermipy.gtanalysis.GTAnalysis.extension` (see `124
<https://github.com/fermiPy/fermipy/pull/124>`_). Cleanup of
columns in `~fermipy.gtanalysis.GTAnalysis.localize`. Add new
columns for 1-sigma errors projected in CEL and GAL coordinates as
well as associated covariance and correlation matrices. Add
positional errors when running
`~fermipy.gtanalysis.GTAnalysis.extension` with
``fit_position=True``.
* Add ``free_radius`` option to
`~fermipy.gtanalysis.GTAnalysis.localize`,
`~fermipy.gtanalysis.GTAnalysis.extension`, and
`~fermipy.gtanalysis.GTAnalysis.sed`. This can be used to free
background sources within a certain distance of the analyzed source.
* Relocalize point-source hypothesis when testing extension of
extended sources.
* Improve speed and accuracy of source map calculation (see `123
<https://github.com/fermiPy/fermipy/pull/123>`_). Exposures are now
extracted directly from the exposure map.
* Write analysis configuration to ``CONFIG`` header keyword of all
FITS output files.
* Add ``jobs`` and ``diffuse`` submodules (see `120
<https://github.com/fermiPy/fermipy/pull/120>`_ and `#122
<https://github.com/fermiPy/fermipy/pull/120>`_). These contain
functionality for peforming all-sky diffuse analysis and setting up
automated analysis pipelines. More detailed documentation on these
features to be provided in a future release.

-------------------
* Rewrite LTCube class to add support for fast LT cube generation.
The ``gtlike.use_local_ltcube`` option can be used to enable the
python-based LT cube calculation in lieu of ``gtltcube``.
* Bug fixes and improvements to lightcurve method (see `102
<https://github.com/fermiPy/fermipy/pull/102>`_). Python-based LT
cube generation is now enabled by default resulting in much faster
execution time when generating light curves over long time spans.
* Add ``fit_position`` option to
`~fermipy.gtanalysis.GTAnalysis.extension` that can be used to
enable a joint fit of extension and position.
* New scheme for auto-generating parameter docstrings.
* Add new `~fermipy.gtanalysis.GTAnalysis.set_source_morphology`
method to update the spatial model of a source at runtime.
* Major refactoring of `~fermipy.gtanalysis.GTAnalysis.extension` and
`~fermipy.gtanalysis.GTAnalysis.localize` (see `106
<https://github.com/fermiPy/fermipy/pull/106>`_ and `#110
<https://github.com/fermiPy/fermipy/pull/110>`_).
* Pulled in many new modules and scripts for diffuse all-sky analysis
(see `105 <https://github.com/fermiPy/fermipy/pull/105>`_).

-------------------
* Add support for phased analysis (`87
<https://github.com/fermiPy/fermipy/pull/87>`_). ``gtlike.expscale``
and ``gtlike.src_expscale`` can be used to apply a constant exposure
correction to a whole component or individual sources within a
component. See :ref:`phased` for examples.
* Add script and tools for calculating flux sensitivity (`88
<https://github.com/fermiPy/fermipy/pull/88>`_ and `#95
<https://github.com/fermiPy/fermipy/pull/95>`_). The
``fermipy-flux-sensitivity`` script evaluates both the differential
and integral flux sensitivity for a given TS threshold and minimum
number of detected counts. See :ref:`sensitivity` for examples.
* Add ``fermipy-healview`` script for generating images of healpix
maps and cubes.
* Improvements to HPX-related classes and utilities.
* Refactoring in ``irfs`` module to support development of new
validation tools.
* Improvements to configuration handling to allow parameter validation
when updating configuration at runtime.
* Add lightcurve method (`80
<https://github.com/fermiPy/fermipy/pull/80>`_). See
:ref:`lightcurve` for documentation.
* Change convention for flux arrays in source object. Values and
uncertainties are now stored in separate arrays (e.g. ``flux`` and
``flux_err``).
* Add :ref:`Docker-based installation <dockerinstall>` instructions.
This can be used to run the RHEL6 SLAC ST builds on any machine that
supports Docker (e.g. OSX Yosemite or later).
* Adopt changes to column name conventions in SED format. All column
names are now lowercase.

-------------------
* Add support for weighted likelihood fits (supported in ST
11-03-00 or later). Weights maps can be specified with the ``wmap``
parameter in :ref:`config_gtlike`.
* Implemented performance improvements in
`~fermipy.gtanalysis.GTAnalysis.tsmap` including switching to
newton's method for step-size calculation and masking of empty
pixels (see `79 <https://github.com/fermiPy/fermipy/pull/79>`_).
* Ongoing development and refactoring of classes for dealing with
CastroData (binned likelihood profiles).
* Added `~fermipy.gtanalysis.GTAnalysis.reload_sources` method for
faster recomputation of source maps.
* Fixed sign error in localization plotting method that gave wrong
orientation for error ellipse..
* Refactored classes in `~fermipy.spectrum` and simplified interface
for doing spectral fits (see `69
<https://github.com/fermiPy/fermipy/pull/69>`_).
* Added DMFitFunction spectral model class in
`~fermipy.spectrum` (see `66
<https://github.com/fermiPy/fermipy/pull/66>`_). This uses the same
lookup tables as the ST DMFitFunction class but provides a pure
python implementation which can be used independently of the STs.

-------------------

* Implement support for more spectral models
(DMFitFunction, EblAtten, FileFunction, Gaussian).
* New options (``outdir_regex`` and ``workdir regex``) for
fine-grained control over input/output file staging.
* Add ``offset_roi_edge`` to source dictionary. Defined as the
distance from the source position to the edge of the ROI (< 0 =
inside the ROI, > 0 = outside the ROI).
* Add new variables in `~fermipy.gtanalysis.GTAnalysis.fit` output
(``edm``, ``fit_status``).
* Add new package scripts (``fermipy-collect-sources``,
``fermipy-cluster-sources``).
* Various refactoring and improvements in code for dealing with castro
data.
* Add ``MODEL_FLUX`` and ``PARAMS`` HDUs to SED FITS file. Many new
elements added SED output dictionary.
* Support NEWTON fitter with the same interface as MINUIT and
NEWMINUIT. Running `~fermipy.gtanalysis.GTAnalysis.fit` with
``optimizer`` = NEWTON will use the NEWTON fitter where applicable
(only free norms) and MINUIT otherwise. The ``optimizer`` argument
to `~fermipy.gtanalysis.GTAnalysis.sed`,
`~fermipy.gtanalysis.GTAnalysis.extension`, and
`~fermipy.gtanalysis.GTAnalysis.localize` can be used to override
the default optimizer at runtime. Note that the NEWTON fitter is
only supported by ST releases *after* 11-01-01.