Merge branch 'RELEASE_next_minor' into RELEASE_next_major

.coveragerc

@@ -4,9 +4,7 @@ source = hyperspy
 include = */hyperspy/*
 omit =
     */hyperspy/external/*
-    */hyperspy/ipython_profile/*
-    */hyperspy/gui/*
+    */hyperspy/gui_traitsui/*
     */setup.py
     */examples/*
-    */bin/*
     */continuous_integration/*

.travis.yml

@@ -33,8 +33,8 @@ before_install:
 install:
 
   - if [[ $MINIMAL_ENV == 'False' ]] ; then
-      DEPS="pip numpy scipy matplotlib ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython lxml ipyparallel dask traits traitsui";
-    else DEPS="pip ipython numpy scipy matplotlib h5py sympy scikit-image";
+      DEPS="pip numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython lxml ipyparallel dask traits traitsui";
+    else DEPS="pip ipython numpy scipy matplotlib>=2.0.2 h5py sympy scikit-image";
     fi
   - conda create -n testenv --yes python=$PYTHON;
     source activate testenv;

CHANGES.txt

@@ -5,18 +5,127 @@ We only cover here the main highlights, for a detailed list of all the changes
 see `the commits in the GITHUB milestones
 <https://github.com/hyperspy/hyperspy/milestones?state=closed>`_.
 
+.. _changes_1.3:
+
+v1.3
+====
+
+This is a minor release. Follow the following links for details on all
+the `bugs fixed
+<https://github.com/hyperspy/hyperspy/issues?q=label%3A"type%3A+bug"+is%3Aclosed+milestone%3Av1.3>`_,
+`feature
+<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.3+label%3A"type%3A+enhancement">`_
+and `documentation
+<https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=is%3Aclosed%20milestone%3Av1.3%20label%3A%22affects%3A%20documentation%22%20>`_ enhancements,
+and `new features
+<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.3+label%3A"type%3A+New+feature">`_.
+
+NEW
+---
+* :py:meth:`~.signal.BaseSignal.rebin` supports upscaling and rebinning to
+  arbitrary sizes through linear interpolation. See :ref:`rebin-label`. It also runs faster if `numba <http://numba.pydata.org/>`_ is installed.
+* :py:attr:`~.axes.AxesManager.signal_extent` and :py:attr:`~.axes.AxesManager.navigation_extent` properties to easily get the extent of each space.
+* New IPywidgets Graphical User Interface (GUI) elements for the `Jupyter Notebook <http://jupyter.org>`_.
+  See the new `hyperspy_gui_ipywidgets <https://github.com/hyperspy/hyperspy_gui_ipywidgets>`_ package.
+  It is not installed by default, see :ref:`install-label` for details.
+* All the :ref:`roi-label` now have a :meth:`gui` method to display a GUI if
+  at least one of HyperSpy's GUI packgages are installed.
+
+Enhancements
+------------
+* Creating many markers is now much faster.
+* New "Stage" metadata node. See :ref:`metadata_structure` for details.
+* The Brucker file reader now supports the new version of the format. See :ref:`bcf-format`.
+* HyperSpy is now compatible with all matplotlib backends, including the nbagg which is
+  particularly convenient for interactive data analysis in the
+  `Jupyter Notebook <http://jupyter.org>`_ in combination with the new
+  `hyperspy_gui_ipywidgets <https://github.com/hyperspy/hyperspy_gui_ipywidgets>`_ package.
+  See :ref:`importing_hyperspy-label`.
+* The ``vmin`` and ``vmax`` arguments of the
+  :py:func:`~.drawing.utils.plot_images` function now accept lists to enable
+  setting these parameters for each plot individually.
+* The :py:meth:`~.signal.MVATools.plot_decomposition_results` and
+  :py:meth:`~.signal.MVATools.plot_bss_results` methods now makes a better
+  guess of the number of navigators (if any) required to visualise the
+  components. (Previously they were always plotting four figures by default.)
+* All functions that take a signal range can now take a :py:class:`~.roi.SpanROI`.
+* The following ROIs can now be used for indexing or slicing (see :ref:`here <roi-slice-label>` for details):
+
+    * :py:class:`~.roi.Point1DROI`
+    * :py:class:`~.roi.Point2DROI`
+    * :py:class:`~.roi.SpanROI`
+    * :py:class:`~.roi.RectangularROI`
+
+
+API changes
+-----------
+* Permanent markers (if any) are now displayed when plotting by default.
+* HyperSpy no longer depends on traitsui (fixing many installation issues) and
+  ipywidgets as the GUI elements based on these packages have now been splitted
+  into separate packages and are not installed by default.
+* The following methods now raise a ``ValueError`` when not providing the
+  number of components if ``output_dimension`` was not specified when
+  performing a decomposition. (Previously they would plot as many figures
+  as available components, usually resulting in memory saturation):
+
+    * :py:meth:`~.signal.MVATools.plot_decomposition_results`.
+    * :py:meth:`~.signal.MVATools.plot_decomposition_factors`.
+
+* The default extension when saving to HDF5 following HyperSpy's specification
+  is now ``hspy`` instead of ``hdf5``. See :ref:`hspy-format`.
+
+* The following methods are deprecated and will be removed in HyperSpy 2.0
+
+    * :py:meth:`~.axes.AxesManager.show`. Use :py:meth:`~.axes.AxesManager.gui`
+      instead.
+    * All :meth:`notebook_interaction` method. Use the equivalent :meth:`gui` method
+      instead.
+    * :py:meth:`~._signals.signal1d.Signal1D.integrate_in_range`.
+      Use :py:meth:`~._signals.signal1d.Signal1D.integrate1D` instead.
+
+* The following items have been removed from
+  :ref:`preferences <configuring-hyperspy-label>`:
+
+    * ``General.default_export_format``
+    * ``General.lazy``
+    * ``Model.default_fitter``
+    * ``Machine_learning.multiple_files``
+    * ``Machine_learning.same_window``
+    * ``Plot.default_style_to_compare_spectra``
+    * ``Plot.plot_on_load``
+    * ``Plot.pylab_inline``
+    * ``EELS.fine_structure_width``
+    * ``EELS.fine_structure_active``
+    * ``EELS.fine_structure_smoothing``
+    * ``EELS.synchronize_cl_with_ll``
+    * ``EELS.preedge_safe_window_width``
+    * ``EELS.min_distance_between_edges_for_fine_structure``
+
+* New ``Preferences.GUIs`` section to enable/disable the installed GUI toolkits.
+
+For developers
+--------------
+* In addition to adding ipywidgets GUI elements, the traitsui GUI elements have
+  been splitted into a separate package. See the new
+  `hyperspy_gui_traitsui <https://github.com/hyperspy/hyperspy_gui_traitsui>`_
+  package.
+* The new :py:mod:`~.ui_registry` enables easy connection of external
+  GUI elements to HyperSpy. This is the mechanism used to split the traitsui
+  and ipywidgets GUI elements.
+
+
 .. _changes_1.2:
 
 v1.2
 ====
 
 This is a minor release. Follow the following links for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?q=label%3Abug+is%3Aclosed+milestone%3Av1.2>`_,
+<https://github.com/hyperspy/hyperspy/issues?q=label%3A"type%3A+bug"+is%3Aclosed+milestone%3Av1.2>`_,
 `enhancements
-<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.2+label%3Aenhancement>`_
+<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.2+label%3A"type%3A+enhancement">`_
 and `new features
-<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.2+label%3Anew>`_.
+<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.2+label%3A"type%3A+New+feature">`_.
 
 NEW
 ---
@@ -58,14 +167,14 @@ For developers
 
 
 
-.. _changes_1.1.2: 
+.. _changes_1.1.2:
 v1.1.2
 ======
 
 This is a maintenance release. Follow the following links for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?q=label%3Abug+is%3Aclosed+milestone%3Av1.1.2>`_
-and `enhancements <https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.1.2+label%3Aenhancement>`_.
+<https://github.com/hyperspy/hyperspy/issues?q=label%3A"type%3A+bug"+is%3Aclosed+milestone%3Av1.1.2>`_
+and `enhancements <https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3Av1.1.2+label%3A"type%3A+enhancement">`_.
 
 
 .. _changes_1.1.1:
@@ -74,7 +183,7 @@ v1.1.1
 
 This is a maintenance release. Follow the following link for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?q=label%3Abug+is%3Aclosed+milestone%3A1.1.1>`_.
+<https://github.com/hyperspy/hyperspy/issues?q=label%3A"type%3A+bug"+is%3Aclosed+milestone%3A1.1.1>`_.
 
 Enhancements
 ------------
@@ -95,7 +204,7 @@ v1.1
 
 This is a minor release. Follow the following links for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?q=label%3Abug+is%3Aclosed+milestone%3A1.1>`_.
+<https://github.com/hyperspy/hyperspy/issues?q=label%3A"type%3A+bug"+is%3Aclosed+milestone%3A1.1>`_.
 
 NEW
 ---
@@ -121,7 +230,7 @@ v1.0.1
 
 This is a maintenance release. Follow the following links for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?q=label%3Abug+is%3Aclosed+milestone%3A1.0.1>`_.
+<https://github.com/hyperspy/hyperspy/issues?q=label%3A"type%3A+bug"+is%3Aclosed+milestone%3A1.0.1>`_.
 
 
 v1.0
@@ -203,8 +312,8 @@ v0.8.5
 
 This is a maintenance release. Follow the following links for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?q=is%3Aissue+milestone%3A0.8.5+label%3Abug+is%3Aclosed>`_,
-`feature <https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=milestone%3A0.8.5+is%3Aclosed++label%3Aenhancement+>`_
+<https://github.com/hyperspy/hyperspy/issues?q=is%3Aissue+milestone%3A0.8.5+label%3A"type%3A+bug"+is%3Aclosed>`_,
+`feature <https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=milestone%3A0.8.5+is%3Aclosed++label%3A"type%3A+enhancement"+>`_
 and `documentation
 <https://github.com/hyperspy/hyperspy/pulls?utf8=%E2%9C%93&q=milestone%3A0.8.5+label%3Adocumentation+is%3Aclosed+>`_ enhancements.
 
@@ -252,11 +361,11 @@ The broadcasting rules have also changed. See :ref:`signal.operations`
 for details.
 
 Follow the following links for details on all the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?page=1&q=is%3Aclosed+milestone%3A0.8.3+label%3Abug&utf8=%E2%9C%93>`_,
+<https://github.com/hyperspy/hyperspy/issues?page=1&q=is%3Aclosed+milestone%3A0.8.3+label%3A"type%3A+bug"&utf8=%E2%9C%93>`_,
 `documentation enhancements
 <https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3Adocumentation>`_,
 `enhancements
-<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3Aenhancement>`_,
+<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3A"type%3A+enhancement">`_,
 `new features
 <https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3ANew>`_
 `and API changes
@@ -277,9 +386,9 @@ v0.8.1
 
 This is a maintenance release. Follow the following links for details on all
 the `bugs fixed
-<https://github.com/hyperspy/hyperspy/issues?page=1&q=is%3Aclosed+milestone%3A0.8.1+label%3Abug&utf8=%E2%9C%93>`_,
+<https://github.com/hyperspy/hyperspy/issues?page=1&q=is%3Aclosed+milestone%3A0.8.1+label%3A"type%3A+bug"&utf8=%E2%9C%93>`_,
 `feature
-<https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=is%3Aclosed+milestone%3A0.8.1++label%3Aenhancement+>`_
+<https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=is%3Aclosed+milestone%3A0.8.1++label%3A"type%3A+enhancement"+>`_
 and `documentation
 <https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.1+label%3Adocumentation>`_ enhancements.
 

README.rst

@@ -2,11 +2,11 @@
 
 |Travis|_ |AppVeyor|_ |Coveralls|_ |pypi_version|_  |rtd|_ |gitter|_ |saythanks|_
 
-.. |Travis| image:: https://api.travis-ci.org/hyperspy/hyperspy.png?branch=RELEASE_next_major
+.. |Travis| image:: https://api.travis-ci.org/hyperspy/hyperspy.png?branch=RELEASE_next_minor
 .. _Travis: https://travis-ci.org/hyperspy/hyperspy
 
-.. |AppVeyor| image:: https://ci.appveyor.com/api/projects/status/github/hyperspy/hyperspy?svg=true&branch=RELEASE_next_major
-.. _AppVeyor: https://ci.appveyor.com/project/hyperspy/hyperspy/branch/RELEASE_next_major
+.. |AppVeyor| image:: https://ci.appveyor.com/api/projects/status/github/hyperspy/hyperspy?svg=true&branch=RELEASE_next_minor
+.. _AppVeyor: https://ci.appveyor.com/project/hyperspy/hyperspy/branch/RELEASE_next_minor
 
 .. |Coveralls| image:: https://coveralls.io/repos/hyperspy/hyperspy/badge.svg
 .. _Coveralls: https://coveralls.io/r/hyperspy/hyperspy
@@ -21,7 +21,7 @@
 .. _gitter: https://gitter.im/hyperspy/hyperspy?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge
 
 .. |saythanks| image:: https://img.shields.io/badge/say%20-thanks!-orange.svg
-.. _saythanks: https://saythanks.io/to/hyperspy 
+.. _saythanks: https://saythanks.io/to/hyperspy
 
 
 HyperSpy is an open source Python library which provides tools to facilitate
@@ -35,8 +35,7 @@ providing easy access to analytical tools that exploit the multidimensionality
 of the dataset.
 
 Its modular structure makes it easy to add features to analyze different kinds
-of signals. Currently there are specialized tools to analyze electron
-energy-loss spectroscopy (EELS) and energy dispersive X-rays (EDX) data.
+of signals.
 
 HyperSpy is released under the GPL v3 license.
 
@@ -50,5 +49,5 @@ Cite
 
 |DOI|_
 
-.. |DOI| image:: https://zenodo.org/badge/doi/10.5281/zenodo.345099.svg
-.. _DOI: http://dx.doi.org/10.5281/zenodo.345099
+.. |DOI| image:: https://zenodo.org/badge/doi/10.5281/zenodo.583693.svg
+.. _DOI: http://dx.doi.org/10.5281/zenodo.583693

appveyor.yml

@@ -21,8 +21,8 @@ environment:
        CONDA_NPY: "19"
        WP_URL: 'https://github.com/winpython/winpython/releases/download/1.3.20160209/WinPython-32bit-3.5.1.2.exe'
        WP_CRC: '172d19a743ccfaf55af779d15f29f67fca83a46f08b0af855dfaf809b4184c0d'
-       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
-    
+       DEPS: "numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+
      - PYTHON: "C:\\Miniconda35-x64"
        PYTHON_VERSION: "3.5.x"
        PYTHON_MAJOR: 3
@@ -31,21 +31,21 @@ environment:
        CONDA_NPY: "19"
        WP_URL: 'https://github.com/winpython/winpython/releases/download/1.3.20160209/WinPython-64bit-3.5.1.2.exe'
        WP_CRC: '07e854b9aa7a31d8bbf7829d04a45b6d6266603690520e365199af2d98751ab1'
-       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+       DEPS: "numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
 
      - PYTHON: "C:\\Miniconda36"
        PYTHON_VERSION: "3.6.x"
        PYTHON_MAJOR: 3
        PYTHON_ARCH: "32"
        CONDA_PY: "36"
-       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
-    
+       DEPS: "numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+
      - PYTHON: "C:\\Miniconda36-x64"
        PYTHON_VERSION: "3.6.x"
        PYTHON_MAJOR: 3
        PYTHON_ARCH: "64"
        CONDA_PY: "36"
-       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+       DEPS: "numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
 
 
 
@@ -132,6 +132,13 @@ before_deploy:
   - "%CMD_IN_ENV% %WP_INSTDIR%/scripts/env.bat"
   # Give info about python vesion and compiler used to compile the python
   - "%CMD_IN_ENV% python.exe -c \"import sys; print(sys.version)\""
+  # Install scikit-image from Christoph Gohlke binaries repository
+  - cinst wget
+  - ps: Add-AppveyorMessage "Downloading scikit-image..."
+  - ps: if($Env:PYTHON_ARCH -eq "64") {$Env:SCIKIT_IMAGE="https://www.dropbox.com/s/1xn8mgudmtph19i/scikit_image-0.13.0-cp35-cp35m-win_amd64.whl?dl=1"} else {$Env:SCIKIT_IMAGE="https://www.dropbox.com/s/6hwotxy9hoalj25/scikit_image-0.13.0-cp35-cp35m-win32.whl?dl=1"}
+  - "ECHO %SCIKIT_IMAGE%"
+  # - "%CMD_IN_ENV% wget http://www.lfd.uci.edu/~gohlke/pythonlibs/tuoh5y4k/%SCIKIT_IMAGE% --header User-Agent:Chrome/23.0.1271.97"
+  - "%CMD_IN_ENV% pip install %SCIKIT_IMAGE%"
   - "%CMD_IN_ENV% pip install --upgrade tqdm notebook cython ipython configobj start_jupyter_cm ipywidgets ipyparallel sympy pytest"
   # uninstall and reinstall matplotlib to get the 2.0 version without using --upgrade option (to avoid upgrading numpy and breaking scipy...)
   - "%CMD_IN_ENV% pip uninstall -y matplotlib"
@@ -143,11 +150,15 @@ before_deploy:
   # setting back the config:
   - "ren %WP_INSTDIR%\\settings\\pydistutils_bak.cfg pydistutils.cfg"
   # Custom installer step
-  # TODO: Re-run tests in WinPython environment
   - ps: Add-AppveyorMessage "Creating installer..."
   - "%PYTHON%/python.exe -m hspy_bundle.configure_installer %APPDATA%/wpdir %PYTHON_ARCH% %APPVEYOR_REPO_TAG_NAME%"
   - "\"%NSIS_DIR%/makensis.exe\" /V3 NSIS_installer_script-%PYTHON_ARCH%bit.nsi"
-  - ps: Add-AppveyorMessage "Installer created! Pushing to GitHub..."
+  - ps: Add-AppveyorMessage "Installer created! Re-run tests in Winpython environment..."
+  # Re-run tests in WinPython environment
+  - ps: if($Env:PYTHON_ARCH -eq "64") {$Env:PYTHON_DIR_NAME="python-3.5.1.amd64"} else {$Env:PYTHON_DIR_NAME="python-3.5.1"}
+  - "SET HYPERSPY_DIR=%WP_INSTDIR%\\%PYTHON_DIR_NAME%\\Lib\\site-packages\\hyperspy"
+  - ps: py.test --mpl $Env:HYPERSPY_DIR
+  - ps: Add-AppveyorMessage "Tests finished! Pushing to GitHub..."
   - "appveyor PushArtifact HyperSpy-%APPVEYOR_REPO_TAG_NAME%-Bundle-Windows-%PYTHON_ARCH%bit.exe"
 
 deploy:
@@ -159,6 +170,8 @@ deploy:
     #secure: KwAfARhGEqOnZHltPB6kKu8xmnoiGSk7NMYJBIEbWvFCuVnepoPV7ZcIjUN3pUpK
     #   sem-geologist:
     #secure: RRqUkx9H5VuFNITmm+YzgB0qnqgVGPH1yrPVxb4oCD+FAjcTch2WZAiPEKn4L6w6
+    #   ericpre:
+    #secure: ae8XsPI+vKJI9AWm0r9+ec71CIkXcnCHlNIQ57v+87hh5k1xuAAxIOi1CFKEmmZv
   artifact: /.*\.exe/, win_wheels  # upload all exe installers and wheels to release assets
   draft: false
   prerelease: false