Merge pull request #241 from spacetelescope/loaders

Enable units for cos and stis loaders

.travis.yml

@@ -1,11 +1,8 @@
-language: python
+language: c
 
-python:
-    - 2.6
-    - 2.7
-    - 3.3
-    - 3.4
-    - 3.5
+os:
+  - linux
+  - osx
 
 # Setting sudo to false opts in to Travis-CI container-based builds.
 sudo: false
@@ -27,45 +24,37 @@ env:
         # The following versions are the 'default' for tests, unless
         # overidden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
-        - NUMPY_VERSION=1.9
         - ASTROPY_VERSION=stable
         - SETUP_CMD='test'
-        - PIP_DEPENDENCIES=''
+        - PIP_DEPENDENCIES='sphinx_automodapi sphinx_rtd_theme'
         # For this package-template, we include examples of Cython modules,
         # so Cython is required for testing. If your package does not include
         # Cython code, you can set CONDA_DEPENDENCIES=''
-        - CONDA_DEPENDENCIES='Cython'
+        - CONDA_CHANNELS='http://ssb.stsci.edu/astroconda astropy-ci-extras'
+        - CONDA_DEPENDENCIES='numpy scipy cython specutils qtpy pyqtgraph pyyaml six'
+
     matrix:
-        # Make sure that egg_info works without dependencies
-        - SETUP_CMD='egg_info'
-        # Try all python versions with the latest numpy
-        - SETUP_CMD='test'
+        - PYTHON_VERSION=2.7 SETUP_CMD='install'
+        - PYTHON_VERSION=2.7 SETUP_CMD='test'
+        - PYTHON_VERSION=2.7 SETUP_CMD='egg_info'
+        - PYTHON_VERSION=3.5 SETUP_CMD='install'
+        - PYTHON_VERSION=3.5 SETUP_CMD='test'
+        - PYTHON_VERSION=3.5 SETUP_CMD='egg_info'
+
 
 matrix:
     include:
-
         # Do a coverage test in Python 2.
-        - python: 2.7
-          env: SETUP_CMD='test --coverage'
+        - env: PYTHON_VERSION=2.7 SETUP_CMD='test --coverage'
 
         # Check for sphinx doc build warnings - we do this first because it
         # may run for a long time
-        - python: 2.7
-          env: SETUP_CMD='build_sphinx -w'
+        - env: PYTHON_VERSION=2.7 SETUP_CMD='build_sphinx -w'
 
         # Try Astropy development version
-        - python: 2.7
-          env: ASTROPY_VERSION=development
-        - python: 3.4
-          env: ASTROPY_VERSION=development
-
-        # Try older numpy versions
-        - python: 2.7
-          env: NUMPY_VERSION=1.8
-        - python: 2.7
-          env: NUMPY_VERSION=1.7
-        - python: 2.7
-          env: NUMPY_VERSION=1.6
+        - env: PYTHON_VERSION=2.7 ASTROPY_VERSION=development
+
+        - env: PYTHON_VERSION=3.5 ASTROPY_VERSION=development
 
 before_install:
 
@@ -93,7 +82,7 @@ install:
     # As described above, using ci-helpers, you should be able to set up an
     # environment with dependencies installed using conda and pip, but in some
     # cases this may not provide enough flexibility in how to install a
-    # specific dependency (and it will not be able to install non-Python 
+    # specific dependency (and it will not be able to install non-Python
     # dependencies). Therefore, you can also include commands below (as
     # well as at the start of the install section or in the before_install
     # section if they are needed before setting up conda) to install any

README.md

@@ -1,4 +1,6 @@
 # SpecViz
+[![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)](http://www.astropy.org/) [![Build Status](https://travis-ci.org/spacetelescope/specviz.svg?branch=loaders)](https://travis-ci.org/spacetelescope/specviz) [![Documentation Status](http://readthedocs.org/projects/specviz/badge/?version=latest)](http://specviz.readthedocs.io/en/latest/?badge=latest)
+
 An gui-based interactive analysis tool for one dimensional astronomical data
 using Python.
 

docs/environment.yml

@@ -0,0 +1,14 @@
+name: specviz
+channels:
+  - http://ssb.stsci.edu/astroconda
+dependencies:
+  - pyyaml
+  - cython
+  - numpy
+  - scipy
+  - astropy
+  - specutils
+  - pyqtgraph
+  - pip:
+    - sphinx_automodapi
+    - sphinx_rtd_theme

docs/make.bat

@@ -19,7 +19,7 @@ if "%1" == "help" (
 	:help
 	echo.Please use `make ^<target^>` where ^<target^> is one of
 	echo.  html       to make standalone HTML files
-	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  dirhtml    to make HTML files named ndex.html in directories
 	echo.  singlehtml to make a single large HTML file
 	echo.  pickle     to make pickle files
 	echo.  json       to make JSON files

docs/source/conf.py

@@ -36,12 +36,14 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.autosummary',
-    'sphinx.ext.pngmath',
+    'sphinx.ext.imgmath',
     'sphinx.ext.intersphinx',
     'sphinx.ext.viewcode',
     'sphinx_automodapi.automodapi'
     ]
 
+suppress_warnings = ['image.nonlocal_uri']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/source/installation.rst

@@ -3,7 +3,7 @@
 Installation
 ============
 
-SpecViz is distributed through the `Anaconda <https://anaconda.org>`_ package
+SpecViz is distributed through the `Anaconda <https://anaconda.org>`__ package
 manager. Specifically, it lives within Space Telescope Science Institute's
 `AstroConda <https://astroconda.readthedocs.io/>`_ channel.
 
@@ -70,7 +70,7 @@ Please keep in mind that PyQt5 is the recommended PyQt implementation as
 `Qt4 development and support has ended <http://blog.qt.io/blog/2015/05/26/qt-4-8-7-released/>`_.
 
 Below are instructions for installing using *either* `Homebrew <http://brew
-.sh/>`_ *or* `Anaconda <https://www.continuum.io/downloads>`_.
+.sh/>`_ *or* `Anaconda <https://www.continuum.io/downloads>`__.
 
 PyQt5
 """""

readthedocs.yml

@@ -0,0 +1,5 @@
+python:
+   setup_py_install: true
+
+conda:
+    file: docs/environment.yml

requirements.txt

@@ -1,11 +1,12 @@
---index-url https://pypi.python.org/simple/
+-index-url https://pypi.python.org/simple/
 
 pyyaml
 cython
 numpy
 scipy
 astropy
-sphinx_automodapi
+sphinx_automodapi 
+sphinx_rtd_theme
 git+https://github.com/nmearl/specutils.git
 git+https://github.com/nmearl/pyqtgraph.git
 -e .

setup.cfg

@@ -1,23 +1,23 @@
 [build_sphinx]
-source-dir = docs
+source-dir = docs/source
 build-dir = docs/_build
 all_files = 1
 
 [upload_docs]
 upload-dir = docs/_build/html
 show-response = 1
 
-[pytest]
+[tool:pytest]
 minversion = 2.2
 norecursedirs = build docs/_build
-doctest_plus = enabled
+doctest_plus = disabled
 
 [ah_bootstrap]
 auto_use = True
 
 [metadata]
 package_name = specviz
-description = An interactive astronomical analysis tool. 
+description = An interactive astronomical analysis tool.
 long_description = SpecViz is a tool for 1-D spectral visualization and analysis of astronomical spectrograms.
 author = Nicholas Earl, Ivo Busko, Pey Lian Lim
 author_email = [email protected]

specviz/analysis/tests/test_statistics.py

@@ -0,0 +1,15 @@
+import numpy as np
+
+from ..statistics import stats
+
+def test_simple_stats():
+    a = np.ones(10)
+    truth = {'mean': 1,
+            'median': 1,
+            'stddev': 0,
+            'total': 9,
+            'npoints': 10}
+
+    calc = stats(a)
+
+    assert calc == truth, "Crazy wrong stats"

specviz/core/comms.py

@@ -16,13 +16,13 @@
 
 
 class EventNode(object):
-    """
-    An event
+    """An event
 
     An event is defined by the arguments the listeners
     of the event expect to be given.
 
     Parameters
+    ----------
     args: [arg, ...]
         The list of keyword arguments that the event
         will provide to its listeners

specviz/io/loaders/hstcos_loader.py

@@ -45,7 +45,12 @@ def cos_spectrum_loader(file_name, **kwargs):
 
         uncertainty = StdDevUncertainty(hdu[1].data["ERROR"].flatten())
         data = hdu[1].data['FLUX'].flatten()
+        dispersion = hdu[1].data['wavelength'].flatten()
         unit = Unit("erg/cm**2 Angstrom s")
 
-    return Spectrum1DRef(data=data, name=name,
-                         uncertainty=uncertainty, unit=unit, meta=meta)
+    return Spectrum1DRef.from_array(data=data,
+                                    dispersion=dispersion,
+                                    dispersion_unit=Unit('Angstrom'),
+                                    uncertainty=uncertainty,
+                                    unit=unit,
+                                    meta=meta)

specviz/io/loaders/hststis_loader.py

@@ -45,7 +45,12 @@ def stis_spectrum_loader(file_name, **kwargs):
 
         uncertainty = StdDevUncertainty(hdu[1].data["ERROR"].flatten())
         data = hdu[1].data['FLUX'].flatten()
+        dispersion = hdu[1].data['wavelength'].flatten()
         unit = Unit("erg/cm**2 Angstrom s")
 
-    return Spectrum1DRef(data=data, name=name,
-                         uncertainty=uncertainty, unit=unit, meta=meta)
+    return Spectrum1DRef.from_array(data=data,
+                                    dispersion=dispersion,
+                                    dispersion_unit=Unit('Angstrom'),
+                                    uncertainty=uncertainty,
+                                    unit=unit,
+                                    meta=meta)