Merge remote-tracking branch 'upstream/RELEASE_next_minor' into RELEA…

…SE_next_major

.github/CONTRIBUTING.md

@@ -0,0 +1,16 @@
+## Discussions
+
+For discussions on the use of hyperspy, please use the [mailing list](http://groups.google.com/group/hyperspy-users): useful to discuss use cases of HyperSpy and ask about specific applications.
+
+Discussion on the [gitter chat](https://gitter.im/hyperspy/hyperspy): useful to ask quick questions.
+
+## Issues
+
+The [issue tracker](https://github.com/hyperspy/hyperspy/issues) can be used to report bugs or propose new features. When reporting a bug, the following is useful:
+- give a minimal example demonstrating the bug,
+- copy and paste the error traceback.
+
+## Contribute
+
+If you want to contribute to the HyperSpy source code, you can send us a [pull requests](https://github.com/hyperspy/hyperspy/pulls). For more information, please read the [developer guide](http://hyperspy.org/hyperspy-doc/current/dev_guide.html).
+

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,29 @@
+### Requirements
+* Read the [developer guide](http://hyperspy.org/hyperspy-doc/current/dev_guide.html).
+* Filling out the template; it helps the review process and it is useful to summarise the PR.
+* This template can be updated during the progression of the PR to summarise its status. 
+
+*You can delete this section after you read it.*
+
+### Description of the change
+A few sentences and/or a bulleted list to describe and motivate the change:
+- Change A.
+- Change B.
+- etc.
+
+### Progress of the PR
+- [ ] Change implemented (can be split into several points),
+- [ ] update docstring (if appropriate),
+- [ ] update user guide (if appropriate),
+- [ ] add tests,
+- [ ] ready for review.
+
+### Minimal example of the bug fix or the new feature
+```python
+>>> import hyperspy.api as hs
+>>> import numpy as np
+>>> s = hs.signals.Signal1D(np.arange(10))
+>>> # Your new feature...
+```
+Note that this example can be useful to update the user guide.
+

.gitignore

@@ -35,6 +35,7 @@ doc/log.txt
 *.DS_Store
 .ropeproject/*
 .idea/*
+desktop.ini
 *.pyproj
 hyperspy/tests/misc/cython/test_cython_integration.c
 hyperspy/io_plugins/unbcf_fast.c

.travis.yml

@@ -33,12 +33,13 @@ before_install:
 install:
 
   - if [[ $MINIMAL_ENV == 'False' ]] ; then
-      DEPS="pip numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython lxml ipyparallel dask traits traitsui";
+      DEPS="pip numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill natsort setuptools scikit-image cython ipyparallel dask traits traitsui";
     else DEPS="pip ipython numpy scipy matplotlib>=2.0.2 h5py sympy scikit-image";
     fi
   - conda create -n testenv --yes python=$PYTHON;
     source activate testenv;
     conda install -y -c conda-forge $DEPS;
+    conda install -y -c conda-forge --no-deps freetype=2.6;
   - if [[ $MINIMAL_ENV == 'False' ]] ; then
       pip install .[all];
     else pip install .;
@@ -54,9 +55,19 @@ before_script: # configure a headless display to test plot generation
 
 script:
   - python -c 'import matplotlib.pyplot as plt; print(plt.get_backend())';
-  - pip install coverage coveralls pytest pytest-cov pytest-mpl;
+  - pip install coverage coveralls pytest pytest-cov pytest-mpl pytest-sugar;
     py.test --mpl --cov=hyperspy --pyargs hyperspy;
 
+#after_failure: # run only on failure in case there is a need to check matplotlib image comparison
+# This needs a service to upload the artifacts (and corresponding configuration)
+# See:
+# https://blog.travis-ci.com/2012-12-18-travis-artifacts/
+# https://docs.travis-ci.com/user/uploading-artifacts/
+# https://github.com/matplotlib/matplotlib/blob/master/.travis.yml
+#  - gem install travis-artifacts
+#  - zip -r image_comparison_failure.zip /tmp/ -i *.png
+#  - travis-artifacts upload image_comparison_failure.zip
+
 after_success:
 - coveralls
 - if [[ $MINIMAL_ENV == 'False' ]]; then

CHANGES.txt → CHANGES.rst

@@ -1,14 +1,17 @@
 What's new
 **********
 
+Current Version
+===============
+
 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
@@ -114,10 +117,16 @@ For developers
   and ipywidgets GUI elements.
 
 
+Changelog
+*********
+
+Previous Versions
+=================
+
 .. _changes_1.2:
 
 v1.2
-====
+++++
 
 This is a minor release. Follow the following links for details on all
 the `bugs fixed
@@ -169,7 +178,7 @@ For developers
 
 .. _changes_1.1.2:
 v1.1.2
-======
+++++++
 
 This is a maintenance release. Follow the following links for details on all
 the `bugs fixed
@@ -179,7 +188,7 @@ and `enhancements <https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+mil
 
 .. _changes_1.1.1:
 v1.1.1
-======
+++++++
 
 This is a maintenance release. Follow the following link for details on all
 the `bugs fixed
@@ -200,7 +209,7 @@ Enhancements
 
 .. _changes_1.1:
 v1.1
-====
+++++
 
 This is a minor release. Follow the following links for details on all
 the `bugs fixed
@@ -226,15 +235,15 @@ Enhancements
 
 
 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%3A"type%3A+bug"+is%3Aclosed+milestone%3A1.0.1>`_.
 
 
 v1.0
-====
+++++
 
 This is a major release. Here we only list the highlist. A detailed list of
 changes `is available in github
@@ -307,7 +316,7 @@ API changes
 
 
 v0.8.5
-======
+++++++
 
 
 This is a maintenance release. Follow the following links for details on all
@@ -342,13 +351,13 @@ deprecate `as_signal1D`, `as_signal2D`, `to_spectrum` and `to_image`. See `#963
 
 
 v0.8.4
-======
+++++++
 
 This release adds support for Python 3 and drops support for Python 2. In all
 other respects it is identical to v0.8.3.
 
 v0.8.3
-======
+++++++
 
 This is a maintenance release that includes fixes for multiple bugs, some
 enhancements, new features and API changes. This is set to be the last HyperSpy
@@ -375,14 +384,14 @@ Follow the following links for details on all the `bugs fixed
 .. _changes_0.8.2:
 
 v0.8.2
-======
+++++++
 
 This is a maintenance release that fixes an issue with the Python installers. Those who have successfully installed v0.8.1 do not need to upgrade.
 
 .. _changes_0.8.1:
 
 v0.8.1
-======
+++++++
 
 This is a maintenance release. Follow the following links for details on all
 the `bugs fixed
@@ -437,7 +446,7 @@ API changes
 .. _changes_0.8:
 
 v0.8
-====
+++++
 
 New features
 ------------
@@ -494,7 +503,7 @@ API changes
     + ``add_axes`` -> ``set_mpl_ax``
 
 v0.7.3
-======
+++++++
 
 This is a maintenance release. A list of fixed issues is available in the
 `0.7.3 milestone
@@ -504,7 +513,7 @@ in the github repository.
 .. _changes_0.7.2:
 
 v0.7.2
-======
+++++++
 
 This is a maintenance release. A list of fixed issues is available in the
 `0.7.2 milestone
@@ -514,7 +523,7 @@ in the github repository.
 .. _changes_0.7.1:
 
 v0.7.1
-======
+++++++
 
 This is a maintenance release. A list of fixed issues is available in the
 `0.7.1 milestone
@@ -529,7 +538,7 @@ New features
 * Add suspend/resume model plot updating. See :ref:`model.visualization`.
 
 v0.7
-====
+++++
 
 New features
 ------------
@@ -674,7 +683,7 @@ API changes
 .. _changes_0.6:
 
 v0.6
-====
+++++
 
 New features
 ------------
@@ -758,7 +767,7 @@ API changes
 .. _changes_0.5.1:
 
 v0.5.1
-======
+++++++
 
 New features
 ------------
@@ -791,7 +800,7 @@ API changes
 .. _changes_0.5:
 
 v0.5
-====
+++++
 
 New features
 ------------
@@ -853,7 +862,7 @@ API changes
 .. _changes_0.4.1:
 
 v0.4.1
-======
+++++++
 
 New features
 ------------
@@ -884,7 +893,7 @@ Syntax changes
 .. _changes_0.4:
 
 v0.4
-====
+++++
 
 New features
 ------------

README.rst

@@ -44,6 +44,13 @@ HyperSpy is released under the GPL v3 license.
     **Since version 0.8.4 HyperSpy only supports Python 3. If you need to install
     HyperSpy in Python 2.7 install HyperSpy 0.8.3.**
 
+
+Contributing
+------------
+
+Everyone is welcome to contribute. Please read our
+`contributing guidelines <https://github.com/hyperspy/hyperspy/blob/RELEASE_next_minor/.github/CONTRIBUTING.md>`_ and get started!
+
 Cite
 ----
 

appveyor.yml

@@ -4,7 +4,7 @@ shallow_clone: true
 environment:
 
   global:
-    TEST_DEPS: "pytest pytest-cov wheel pip"
+    TEST_DEPS: "pytest pytest-cov wheel"
     NSIS_DIR: "%PROGRAMFILES(x86)%/NSIS"
     MPLBACKEND: "agg"
 
@@ -21,7 +21,7 @@ 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>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython ipyparallel dask"
 
      - PYTHON: "C:\\Miniconda35-x64"
        PYTHON_VERSION: "3.5.x"
@@ -31,21 +31,22 @@ 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>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython ipyparallel dask"
 
      - PYTHON: "C:\\Miniconda36"
        PYTHON_VERSION: "3.6.x"
        PYTHON_MAJOR: 3
        PYTHON_ARCH: "32"
        CONDA_PY: "36"
-       DEPS: "numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython ipyparallel dask"
 
      - PYTHON: "C:\\Miniconda36-x64"
        PYTHON_VERSION: "3.6.x"
        PYTHON_MAJOR: 3
        PYTHON_ARCH: "64"
        CONDA_PY: "36"
-       DEPS: "numpy scipy matplotlib>=2.0.2 ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython lxml ipyparallel dask=0.13"
+       DEPS: "numpy scipy matplotlib ipython h5py sympy scikit-learn dill setuptools natsort scikit-image cython ipyparallel dask"
+
 
 
 
@@ -69,12 +70,11 @@ install:
   - ps: Add-AppveyorMessage "Installing conda packages..."
   - "%CMD_IN_ENV% conda install -yq %TEST_DEPS%"
   - "%CMD_IN_ENV% conda install -yq %DEPS%"
-    # Having 'sip' folder on path confuses import of `sip`.
-  - "%CMD_IN_ENV% conda install pip"
+  # install freetype=2.6 from conda-forge to pass the plotting tests
+  - "%CMD_IN_ENV% conda install -yq -c conda-forge --no-deps freetype=2.6"
+  # Having 'sip' folder on path confuses import of `sip`.
+  #- "%CMD_IN_ENV% conda install -yq pip"
   - "pip install pytest-mpl"
-    # Force to have the freetype font in matplotlib from pip for plot testing
-  - "pip uninstall -y matplotlib"
-  - "pip install matplotlib"
   # TODO: Remove once anaconda taitsui package is at v5:
   - "IF \"%PYTHON_MAJOR%\" EQU \"3\" pip install --upgrade traitsui tqdm"
   - ps: Add-AppveyorMessage "Installing hyperspy..."
@@ -97,6 +97,11 @@ artifacts:
   - path: dist\*.whl
     name: win_wheels
 
+on_failure:
+  - ps: $Env:image_comparison_filename = 'image_comparison_' + $Env:PYTHON_VERSION + '_' + $Env:PYTHON_ARCH + 'bits.zip'
+  - ps: 7z a -r $Env:image_comparison_filename C:\Users\appveyor\AppData\Local\Temp\1\*png
+  - ps: Push-AppveyorArtifact $Env:image_comparison_filename
+
   #Auto-deployment of bundle installer for tags:
 before_deploy:
   - ps: Add-AppveyorMessage "Running deployment step..."

doc/README.txt

@@ -1 +1,6 @@
-To build the documentation you need to install python-sphinx and numpydoc and to run the make command in this folder, for example 'make html' to build the whole documentation in html format. See the make command documentation for more details.
+1. To build the documentation you need the following libraries to be installed:
+- sphinx
+- numpydoc
+- sphinxcontrib-napoleon
+- sphinx_rtd_theme
+2. Run the make command in this folder, for example 'make html' to build the whole documentation in html format. See the make command documentation for more details.