Merge pull request #284 from nmearl/master

Bug squashing and polish

.travis.yml

@@ -5,7 +5,7 @@ os:
   - osx
 
 # Setting sudo to false opts in to Travis-CI container-based builds.
-sudo: false
+sudo: true
 
 # The apt packages below are needed for sphinx builds. A full list of packages
 # that can be included can be found here:
@@ -95,4 +95,4 @@ after_success:
     # If coveralls.io is set up for this package, uncomment the line
     # below and replace "packagename" with the name of your package.
     # The coveragerc file may be customized as needed for your package.
-    # - if [[ $SETUP_CMD == 'test --coverage' ]]; then coveralls --rcfile='packagename/tests/coveragerc'; fi
+# - if [[ $SETUP_CMD == 'test --coverage' ]]; then coveralls --rcfile='packagename/tests/coveragerc'; fi

docs/source/conf.py

@@ -68,9 +68,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.1'
+version = '0.3'
 # The full version, including alpha/beta/rc tags.
-release = '0.1.0a1'
+release = '0.3.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/source/index.rst

@@ -23,18 +23,18 @@ emission and absorption lines in addition to regions of flat continuua).
 SpecViz incorporates various methods for fitting such models to data. For more
 details, see :ref:`doc_model_fitting`.
 
-Furthermore, SpecViz allows for overplotting or simple combining of spectra.
+Furthermore, SpecViz allows for overplotting or combining of spectra.
 
 SpecViz will soon include the ability to
-   - Measure the average of multiple spectra, splice a spectrum, and apply Fourier filters.
+   - Measure the average of multiple spectra, detrending, and apply Fourier filters.
    - Interactively renormalize data from spectral templates.
    - Overplot spectral line lists.
    - And more...
 
 Demo
 ----
 
-.. image:: https://i.vimeocdn.com/video/571749719_640.jpg
+.. image:: _static/demo.png
    :target: https://stsci.box.com/s/6ynrfshzrix3yaxvd3c8bcs4hzltpadz
 
 
@@ -45,6 +45,7 @@ Installation and Setup
    :maxdepth: 2
 
    installation
+   launching
 
 
 Using SpecViz

docs/source/installation.rst

@@ -31,21 +31,13 @@ any terminal::
     $ specviz
 
 
-PyQt5 version (optional)
-^^^^^^^^^^^^^^^^^^^^^^^^
+Uninstalling
+^^^^^^^^^^^^
 
-While the PyQt4 version of SpecViz is currently the default distributed, it
-is recommended that you upgrade to using the PyQt5 version if you know that
-you do not have any system conflicts. Note that this is entirely optional,
-but encouraged due to the fact that `Qt4 development and support has ended
-<http://blog.qt.io/blog/2015/05/26/qt-4-8-7-released/>`_. ::
+To uninstall via Anaconda, simply type the following at a command line::
 
-    $ conda install --channel https://conda.anaconda.org/spyder-ide pyqt5
-    $ conda install --channel https://conda.anaconda.org/nmearl specviz
+    $ conda uninstall specviz
 
-SpecViz can then be launched via the command line::
-
-    $ specviz
 
 Install via source
 ------------------
@@ -60,70 +52,58 @@ handled automatically by the setup functions, with the exception of PyQt/PySide.
 * Numpy
 * Scipy
 * PyQtGraph
+* qtpy
 
 
-Installing PyQt/PySide
-^^^^^^^^^^^^^^^^^^^^^^
-
-The easiest way to install PyQt/PySide is through some package manager.
-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>`__.
+Installing
+^^^^^^^^^^
 
-PyQt5
-"""""
+Clone the SpecViz repository somewhere on your system, and install locally using
+``pip``. If you are using an Anaconda virtual environment, please be sure to
+activate it first before installing: ``$ source activate <environment_name>``.
 
-Homebrew
-   `Install using Homebrew for Qt5 <http://brewformulas.org/Pyqt5>`_.
+::
 
-Anaconda
-   Installing PyQt5 with Anaconda will require installing from the Spyder-IDE
-   channel as it is not currently a core package (but they're working on it).
-   ::
+    $ git clone https://github.com/spacetelescope/specviz.git
+    $ cd specviz
+    $ git checkout tags/v0.3.0
+    $ pip install -r requirements.txt
 
-    $ conda install --channel https://anaconda.org/m-labs/pyqt5 pyqt5
+This uses the ``pip`` installation system, so please note that
 
+1. You need to have ``pip`` installed (included in most Python installations).
+2. You do **not** need to run ``python setup.py install``.
+3. You do **not** need to install the dependencies by hand (except for PyQt).
 
-PyQt4
-"""""
+Likewise, the ``pip`` command will use your default Python to install.
+You can specify by using ``pip2`` or ``pip3``, if you're not using a virtual
+environment.
 
-Homebrew
-   `Install using Homebrew for Qt4 <http://brewformulas.org/Pyqt4>`_.
 
-Anaconda
-   Install using Anaconda::
+PyQt/PySide bindings
+^^^^^^^^^^^^^^^^^^^^
 
-    $ conda install pyqt
+SpecViz requires PyQt. Currently, only python environments with 3.5 or higher
+installed can use ``pip`` to install PyQt5, in which case simply type::
 
+    $ pip install pyqt5
 
-Installing
-^^^^^^^^^^
+to install it on your system.
 
-Clone the SpecViz repository somewhere on your system, and install locally using
-``pip``. If you are using an Anaconda virtual environment, please be sure to
-activate it first before installing: ``$ source activate <environment_name>``.
+In any other case, PyQt can be installed via anaconda::
 
-::
+    $ conda install pyqt
 
-    $ git clone https://github.com/spacetelescope/specviz.git
-    $ cd specviz
-    $ git checkout tags/v0.1.2rc3
-    $ pip install -r requirements.txt
+SpecViz works with with PyQt4 and PySide, but it is recommended that users use
+PyQt5 if available.
 
-.. note::
 
-   This uses the ``pip`` installation system, so please note that
+Uninstalling
+^^^^^^^^^^^^
 
-   1. You need to have ``pip`` installed (included in most Python
-      installations).
-   2. You do **not** need to run ``python setup.py install``.
-   3. You do **not** need to install the dependencies by hand (except for PyQt).
+To uninstall via ``pip``, simply type the following at a command line::
 
-   Likewise, the ``pip`` command will use your default Python to install.
-   You can specify by using ``pip2`` or ``pip3``, if you're not using a virtual
-   environment.
+    $ pip uninstall specviz
 
 
 Known Issues
@@ -154,19 +134,3 @@ This issue can be solved with the following command::
 
     $ conda uninstall pyqt5 qt5
 
-
-.. _doc_launching:
-
-Launching SpecViz
-=================
-
-Once you've installed SpecViz, you can launch it via the command line::
-
-    $ specviz
-
-
-If you only wish to inspect a single FITS or ASCII file using the default
-:ref:`doc_custom_loaders` file formatting, you can also pass in the filename
-as a command line argument, as follows::
-
-    $ specviz filename

docs/source/launching.rst

@@ -0,0 +1,20 @@
+.. _doc_launching:
+
+Launching SpecViz
+=================
+
+Once you've installed SpecViz, you can launch it via the command line::
+
+    $ specviz
+
+
+If you only wish to inspect a single FITS or ASCII file using the default
+:ref:`doc_custom_loaders` file formatting, you can also pass in the filename
+as a command line argument, as follows::
+
+    $ specviz filename
+
+
+You may also include the name of a custom loader as second optional argument::
+
+    $ specviz filename --format="my-custom-format"

docs/source/model_fitting.rst

@@ -44,19 +44,22 @@ SLSQP               `~astropy.modeling.fitting.SLSQPLSQFitter`
 
 To use a model:
 
-#. Select the layer you wish to operate on from the LAYERS window in the upper left.
-#. Create and position a region of interest (ROI) as described in the :ref:`doc_viewer` section of
-     the documentation.”
+#. Select the layer you wish to operate on from the "Layer List" window in the
+   bottom left. For example, you can choose the layer containing your emission
+   or absorption line.
+#. Create and position a region of interest (ROI) as described in the
+   :ref:`doc_viewer` section of the documentation.
 #. Select the desired model from the ``Add Model`` drop-down box and click
    ``Select`` to add it to ``Current Models``.
 #. If desired, repeat the above step to add additional models.
-#. A new model layer will be created under ``Layers`` (left panel) and it is
-   attached to the selected data layer.
+#. A new model layer will be created under your data layer in the "Layer List"
+   window.
 
-To edit model parameters or enter a better first estimate of the model parameters:
+To edit model parameters or enter a better first estimate of the model
+parameters:
 
-#. Select the model layer under ``Layers`` (left panel) that contains the desired
-   model.
+#. Select the model layer in the "Layer List" window that contains the
+   desired model.
 #. If desired, double-click on the model name to rename it. When you see a
    blinking cursor, enter its new name and press "Enter".
 #. Expand the model listing under ``Current Models`` on the right of the viewer.
@@ -135,7 +138,7 @@ accessed, and varied, by the fitter. Thus, the spline parameters are not fitted,
 they are just a convenient mechanism that enables user access to the parameter's
 values.
 
-The documentation for the spline model can be seen here:
+The documentation for the spline model can be found here:
 
 http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.interpolate.UnivariateSpline.html
 
@@ -152,44 +155,45 @@ value.
     Model arithmetic is a work in progress.
 
 
-Saving and Exporting Models to File
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Saving and exporting models to a file
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Selecting a model layer under "Layers" will enable the
 :ref:`Save <doc_model_save>` (the "floppy disk" icon) and
 :ref:`doc_model_export` (the "out the door" icon) buttons under
-"Current Models" on the right of the viewer. Saving a model to a file will
-enable SpecViz to read back that model into a new model layer. Exporting a model
+"Current Models" on the right of the viewer. When a model is saved as a file on
+disk, it can later be read into SpecViz as described below. Exporting a model
 to a file wil create a Python script in a ``.py`` file. This file can be
 directly imported by Python in a command-line session.
 
-Click on either button to get a file dialog window. Type in a file name.
-If this file name does not end with the correct suffix, the suffix will
-automatically be appended. Click "Save", or just the Return/Enter key.
-The correct suffix for saved and exported files are ``.yaml`` and ``.py``,
-respectively.
+Click on either button to get a file dialog window. Provide a name for the model
+file, if this file name does not end with the
+correct suffix, the suffix will automatically be appended. Click "Save", or
+just press the Return/Enter key. The correct suffix for saved and exported files are
+``.yaml`` and ``.py``, respectively.
 
 
 .. _doc_model_save:
 
-Save and Load
+Save and load
 ^^^^^^^^^^^^^
 
 Saving the model to a file works in the same way as :ref:`doc_model_export`.
 The difference is that a saved model can be later read back into SpecViz via
-the "Load" button (the "folder" icon), also under "Current Models".
+the "Load" button (the "folder" icon), also under "Current Models", whereas the
+exported model cannot.
 
 For the "Load" button to be enabled, a data (spectrum) layer (not a model layer)
-must be selected under "Layers" listing. The selected ``.yaml`` model file will
-generate a model that will be attached to a new model layer associated under the
-selected data layer.
+must be selected in the "Layer List" window. The selected ``.yaml`` model file
+will generate a model that will be attached to a new model layer associated
+with the selected data layer.
 
-The file is writen using the YAML format. Being a plain text file with a
+The file is writen in the YAML format. Being a plain text file with a
 self-explanatory structure, it can be edited at will by the user, e.g., to add
 bounds, fixed flags, and ties to the model parameters. Note that these extra,
 user-defined attributes, won't be accessible from SpecViz's user interface.
-They will however, be accessible by the fitter when a fit is run on the
-model. They will also be written ou correctly, either when saving or exporting
+They will however, be used by the fitter when a fit is run on the
+model. They will also be written out correctly, either when saving or exporting
 the model.
 
 .. note::
@@ -205,8 +209,8 @@ Export
 
 This will save the model in the currently selected model layer to a file
 that can be directly imported by Python. The file is just a plain text
-file with the model expressed recorded as a Python expression. The model
-is associated to a variable named ``'model1'``.
+file with the model given as a Python expression. The model
+is associated a variable named ``'model1'``.
 
 The following example uses the ``'test3.py'`` file name, and a model comprised
 of a constant and a gaussian:
@@ -228,11 +232,11 @@ of a constant and a gaussian:
      -------------- ------------- ------------- -------------
      0.297160787184 2.25396100263 15117.1710847 948.493577186
 
-The file can be edited at will by the user, e.g., to add bounds, fixed flags,
+The file can be edited by the user, e.g., to add bounds, fixed flags,
 and ties to the model parameters.
 
-.. note::
+.. warning::
 
-    Security issues importing model this way into Python and usage of advanced
-    features like bounds and fixed flags are work in progress.
+    Security issues with importing model this way into Python and usage of
+    advanced features like bounds and fixed flags are work in progress.