Update copyright to 2019-2020, Black code style, and pre-commit

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
pyxem · Jan 1, 2020 · bcde148 · bcde148
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,6 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: master
+    hooks:
+      - id: black
+        language_version: python3.7
diff --git a/.travis.yml b/.travis.yml
@@ -1,5 +1,5 @@
-# The setup of different files for installation and tests on different operating
-# systems are based upon HyperSpy:
+# The setup of different files for installation and tests on different
+# operating systems are based upon how HyperSpy does it:
 # https://github.com/hyperspy/hyperspy/blob/RELEASE_next_minor/.travis.yml
 
 language: shell
@@ -74,6 +74,7 @@ after_success:
 before_deploy:
   - export DISTRIBUTIONS=$(ls ./dist/*)
 
+# Source: https://docs.travis-ci.com/user/deployment/pypi/
 deploy:
   provider: pypi
   user: "__token__"

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -36,8 +36,9 @@ standard.
 Code formatting
 ===============
 
-All code in KikuchiPy is formatted according to the `Style Guide for Python Code
-<https://www.python.org/dev/peps/pep-0008/>`_.
+The code making up KikuchiPy is formatted closely following the `Style Guide for
+Python Code <https://www.python.org/dev/peps/pep-0008/>`_ with `The *Black* Code
+style <https://black.readthedocs.io/en/stable/the_black_code_style.html>`_.
 
 .. _writing-documentation:
 

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![Build Status](https://api.travis-ci.org/kikuchipy/kikuchipy.svg?branch=master)](https://travis-ci.org/kikuchipy/kikuchipy) [![Coverage Status](https://coveralls.io/repos/github/kikuchipy/kikuchipy/badge.svg?branch=master)](https://coveralls.io/github/kikuchipy/kikuchipy?branch=master) [![Documentation Status](https://readthedocs.org/projects/kikuchipy/badge/?version=latest)](https://kikuchipy.readthedocs.io/en/latest/?badge=latest)
+[![Build Status](https://api.travis-ci.org/kikuchipy/kikuchipy.svg?branch=master)](https://travis-ci.org/kikuchipy/kikuchipy) [![Coverage Status](https://coveralls.io/repos/github/kikuchipy/kikuchipy/badge.svg?branch=master)](https://coveralls.io/github/kikuchipy/kikuchipy?branch=master) [![Documentation Status](https://readthedocs.org/projects/kikuchipy/badge/?version=latest)](https://kikuchipy.readthedocs.io/en/latest/?badge=latest) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 *KikuchiPy is an open-source Python library for processing and analysis of
 electron backscatter diffraction (EBSD) patterns.*
@@ -8,6 +8,9 @@ by the [HyperSpy](https://hyperspy.org/) library. This means that the `EBSD`
 class, which has several common methods for processing of EBSD patterns, also
 inherits all relevant methods from HyperSpy's `Signal2D` and `Signal` classes.
 
+Note that the project is in an alpha stage, and there will likely be breaking
+changes with each release.
+
 KikuchiPy is released under the GPL v3 license.
 
 #### User guide

diff --git a/doc/background_correction.rst b/doc/background_correction.rst
@@ -102,14 +102,13 @@ for the effect of varying ``kernel_size``.
     S. Koizuimi, "Quantitative electron backscatter diffraction (EBSD) data
     analyses using the dictionary indexing (DI) approach: Overcoming indexing
     difficulties on geological materials," *American Mineralogist* **102**
-    (2017) [`link <https://doi.org/10.2138/am-2017-6062>`_].
-
+    (2017), doi: https://doi.org/10.2138/am-2017-6062.
 
 .. [Jackson2019]
     M. A. Jackson, E. Pascal, M. De Graef, "Dictionary Indexing of Electron
     Back-Scatter Diffraction Patterns: a Hands-On Tutorial," *Integrating
-    Materials and Manufacturing Innovation* **8** (2019) [`link
-    <https://doi.org/10.1007/s40192-019-00137-4>`_].
+    Materials and Manufacturing Innovation* **8** (2019), doi:
+    https://doi.org/10.1007/s40192-019-00137-4.
 
 .. _rescale-intensities:
 

diff --git a/doc/changelog.rst b/doc/changelog.rst
@@ -1,3 +1,70 @@
 =========
 Changelog
 =========
+
+0.1.0 / 2020-01-02
+==================
+
+We're happy to announce the release of KikuchiPy v0.1.0!
+
+KikuchiPy is an open-source Python library for processing and analysis of
+electron backscatter diffraction (EBSD) patterns. The library builds upon the
+tools for multi-dimensional data analysis provided by the HyperSpy library.
+
+For more information, a user guide, and the full reference API documentation,
+please visit: https://kikuchipy.readthedocs.io
+
+This is the initial pre-release, where things start to get serious... seriously
+fun!
+
+Features
+--------
+- Load EBSD patterns and metadata from the NORDIF binary format (.dat) and
+  Bruker Nano and EDAX TSL's h5ebsd formats (.h5) into an ``EBSD`` object, e.g.
+  ``s``, based upon HyperSpy's `Signal2D` class, using ``s = kp.load()``. This
+  ensures easy access to patterns and metadata in the attributes ``s.data`` and
+  ``s.metadata``, respectively.
+- Save EBSD patterns to the NORDIF binary format (.dat) and our own h5ebsd
+  format (.h5), using ``s.save()``. Both formats are readable by EMsoft's NORDIF
+  and EMEBSD readers, respectively.
+- Lazy alternative for all functionality (except some multivariate analysis
+  algorithsm), meaning all operations on a scan, including plotting, can be done
+  loading only necessary parts of the scan into memory at a time.
+- Visualize patterns easily with HyperSpy's powerful and versatile ``s.plot()``.
+  Any image, e.g. a virtual backscatter electron image, quality map, phase map
+  or orientation map, can be used to navigate in. Multiple scans of the same
+  size, e.g. best matching simulated patterns to a scan, can be plotted
+  simultaneously alongside the experimental patterns with HyperSpy's
+  ``plot_signals()``.
+- Virtual backscatter electron (VBSE) imaging is easily performed with
+  ``s.virtual_backscatter_electron_imaging()`` based upon similar functionality
+  in pyXem. Arbitrary region of interests can be used, and the corresponding
+  VBSE image can be inspected interactively. Finally, the VBSE image can be
+  obtained in a new ``EBSD`` object with ``vbse = s.get_virtual_image()``,
+  before writing the data to an image file in your desired format with
+  matplotlib's ``imsave('filename.png', vbse.data)``.
+- Change scan and pattern size, e.g. by cropping on the detector or extracting
+  a region of interest, by using ``s.isig`` or ``s.inav``, respectively.
+  Patterns can be binned (upscaled or downscaled) using ``s.rebin``. These
+  methods are provided by HyperSpy.
+- Perform static and dynamic background correction by subtraction or division
+  with ``s.static_background_correction()`` and
+  ``s.dynamic_background_correction()``. For the former connection, relative
+  intensities between patterns can be kept if desired.
+- Perform adaptive histogram equalization by setting an appropriate contextual
+  region (kernel size) with ``s.adaptive_histogram_equalization()``.
+- Rescale pattern intensities to desired data type and range using
+  ``s.rescale_intensities()``.
+- Multivariate statistical analysis, like principal component analysis and many
+  other decomposition algorithms, can be easily performed with
+  ``s.decomposition()``, provided by HyperSpy.
+- Since the ``EBSD`` class is based upon HyperSpy's ``Signal2D`` class, which
+  itself is based upon their ``BaseSignal`` class, all functionality available
+  to ``Signal2D`` is also available to the ``EBSD`` class. See HyperSpy's user
+  guide (http://hyperspy.org/hyperspy-doc/current/user_guide/tools.html) for
+  details.
+
+Contributions to this release (alphabetical by first name)
+----------------------------------------------------------
+- Håkon Wiik Ånes
+- Tina Bergh
diff --git a/doc/load_save_patterns.rst b/doc/load_save_patterns.rst
@@ -237,11 +237,6 @@ containing only ``Scan 1``, by passing:
 
 Here the h5ebsd :func:`~kikuchipy.io.plugins.h5ebsd.file_writer` is called.
 
-.. [Jackson2014] M. A. Jackson, M. A. Groeber, M. D. Uchic, D. J. Rowenhorst
-    and M. De Graef, "h5ebsd: an archival data format for electron back-scatter
-    diffraction data sets," *Integrating Materials and Manufacturing Innovation*
-    **3** (2014) [`link <https://doi.org/10.1186/2193-9772-3-4>`_].
-
 .. _nordif-format:
 
 NORDIF binary

diff --git a/doc/release/release_0.1.rst b/doc/release/release_0.1.rst
diff --git a/doc/visualizing_patterns.rst b/doc/visualizing_patterns.rst
@@ -4,7 +4,7 @@ Visualizing patterns
 
 The :class:`~kikuchipy.signals.ebsd.EBSD` object has a powerful and versatile
 :meth:`~hyperspy.signal.BaseSignal.plot` method provided by HyperSpy, and its
-uses are greatly detailed in the `HyperSpy user guide
+uses are greatly detailed in HyperSpy's `visualisation user guide
 <http://hyperspy.org/hyperspy-doc/current/user_guide/visualisation.html>`_. This
 section details example uses specific to
 :class:`~kikuchipy.signals.ebsd.EBSD` objects.

diff --git a/kikuchipy/__init__.py b/kikuchipy/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The KikuchiPy developers
+# Copyright 2019-2020 The KikuchiPy developers
 #
 # This file is part of KikuchiPy.
 #

diff --git a/kikuchipy/conftest.py b/kikuchipy/conftest.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The KikuchiPy developers
+# Copyright 2019-2020 The KikuchiPy developers
 #
 # This file is part of KikuchiPy.
 #
@@ -33,24 +33,28 @@ def dummy_signal():
     methods using this signal (as input) to hard-coded outputs.
     """
 
+    # fmt: off
     dummy_array = np.array(
         [5, 6, 5, 7, 6, 5, 6, 1, 0, 9, 7, 8, 7, 0, 8, 8, 7, 6, 0, 3, 3, 5, 2, 9,
          3, 3, 9, 8, 1, 7, 6, 4, 8, 8, 2, 2, 4, 0, 9, 0, 1, 0, 2, 2, 5, 8, 6, 0,
          4, 7, 7, 7, 6, 0, 4, 1, 6, 3, 4, 0, 1, 1, 0, 5, 9, 8, 4, 6, 0, 2, 9, 2,
-         9, 4, 3, 6, 5, 6, 2, 5, 9], dtype=np.uint8).reshape((3, 3, 3, 3))
+         9, 4, 3, 6, 5, 6, 2, 5, 9],
+        dtype=np.uint8
+    ).reshape((3, 3, 3, 3))
+    # fmt: on
+
     return kp.signals.EBSD(dummy_array)
 
 
 @pytest.fixture
 def dummy_background():
-    """Dummy static background pattern for the dummy signal. If this
-    is changed, all tests using this background will fail since they
+    """Dummy static background pattern for the dummy signal. If this is
+    changed, all tests using this background will fail since they
     compare the output from methods using this background (as input) to
     hard-coded outputs.
     """
 
-    return np.array(
-        [5, 4, 5, 4, 3, 4, 4, 4, 3], dtype=np.uint8).reshape((3, 3))
+    return np.array([5, 4, 5, 4, 3, 4, 4, 4, 3], dtype=np.uint8).reshape((3, 3))
 
 
 @pytest.fixture()
@@ -60,6 +64,6 @@ def save_path_h5ebsd():
     """
 
     with tempfile.TemporaryDirectory() as tmp:
-        file_path = os.path.join(tmp, 'patterns_temp.h5')
+        file_path = os.path.join(tmp, "patterns_temp.h5")
         yield file_path
         gc.collect()
diff --git a/kikuchipy/hyperspy_extension.yaml b/kikuchipy/hyperspy_extension.yaml
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The KikuchiPy developers
+# Copyright 2019-2020 The KikuchiPy developers
 #
 # This file is part of KikuchiPy.
 #

diff --git a/kikuchipy/io/__init__.py b/kikuchipy/io/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2019 The KikuchiPy developers
+# Copyright 2019-2020 The KikuchiPy developers
 #
 # This file is part of KikuchiPy.
 #