Merge pull request #21 from chummels/release

Prepare for Stable Release

CITATION

@@ -1,18 +1,22 @@
 If you use Trident for your scientific research, please include the following
 bibtex to cite our Trident method paper:
 
-@ARTICLE{2016arXiv161203935H,
-       author = {{Hummels}, C. and {Smith}, B. and {Silvia}, D.},
-        title = "{Trident: a universal tool for generating synthetic absorption spectra from astrophysical simulations}",
-      journal = {ArXiv e-prints},
-archivePrefix = "arXiv",
-       eprint = {1612.03935},
- primaryClass = "astro-ph.IM",
-     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Astrophysics of Galaxies},
-         year = 2016,
-        month = dec,
-       adsurl = {http://adsabs.harvard.edu/abs/2016arXiv161203935H},
-      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+@ARTICLE{2017ApJ...847...59H,
+    author = {{Hummels}, C.~B. and {Smith}, B.~D. and {Silvia}, D.~W.},
+    title = "{Trident: A Universal Tool for Generating Synthetic Absorption Spectra from Astrophysical Simulations}",
+    journal = {\apj},
+    archivePrefix = "arXiv",
+    eprint = {1612.03935},
+    primaryClass = "astro-ph.IM",
+    keywords = {cosmology: theory, methods: data analysis, methods: numerical, radiative transfer },
+    year = 2017,
+    month = sep,
+    volume = 847,
+    eid = {59},
+    pages = {59},
+    doi = {10.3847/1538-4357/aa7e2d},
+    adsurl = {http://adsabs.harvard.edu/abs/2017ApJ...847...59H},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
 In addition, you can add a footnote to the Trident webpage in the body of the 

CREDITS

@@ -1,10 +1,14 @@
 Trident is a collaborative effort from multiple developers.
 
 Contributors:   
-                Cameron Hummels (chummels@gmail.com)
-                Devin Silvia (devin.silvia@gmail.com)
-                Britton Smith (brittonsmith@gmail.com)
-                Bili Dong (qobilidop@gmail.com)
-                Hilary Egan (hilaryye@gmail.com)
-                Matthew Turk (matthewturk@gmail.com)
-                Lauren Corlies (lcorlie1@jhu.edu)
+
+Cameron Hummels
+Britton Smith
+Devin Silvia
+Matthew Turk
+Nathan Goldbaum
+Kacper Kowalik
+Lauren Corlies
+Bili Dong
+Hilary Egan
+Clayton Strawn

LICENSE

@@ -64,7 +64,7 @@ With this in mind, the following banner should be used in any source code file
 to indicate the copyright and license terms:
 
 #-----------------------------------------------------------------------------
-# Copyright (c) 2016, Trident Development Team.
+# Copyright (c) 2017, Trident Development Team.
 #
 # Distributed under the terms of the Modified BSD License.
 #

doc/source/advanced_spectra.rst

@@ -13,7 +13,7 @@ setting these properties and shows what impact it has on resulting spectra.
 For this demonstation, we'll be using a light ray passing through a very dense
 disk of gas, taken from the initial output from the AGORA isolated box 
 simulation using ART-II in `Kim et al. (2016)
-<http://adsabs.harvard.edu/abs/2016arXiv161003066K>`_.
+<http://adsabs.harvard.edu/abs/2016ApJ...833..202K>`_.
 If you'd like to try to reproduce the spectra included below you can get 
 the :class:`~trident.LightRay` file from the Trident sample data using the 
 command:

doc/source/changelog.rst

@@ -0,0 +1,80 @@
+.. _changelog:
+
+Changelog
+=========
+
+This document summarizes changes to the codebase with time for Trident.
+
+Contributors
+------------
+
+The `CREDITS file <https://github.com/trident-project/trident/blob/master/CREDITS>`_
+has an updated list of contributors to the codebase.
+
+Version 1.1
+-----------
+
+- Trident development has changed from mercurial to git, and the source has
+  moved from bitbucket to github.  This was done in recognition that more
+  people interact with git/github than do with hg/bitbucket, as well as to
+  follow our major dependency yt in making the same transition.  All previous
+  repository history (e.g., commits, versions, tags, etc.) is retained under
+  this transition. For users operating on the development branch of
+  Trident, you must re-install Trident in order to continue to get updates.
+  The :ref:`installation instructions <installation>` were updated accordingly.
+- We totally rebuilt the testing interface to Trident, which includes
+  more coverage in unit tests and answer tests over both grid-based and
+  particle-based datasets.  We now have continuous integration through
+  `Travis <https://travis-ci.org/trident-project/trident>`_ that tests the code
+  daily and with each new pull request to assure consistent code results and to
+  minimize bugs.  For more information, see :ref:`testing`.
+- Much of the original Trident codebase was developed in yt as the base classes
+  :class:`~trident.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum`
+  and :class:`~trident.LightRay`.  We have now stripped these classes out of
+  yt and moved them entirely into Trident for more flexibility, stability, and
+  autonomy moving forward.  This should not affect the user as these changes
+  were behind the scenes.
+- Added ``store_observables`` keyword to
+  :func:`~trident.SpectrumGenerator.make_spectrum` to store a
+  dictionary of observable properties (e.g., tau, column density, and thermal_b)
+  for each cell along a line of sight for use in post-processing.  See source
+  of :class:`~trident.SpectrumGenerator` for more information.
+- Added an approximate ``flux_error`` field to output spectra, since many
+  observational tools require its presence.  See
+  :func:`~trident.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum.error_func`
+  for more details.
+- Made ``min_tau`` a keyword to
+  :func:`~trident.SpectrumGenerator.make_spectrum` to enable higher precision
+  (although more time intensive) absorption line deposition.
+- Added ability to specify an arbitrary noise vector with
+  :func:`~trident.SpectrumGenerator.add_noise_vector`.
+- A `bugfix <https://github.com/yt-project/yt/pull/1611>`_ was made
+  in yt to the temperature field for Gadget-based code outputs.  The internal
+  energy field was mistakenly being read in co-moving instead of physical units,
+  which led to gas temperatures being low by a factor of (1+z).
+  This is now resolved in yt dev and thus we recommend Trident users use
+  yt dev until yt 3.5 stable is released.
+- `Another bugfix <https://github.com/astropy/astropy/pull/5782>`_ was made
+  in Trident dependency `astropy <https://github.com/astropy/astropy/>`_ to
+  the convolve function, which is used in
+  :func:`~trident.SpectrumGenerator.apply_lsf`.  This may cause slight
+  backwards-incompatible changes when applying line spread functions to
+  post-process spectra.
+- Replaced internal instances of ``particle_type`` with ``sampling_type`` to
+  match similar yt conversion.
+
+Version 1.0
+-----------
+
+Initial release.  See our :ref:`method paper <citation>` for details.
+
+- Create absorption-line spectra for any trajectory through a simulated
+  data set mimicking both background quasar and down-the-barrel configurations.
+- Reproduce the spectral characteristics of common instruments like the
+  Cosmic Origins Spectrograph.
+- Operate across the ultraviolet, optical, and infrared using customizable
+  absorption-line lists.
+- Trace simulated physical structures directly to spectral features.
+- Approximate the presence of ion species absent from the simulation outputs.
+- Generate column density maps for any ion.
+- Provide support for all major astrophysical hydrodynamical codes.

doc/source/conf.py

@@ -56,7 +56,7 @@
 
 # General information about the project.
 project = u'Trident'
-copyright = u'2015-2016, Trident Project'
+copyright = u'2015-2017, Trident Project'
 author = u'Trident Project'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -66,7 +66,7 @@
 # The short X.Y version.
 version = '1.1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.1.0.dev1'
+release = '1.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/index.rst

@@ -25,4 +25,5 @@ information, see :ref:`versions`.
    faq.rst
    reference.rst
    citation.rst
+   changelog.rst
    help.rst

environment.yml

@@ -44,6 +44,6 @@ dependencies:
   - simplegeneric==0.8.1
   - sympy==1.0
   - traitlets==4.3.2
-  - trident==1.0.1
+  - trident==1.1
   - wcwidth==0.1.7
-  - yt==3.3.5
+  - yt==3.4.0

setup.py

@@ -11,7 +11,7 @@ def read(fname):
 
 setup(
     name = "trident",
-    version = "1.1.0.dev1",
+    version = "1.1.0",
     author = "Cameron Hummels, Devin Silvia, Britton Smith",
     author_email = "trident-project-users@googlegroups.com",
     description = ("Spectrum generator for astrophysical simulation data"),
@@ -33,10 +33,11 @@ def read(fname):
         "Programming Language :: Python :: 2",
         "Programming Language :: Python :: 2.7",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.4",
+        "Programming Language :: Python :: 3.5",
+        "Programming Language :: Python :: 3.6",
         "Topic :: Scientific/Engineering :: Astronomy",
         "Topic :: Scientific/Engineering :: Physics",
         "Topic :: Scientific/Engineering :: Visualization",
     ],
-    install_requires=['yt>=3.3.5', 'h5py', 'numpy', 'matplotlib', 'astropy', 'requests', 'setuptools', 'future'],
+    install_requires=['yt>=3.4.0', 'h5py', 'numpy', 'matplotlib', 'astropy', 'requests', 'setuptools', 'future'],
 )