Merge branch 'master' of github.com:sunpy/sunpy into rtdio

.gitignore

@@ -18,7 +18,9 @@ sunpy.egg-info
 paver-minilib.zip
 doc/build/*
 doc/source/api
+doc/source/modules
 doc/html
+doc/source/auto_examples
 docs
 .tox/
 .coverage
@@ -30,7 +32,7 @@ sunpy/cython_version.py
 sunpy/data/sample/*.fits
 sunpy/data/sample/*.csv
 sunpy/data/sample/*.fit
-
+.cache
 
 ### https://raw.github.com/github/gitignore/master/Global/OSX.gitignore
 

.rtd-environment.yml

@@ -1,8 +1,6 @@
 name: sunpy-rtd
 channels:
-    - astropy
-    - sunpy
-    - jevans
+    - openastronomy
 dependencies:
 - astropy
 - beautiful-soup
@@ -60,3 +58,5 @@ dependencies:
 - zlib
 - glymur
 - openjpeg
+- pip:
+    - sphinx-gallery

.travis.yml

@@ -41,9 +41,10 @@ env:
         - TEST_MODE='offline'
         - NUMPY_VERSION='stable'
         - MAIN_CMD='python setup.py'
-        - CONDA_CHANNELS='astropy astropy-ci-extras sunpy jevans'
-        - CONDA_ALL_DEPENDENCIES='Cython jinja2 scipy matplotlib requests beautiful-soup sqlalchemy scikit-image pytest wcsaxes pyyaml pandas'
-        - CONDA_ALL_DEPENDENCIES2="suds-jurko glymur openjpeg $CONDA_ALL_DEPENDENCIES"
+        - CONDA_CHANNELS='astropy astropy-ci-extras sunpy jevans https://conda.anaconda.org/sunpy/label/citesting openastronomy'
+        - CONDA_ALL_DEPENDENCIES='glymur Cython jinja2 scipy matplotlib requests beautifulsoup4 sqlalchemy scikit-image pytest wcsaxes pyyaml pandas'
+        - CONDA_ALL_DEPENDENCIES2='glymur openjpeg Cython jinja2 scipy matplotlib requests beautifulsoup4 sqlalchemy scikit-image pytest wcsaxes pyyaml pandas'
+        - PIP_DEPENDENCIES='suds-jurko sphinx-gallery pytest-cov'
 
 
 #    matrix:
@@ -57,7 +58,7 @@ matrix:
          # # Try MacOS X
          - os: osx
            env: JOB="Py2" PYTHON_VERSION=2.7 SETUP_CMD='test'
-                CONDA_DEPENDENCIES="suds-jurko glymur $CONDA_ALL_DEPENDENCIES" #Without openjpeg
+                CONDA_DEPENDENCIES="$CONDA_ALL_DEPENDENCIES" #Without openjpeg
 
          # Try on Linux
          - os: linux
@@ -71,10 +72,10 @@ matrix:
                 ASTROPY_VERSION='development' CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
          - os: linux
            env: JOB="Py2Sphinx" PYTHON_VERSION=2.7 SETUP_CMD='build_sphinx -w'
-                CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
+                CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES
          - os: linux
            env: JOB="Py2Coverage" PYTHON_VERSION=2.7 SETUP_CMD='test --online --coverage'
-                CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2 PIP_DEPENDENCIES='pytest-cov'
+                CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
          - os: linux
            env: JOB="Py2Doctest" PYTHON_VERSION=2.7 SETUP_CMD='build_sphinx -b doctest'
                 CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
@@ -86,22 +87,25 @@ matrix:
                 CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
                 NUMPY_VERSION=$FIGURES_NUMPY MATPLOTLIB_VERSION=$FIGURES_MPL
          - os: linux
-           env: JOB="Py3" PYTHON_VERSION=3.4 MAIN_CMD='continuous-integration/python3.sh'
-                SETUP_CMD='' CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES
+           env: JOB="Py3.4" PYTHON_VERSION=3.4 SETUP_CMD='test' ASTROPY_VERSION='stable'
+                CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES DEBUG=True
+         - os: linux
+           env: JOB="Py3.5" PYTHON_VERSION=3.5 SETUP_CMD='test' ASTROPY_VERSION='stable'
+                DEBUG=True CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES
 
     # allow_failures has to repeat the environment from the matrix above to mark it as such
     allow_failures:
       - env: JOB="Py2Doctest" PYTHON_VERSION=2.7 SETUP_CMD='build_sphinx -b doctest'
              CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
       - env: JOB="Py2Coverage" PYTHON_VERSION=2.7 SETUP_CMD='test --online --coverage'
-             CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2 PIP_DEPENDENCIES='pytest-cov'
+             CONDA_DEPENDENCIES=$CONDA_ALL_DEPENDENCIES2
 
 install:
-    - echo $CONDA_DEPENDENCIES
     - git clone git://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
-    - source continuous-integration/travis/openjpeg.sh # so glymur knows where to look
+    - source continuous-integration/travis/openjpeg.sh  # so glymur knows where to look
 
+before_script:
     # Download the sample data for the build of the documentation.
     - if [[ $SETUP_CMD == *sphinx* ]]; then python -c "import sunpy.data; sunpy.data.download_sample_data()"; fi
     - if [[ $SETUP_CMD == *figure* ]]; then wget http://raw.githubusercontent.com/dpshelio/sunpy-figure-tests/np1104/conda_env; conda create --name testFigure --file conda_env ; source activate testFigure; fi
@@ -111,7 +115,7 @@ script:
 
 # after_success:
 #     - if [[ $SETUP_CMD == *coverage* ]]; then coveralls --rcfile='./sunpy/tests/coveragerc'; fi
-      
+
 # Notify the IRC channel of build status
 notifications:
   irc: "chat.freenode.net#SunPy"

CHANGELOG.md

@@ -1,21 +1,38 @@
 Latest
 ------
 
+* Sunpy is now Python 3.x compatible (3.4 and 3.5).
+* Added a unit check and warnings for map metadata.
 * Added IRIS SJI color maps.
 * Updated `show_colormaps()` with new string filter to show a subset of color maps.
 * Fixed MapCube animations by working around a bug in Astropy's ImageNormalize
 * Remove ``vso.QueryResponse.num_records()`` in favour of `len(qr)`
-* add a `draw_rectangle` helper to `GenericMap` which can plot rectanges in the
+* Add a `draw_rectangle` helper to `GenericMap` which can plot rectangles in the
   native coordinate system of the map.
+* Added the ability to shift maps to correct for incorrect map location, for example.
+* Bug fix for RHESSI summary light curve values.
+* Mapcube solar derotation and coalignment now pass keywords to the routine used to
+  shift the images, scipy.ndimage.interpolation.shift.
 * Add automatic registration of ``GenericMap`` subclasses with the factory as
   long as they define an ``is_datasource_for`` method.
-
-* Added the ability to shift maps to correct for incorrect map location, for example.
-* Added functions flareclass_to_flux and flux_to_flareclass which convert
+* Added functions ``flareclass_to_flux`` and ``flux_to_flareclass`` which convert
   between GOES flux to GOES class numbers (e.g. X12, M3.4).
-* Removed old sunpy.util.goes_flare_class()
-* Bug fix for rhessi summary light curve values.
+* Removed old ``sunpy.util.goes_flare_class()``
+* Bug fix for RHESSI summary light curve values.
+* The ``MapCube.as_array`` function now returns a masked numpy array if at least
+  one of the input maps in the MapCube has a mask.
+* Map superpixel method now respects maps that have masks.
+* Map superpixel method now accepts numpy functions as an argument, or any user-defined
+  function.
+* Map superpixel method no longer has the restriction that the number of original pixels
+  in the x (or y) side of the superpixel exactly divides the number of original
+  pixels in the x (or y) side of the original map data.
 * `sunpy.physics.transforms` has been deprecated and the code moved into `sunpy.physics`.
+* Add the `sunpy.coordinates` module, this adds the core physical solar coordinates frame within the astropy coordinates framework.
+* Added ability of maps to draw contours on top of themselves (`draw_contours`)
+* Added concatenate functionality to lightcurve base class.
+* Fix Map to allow astropy.io.fits Header objects as valid input for meta arguments.
+* Added an examples gallery using `sphinx-gallery`.
 
 0.6.0
 -----

CITATION.md

@@ -0,0 +1,42 @@
+#Acknowledging or Citing SunPy
+
+###If you have used SunPy in your scientific work we would appreciate it if you would acknowledge it.
+The continued growth and development of SunPy is dependent on the community being aware of the use SunPy. If you use SunPy, we therefore ask that you acknowledge SunPy appropriately in a publication, presentation, poster, or talk. 
+
+* **For a publication**, we recommend the following line be added to the conclusion or acknowledgements:
+
+	*This research has made use of SunPy, an open-source and free community-developed solar data analysis package written in Python (citation).*
+
+	The citation is to the [SunPy v0.5 paper](https://iopscience.iop.org/article/10.1088/1749-4699/8/1/014009)/[arXiv(open access)](http://arxiv.org/abs/1505.02563). If the journal allows please also include a link to sunpy.org. If you have the time, please email us to let us know about your paper, as we maintain a [public list](https://www.zotero.org/groups/sunpy_-_python_for_solar_physicists) of papers on [Zotero](https://www.zotero.org/). 
+	A BibTeX entry for LaTeX users is:
+
+```
+	@ARTICLE{2015CS&D....8a4009S,
+	   author = {{SunPy Community}, T. and {Mumford}, S.~J. and {Christe}, S. and 
+		{P{\'e}rez-Su{\'a}rez}, D. and {Ireland}, J. and {Shih}, A.~Y. and 
+		{Inglis}, A.~R. and {Liedtke}, S. and {Hewett}, R.~J. and {Mayer}, F. and 
+		{Hughitt}, K. and {Freij}, N. and {Meszaros}, T. and {Bennett}, S.~M. and 
+		{Malocha}, M. and {Evans}, J. and {Agrawal}, A. and {Leonard}, A.~J. and 
+		{Robitaille}, T.~P. and {Mampaey}, B. and {Iv{\'a}n Campos-Rozo}, J. and 
+		{Kirk}, M.~S.},
+	    title = "{SunPy{\mdash}Python for solar physics}",
+	  journal = {Computational Science and Discovery},
+	archivePrefix = "arXiv",
+	   eprint = {1505.02563},
+	 primaryClass = "astro-ph.IM",
+	     year = 2015,
+	    month = jan,
+	   volume = 8,
+	   number = 1,
+	      eid = {014009},
+	    pages = {014009},
+	      doi = {10.1088/1749-4699/8/1/014009},
+	   adsurl = {http://adsabs.harvard.edu/abs/2015CS%26D....8a4009S},
+	  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+	}
+
+```
+
+* **For a poster, talks, or project websites**, please include the [Sunpy logo](http://sunpy.org/about/#acknowledging) on the title, conclusion slide, or about page. For websites please link the image to [sunpy.org](http://sunpy.org/). Other versions of the logo are available in the [sunpy-logo repository](https://github.com/sunpy/sunpy-logo/).
+
+Thank you, in advance, for your support. 

INSTALL.txt

@@ -9,4 +9,4 @@ Enter the top-level directory in the extracted files and run:
 
 For detailed installation instructions, see:
 
- http://www.sunpy.org/doc/guide/installation/index.html
+ http://docs.sunpy.org/en/latest/guide/installation/index.html

README.md

@@ -1,10 +1,10 @@
 # [SunPy](http://sunpy.org)
 [![Downloads](https://img.shields.io/pypi/dm/sunpy.svg)](https://pypi.python.org/pypi/sunpy/) [![Latest Version](https://img.shields.io/pypi/v/sunpy.svg)](https://pypi.python.org/pypi/sunpy/) [![Build Status](https://secure.travis-ci.org/sunpy/sunpy.svg)] (http://travis-ci.org/sunpy/sunpy)[![Build status](https://ci.appveyor.com/api/projects/status/xow461iejsjvp9vl?svg=true)](https://ci.appveyor.com/project/sunpy/sunpy)[![Coverage Status](https://coveralls.io/repos/sunpy/sunpy/badge.svg?branch=master)](https://coveralls.io/r/sunpy/sunpy?branch=master) [![Code Health](https://landscape.io/github/sunpy/sunpy/master/landscape.svg)](https://landscape.io/github/sunpy/sunpy/master)
-[![Code Issues](https://www.quantifiedcode.com/api/v1/project/9edd3e28230840038713e1c7dc3eb141/badge.svg)](https://www.quantifiedcode.com/app/project/9edd3e28230840038713e1c7dc3eb141)
+[![Code Issues](https://www.quantifiedcode.com/api/v1/project/9edd3e28230840038713e1c7dc3eb141/badge.svg)](https://www.quantifiedcode.com/app/project/9edd3e28230840038713e1c7dc3eb141)[![Research software impact](http://depsy.org/api/package/pypi/sunpy/badge.svg)](http://depsy.org/package/python/sunpy)
 
 SunPy is an open-source Python library for solar physics data analysis.
 
-[![Research software impact](http://depsy.org/api/package/pypi/sunpy/badge.svg)](http://depsy.org/package/python/sunpy)
+[![Visit our IRC channel](https://kiwiirc.com/buttons/chat.freenode.com/sunpy.png)](https://kiwiirc.com/client/chat.freenode.com/#sunpy)
 
 Installation
 ------------

appveyor.yml

@@ -11,7 +11,8 @@ environment:
       # See: http://stackoverflow.com/a/13751649/163740
       CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\ci-helpers\\appveyor\\windows_sdk.cmd"
       CONDA_CHANNELS: "astropy astropy-ci-extras sunpy jevans"
-      CONDA_DEPENDENCIES: "numpy scipy astropy matplotlib pandas requests beautiful-soup sqlalchemy scikit-image pytest wcsaxes suds-jurko glymur"
+      CONDA_DEPENDENCIES: "numpy scipy astropy matplotlib pandas requests beautifulsoup4 sqlalchemy scikit-image pytest wcsaxes suds-jurko"
+      PIP_DEPENDENCIES: "Glymur"
 
   matrix:
       - PYTHON_VERSION: "2.7"
@@ -20,9 +21,6 @@ environment:
         NUMPY_VERSION: "stable"
 matrix:
     fast_finish: true
-    allow_failures:
-        - PYTHON_VERSION: "3.5"
-          NUMPY_VERSION: "stable"
 
 platform:
     - x64