Merge pull request #1425 from astrofrog/misc-bug-fixes

Miscellaneous bug fixes

.travis.yml

@@ -20,18 +20,16 @@ env:
     - PYTHON_VERSION=3.6
   global:
     # We add astropy-ci-extras to have the latest version of Astropy with older Numpy versions.
-    - CONDA_CHANNELS=astropy-ci-extras
-    - MATPLOTLIB_VERSION=1.5
-    - NUMPY_VERSION=1.11
-    - ASTROPY_VERSION=1.3
-    - IPYTHON_VERSION=5
+    - CONDA_CHANNELS="astropy-ci-extras astropy"
     - PYTEST_ARGS="--cov glue -vs"
+    - ASTROPY_VERSION=stable
+    - NUMPY_VERSION=stable
     - NO_CFG_FILES=false
     - QT_PKG=pyqt5
     - SETUP_XVFB=True
-    - SPHINX_VERSION=1.5
-    - CONDA_DEPENDENCIES="pip dill ipython matplotlib scipy cython h5py pygments pyzmq scikit-image pandas sphinx xlrd pillow pytest mock coverage pyyaml sphinx_rtd_theme qtpy traitlets ipykernel qtconsole"
-    - PIP_DEPENDENCIES="pytest-cov coveralls pyavm astrodendro awscli plotly spectral-cube"
+    - CONDA_DEPENDENCIES="pip dill ipython matplotlib scipy cython h5py pygments pyzmq scikit-image pandas sphinx xlrd pillow pytest mock coverage pyyaml sphinx_rtd_theme qtpy traitlets ipykernel qtconsole spectral-cube pytest-cov"
+    - PIP_DEPENDENCIES="coveralls pyavm astrodendro awscli plotly"
+    - PIP_FALLBACK=false
     - REMOVE_INSTALL_REQUIRES=0
     - secure: NvQVc3XmmjXNVKrmaD31IgltsOImlnt3frAl4wU0pM223iejr7V57hz/V5Isx6sTANWEiRBMG27v2T8e5IiB7DQTxFUleZk3DWXQV1grw/GarEGUawXAgwDWpF0AE/7BRVJYqo2Elgaqf28+Jkun8ewvfPCiEROD2jWEpnZj+IQ=
     - secure: "SU9BYH8d9eNigypG3lC83s0NY6Mq9AHGKXyEGeXDtz1npJIC1KHdzPMP1v1K3dzCgl1p6ReMXPjZMCENyfNkad/xvzTzGk0Nu/4BjihrUPV6+ratVeLpv0JLm8ikh8q+sZURkdtzUOlds+Hfn5ku4LdpT87tcKHY9TINAGA34ZM="
@@ -64,20 +62,14 @@ matrix:
                PIP_DEPENDENCIES="pytest-cov coveralls"
                REMOVE_INSTALL_REQUIRES=1
 
-        # We need to keep the following on 2.7 because of linkchecker
         - os: linux
-          env: PYTHON_VERSION=2.7
+          env: PYTHON_VERSION=3.6
                DOC_TRIGGER=1
-               APP_TRIGGER=1
                PYTEST_ARGS="--cov glue --no-optional-skip"
                NO_CFG_FILES=true
 
         # Test with older package versions:
 
-        - os: linux
-          env: PYTHON_VERSION=2.7
-               QT_PKG=pyqt
-
         - os: linux
           env: PYTHON_VERSION=2.7
                MATPLOTLIB_VERSION=1.4
@@ -125,9 +117,7 @@ before_install:
   - if [[ $QT_PKG == pyqt5 ]]; then export CONDA_DEPENDENCIES="pyqt=5 "$CONDA_DEPENDENCIES; fi
 
   # Documentation dependencies
-  # Note that we need to specify requests 2.9 because of a bug in the version check in linkchecker,
-  # and we can't use conda since requests 2.9 won't exist for e.g. Python 3.6
-  - if [ $DOC_TRIGGER ]; then export PIP_DEPENDENCIES="sphinx-automodapi numpydoc linkchecker requests==2.9 "$PIP_DEPENDENCIES; fi
+  - if [ $DOC_TRIGGER ]; then export PIP_DEPENDENCIES="sphinx-automodapi numpydoc requests "$PIP_DEPENDENCIES; fi
 
   # Install ci-helpers and set up conda
   - git clone git://github.com/astropy/ci-helpers.git
@@ -204,16 +194,19 @@ script:
 
   - if [[ $QT_PKG == False ]]; then glue --version; fi
 
-  - python setup.py test -a "$PYTEST_ARGS";
+  - python setup.py test -a "$PYTEST_ARGS"
 
   # In the following, we use separate if statements for each line, to make
   # sure the exit code from each one is taken into account for the overall
   # exit code.
-  - if [ $DOC_TRIGGER ]; then cd doc; make html 2> warnings.log; cd ..; fi
+  - if [ $DOC_TRIGGER ]; then cd doc; make html linkcheck 2> warnings.log; cd ..; fi
   - if [ $DOC_TRIGGER ]; then cat doc/warnings.log; fi
   # make sure stderr was empty, i.e. no warnings
   - if [ $DOC_TRIGGER ]; then test ! -s doc/warnings.log; fi
-  - if [ $DOC_TRIGGER ]; then linkchecker --ignore-url=".*fontawesome.*" doc/_build/html; fi
+
+  # Check for any broken links, ignore 'redirected with Found'
+  - if [ $DOC_TRIGGER ]; then grep -v "redirected with Found" doc/_build/linkcheck/output.txt > doc/_build/linkcheck/output_no_found_redirect.txt; fi
+  - if [ $DOC_TRIGGER ]; then test ! -s doc/_build/linkcheck/output_no_found_redirect.txt; fi
 
 after_success:
 

CHANGES.md

@@ -16,6 +16,29 @@ v0.11.2 (unreleased)
 * Fixed bug in spectrum tool that caused the upper range in aggregations
   to be incorrectly calculated. [#1402]
 
+* Fixed icon for scatter plot layer when a colormap is used, and fix issues with
+  viewer layer icons not updating immediately. [#1425]
+
+* Fixed dragging and dropping session files onto glue (this now loads the session
+  rather than trying to load it as a dataset). Also now show a warning when
+  the application is about to be reset to open a new session. [#1425]
+
+* Make sure no errors happen if making a selection in an empty viewer. [#1425]
+
+* Fix creating faceted subsets on Python 3.x when no dataset is selected. [#1425]
+
+* Fix issues with overlaying a scatter layer on an image. [#1425]
+
+* Fix issues with labels for categorical axes in the scatter and histogram
+  viewers, in particular when loading viewers with categorical axes from
+  session files. [#1425]
+
+* Make sure a GUI error message is shown when adding non-1-dimensional data
+  to a table viewer. [#1425]
+
+* Fix issues when trying to launch glue multiple times from a Jupyter session.
+  [#1425]
+
 v0.11.1 (2017-08-25)
 --------------------
 

appveyor.yml

@@ -12,6 +12,7 @@ environment:
                         # to the matrix section.
       CONDA_DEPENDENCIES: "astropy scipy cython pyqt matplotlib h5py pygments pyzmq scikit-image pandas xlrd pillow pytest mock coverage ipython ipykernel qtconsole traitlets qtpy"
       PIP_DEPENDENCIES: "plotly"
+      PIP_FALLBACK: "False"
 
   matrix:
       - PYTHON_VERSION: "2.7"

doc/customizing_guide/customization.rst

@@ -38,7 +38,7 @@ specify custom translation functions. Here's how:
 .. literalinclude:: scripts/config_link_example.py
 
 Some remarks about this code:
- #. ``link_function`` is used as a `decorator <http://stackoverflow.com/questions/739654/understanding-python-decorators/1594484#1594484>`_. The decorator adds the function to Glue's list of link functions
+ #. ``link_function`` is used as a `decorator <https://stackoverflow.com/a/1594484/180783>`_. The decorator adds the function to Glue's list of link functions
  #. We provide a short summary of the function in the ``info`` keyword, and a list of ``output_labels``. Usually, only one quantity is returned, so ``output_labels`` has one element.
  #. Glue will always pass numpy arrays as inputs to a link function, and expects a numpy array (or a tuple of numpy arrays) as output
 

doc/developer_guide/coding_guidelines.rst

@@ -4,7 +4,7 @@ Coding guidelines
 Glue is written entirely in Python, and we abide by the following guidelines:
 
 * All code should be Python 2 and 3-compatible. We do this by using the `six
-  <https://pythonhosted.org/six/>`_ package, which we bundle in
+  <https://pypi.python.org/pypi/six>`_ package, which we bundle in
   ``glue.external.six``.
 
 * We follow many of the same guidelines as the `Astropy <http://www.astropy.org>`_ project, which you can find `here <http://docs.astropy.org/en/stable/development/codeguide.html#coding-style-conventions>`__.

doc/developer_guide/testing.rst

@@ -47,13 +47,13 @@ Continuous integration
 
 Every time someone opens a pull request to the Glue repository, and every time
 we merge changes into the code base, all the tests are run on `Travis
-<http://travis-ci.org>`_ and `AppVeyor <http://www.appveyor.com/>`_. This is
+<https://travis-ci.org>`_ and `AppVeyor <https://www.appveyor.com/>`_. This is
 referred to as *Continuous Integration*. One of the nice things about continuous integration is that it allows us to
 automatically run the tests for different operating systems, Python versions,
 versions of Numpy, and Qt frameworks (PyQt4, PyQt5, and PySide).
 
-`Travis <http://travis-ci.org>`_ runs tests on Linux and MacOS X, and `AppVeyor
-<http://www.appveyor.com/>`_ runs the tests on Windows. When you open a pull
+`Travis <https://travis-ci.org>`_ runs tests on Linux and MacOS X, and `AppVeyor
+<https://www.appveyor.com/>`_ runs the tests on Windows. When you open a pull
 request, you will be able to check the status of the tests at the bottom, which
 will look something like this:
 

doc/faq.rst

@@ -78,7 +78,7 @@ Something is broken, or confusing. What should I do?
 ----------------------------------------------------
 
 If you think you've found a bug in Glue, feel free to add an issue to the
-`GitHub issues page <https://github.com/glue-viz/glue/issues?state=open>`_. If
+`GitHub issues page <https://github.com/glue-viz/glue/issues?q=is%3Aopen>`_. If
 you have general questions, feel free to post a message to the `Glue mailing
 list <https://groups.google.com/forum/#!forum/glue-viz>`_, or send us an `email
 <mailto:glue.viz@gmail.com>`_ directly.

doc/getting_started/index.rst

@@ -40,7 +40,7 @@ There are multiple ways to open data:
   Find and open the file ``w5.fits`` which should be in the ``w5.tgz`` or
   ``w5.zip`` archive you downloaded above. This is a `WISE image
   <http://wise.ssl.berkeley.edu/>`_ of the `W5 Star Forming Region
-  <http://en.wikipedia.org/wiki/Soul_Nebula>`_. While this is an astronomical
+  <https://en.wikipedia.org/wiki/Soul_Nebula>`_. While this is an astronomical
   dataset, glue can be used for data in any discipline, and many of the concepts
   shown below are applicable to many types of dataset.
 

doc/gui_guide/3d_viewers.rst

@@ -3,7 +3,7 @@
 3D viewers in Glue
 ==================
 
-A plugin with 3D viewers for glue, powered by `VisPy <http://www.vispy.org>`_,
+A plugin with 3D viewers for glue, powered by `VisPy <http://vispy.org/>`_,
 is available. Provided that you installed glue with ``conda`` or with ``pip``,
 you should already have the 3D viewers available. You can check this by going to
 the **Canvas** menu in glue and selecting **New Data Viewer**, or alternatively
@@ -15,7 +15,7 @@ installed, you should see the 3D viewers in the list:
    :width: 339
 
 If you don't see these in the list, then if you are using
-`Anaconda <https://www.continuum.io/downloads>`_ to manage your Python
+`Anaconda <https://www.anaconda.com/download/>`_ to manage your Python
 distribution, you can install the 3D viewers plugin using::
 
     pip install glue-vispy-viewers
@@ -97,13 +97,13 @@ experimental and currently very slow for displaying isosurfaces. In addition, it
 is only able to show a single isosurface level. We do not recommend using it at
 this time, and have disabled it by default. If you are interested in trying it
 out, see the `README.md
-<https://github.com/glue-viz/glue-vispy-viewers/blob/master/README.md>`_ file in
+<https://github.com/glue-viz/glue-vispy-viewers/blob/master/README.rst>`_ file in
 the glue-vispy-viewers repository.
 
 Reporting issues
 ----------------
 
 Please report any issues with the 3D viewers in the following `issue tracker
-<https://github.com/glue-viz/glue-3d-viewer/issues>`_. Please first check that
+<https://github.com/glue-viz/glue-vispy-viewers/issues>`_. Please first check that
 there is not already a similar issue open -- if there is, please feel free to
 comment on that issue to let us know you ran into that problem too!

doc/gui_guide/spectrum.rst

@@ -151,7 +151,7 @@ parameter names. Each value is itself a dictionary with 4 entries:
 Astropy-based models
 ^^^^^^^^^^^^^^^^^^^^
 
-The :class:`~glue.core.fitters.AstropyFitter1D` base class can be subclassed to plug custom `astropy models and fitters <http://astropy.readthedocs.org/en/latest/modeling/>`_ into Glue. This is very easy::
+The :class:`~glue.core.fitters.AstropyFitter1D` base class can be subclassed to plug custom `astropy models and fitters <http://astropy.readthedocs.io/en/stable/modeling/>`_ into Glue. This is very easy::
 
     from astropy.modeling import models, fitting
 
@@ -181,4 +181,4 @@ of these ideas.
 
 .. figure:: images/emcee_screenshot.png
    :align: center
-   :width: 400
+   :width: 400

doc/installation/conda.rst

@@ -4,7 +4,7 @@ Anaconda Python Distribution (Recommended)
 
 **Platforms:** MacOS X, Linux, and Windows
 
-We recommend using the `Anaconda <http://continuum.io/downloads.html>`__ Python
+We recommend using the `Anaconda <https://www.anaconda.com/download/>`__ Python
 distribution from Continuum Analytics (or the related Miniconda distribution).
 Anaconda includes all of Glue's main dependencies. There are two ways of
 installing Glue with the Anaconda Python Distribution: :ref:`graphically using the

doc/installation/dependencies.rst

@@ -7,26 +7,26 @@ Glue has the following required dependencies:
 
 * Python 2.7, or 3.3 and higher
 * `Numpy <http://www.numpy.org>`_ 1.9 or later
-* `Matplotlib <http://www.matplotlib.org>`_ 1.4 or later
+* `Matplotlib <http://matplotlib.org/>`_ 1.4 or later
 * `Pandas <http://pandas.pydata.org/>`_ 0.14 or later
 * `Astropy <http://www.astropy.org>`_ 1.0 or higher
 * `setuptools <http://setuptools.readthedocs.io/en/latest/>`_ 1.0 or later
-* Either `PySide <http://pyside.org>`__ or `PyQt
+* Either `PySide <https://wiki.qt.io/PySide>`__ or `PyQt
   <https://riverbankcomputing.com/software/pyqt/intro>`__ (both PyQt4 and PyQt5 are supported)
-* `QtPy <https://pypi.python.org/pypi/QtPy/>`__ 1.1.1 or higher - this is an
+* `QtPy <https://pypi.python.org/pypi/QtPy/>`__ 1.2 or higher - this is an
   abstraction layer for the Python Qt packages
 * `IPython <http://ipython.org>`_ 4.0 or higher
 * `ipykernel <https://pypi.python.org/pypi/ipykernel>`_
 * `qtconsole <http://jupyter.org/qtconsole/>`_
-* `dill <http://pythonhosted.org/dill/>`_ 0.2 or later (which improves session saving)
+* `dill <https://pypi.python.org/pypi/dill>`_ 0.2 or later (which improves session saving)
 * `h5py <http://www.h5py.org>`_ 2.4 or later, for reading HDF5 files
 * `xlrd <https://pypi.python.org/pypi/xlrd>`_ 1.0 or later, for reading Excel files
 * `glue-vispy-viewers <https://pypi.python.org/pypi/glue-vispy-viewers>`_, which provide 3D viewers
 
 The following optional dependencies are also highly recommended and
 domain-independent:
 
-* `SciPy <http://www.scipy.org>`_
+* `SciPy <https://www.scipy.org>`_
 * `scikit-image <http://scikit-image.org>`_
 * `plotly <https://plot.ly>`_ for exporting to plot.ly
 

doc/installation/pip.rst

@@ -3,10 +3,10 @@ Installing with pip
 
 **Platforms:** MacOS X, Linux, and Windows
 
-Installing glue with `pip <https://pip.pypa.io>`__ is possible, although you
+Installing glue with `pip <https://pip.pypa.io/en/stable/>`__ is possible, although you
 will need to first make sure that you install Qt and either `PyQt
 <https://riverbankcomputing.com/software/pyqt/intro>`__ or `PySide
-<http://pyside.org>`__, since these cannot be automatically installed with the
+<https://wiki.qt.io/PySide>`__, since these cannot be automatically installed with the
 ``pip`` command. See the section on :ref:`installing-qt` for more details.
 
 Assuming that you have either PyQt or PySide installed, you can install glue

doc/python_guide/data_tutorial.rst

@@ -201,7 +201,7 @@ If you using the Glue application, you can then change the visual properties of
 
 This method of creating subsets can be a powerful technique. For a demo of
 using sending Scikit-learn-identified clusters back into Glue as subsets, see
-`this notebook <http://nbviewer.ipython.org/github/ChrisBeaumont/crime/blob/master/glue_startup.ipynb>`_.
+`this notebook <http://nbviewer.jupyter.org/github/ChrisBeaumont/crime/blob/master/glue_startup.ipynb>`_.
 
 The following example demonstrates how to access subsets defined graphically in data viewers. Let's say that you have two subsets that you defined in the scatter plot and histogram data viewers:
 

doc/videos.rst

@@ -46,7 +46,7 @@ Glue, FBI Crime Data, and Plotly (5 minutes)
  <iframe src="http://player.vimeo.com/video/97436621" width="500" height="313" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe> <
  </center>
 
-See also the `IPython notebook <http://nbviewer.ipython.org/github/ChrisBeaumont/crime/blob/master/glue_plotly_fbi.ipynb>`_ that accompanies this video.
+See also the `IPython notebook <http://nbviewer.jupyter.org/github/ChrisBeaumont/crime/blob/master/glue_plotly_fbi.ipynb>`_ that accompanies this video.
 
 Extracting slices from cubes
 ----------------------------

doc/whatsnew/0.11.rst

@@ -96,7 +96,7 @@ Experimental WorldWide Telescope plugin
 ---------------------------------------
 
 We have developed a plugin that provides a `WorldWide Telescope (WWT)
-<http://worldwidetelescope.org>`_ viewer inside glue:
+<http://worldwidetelescope.org/webclient/>`_ viewer inside glue:
 
 .. image:: images/v0.11/plugin_wwt.jpg
    :align: center