Merge pull request #590 from hakonanes/ebsd-hough-indexing-method

Add EBSD Hough indexing with a thin wrapper around PyEBSDIndex

.github/workflows/tests.yml

@@ -80,7 +80,7 @@ jobs:
       - name: Install optional dependencies
         shell: bash
         run: |
-          pip install -e .'[opt,viz]'
+          pip install -e .'[all]'
 
       - name: Display Python, pip and package versions
         run: |

CHANGELOG.rst

@@ -18,6 +18,13 @@ Unreleased
 
 Added
 -----
+- Method to get a PyEBSDIndex ``EBSDIndexer`` instance from an ``EBSDDetector``,
+  convenient for either indexing with PyEBSDIndex or for use with kikuchipy.
+  (`#590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
+- Convenience function to get a ``CrystalMap`` from a PyEBSDIndex Hough indexing result
+  array. (`#590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
+- PyEBSDIndex as an optional dependency.
+  (`#590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
 - Two tutorials showing projection center (PC) fitting and extrapolation to obtain a
   plane of PCs to index a full dataset.
   (`#588 <https://github.com/pyxem/kikuchipy/pull/588>`_)
@@ -94,6 +101,10 @@ Changed
 
 Deprecated
 ----------
+- The PyPI selector ``viz`` is replaced by ``all``, which installs all optional
+  dependencies. ``viz`` will be removed in version 0.9. Install optional dependencies
+  manually or via ``pip install kikuchipy[all]``.
+  (`#590 <https://github.com/pyxem/kikuchipy/pull/590>`_)
 - ``projections`` module with classes ``GnomonicProjection``, ``HesseNormalForm``,
   ``LambertProjection`` and ``SphericalProjection``. These will be removed in version
   0.9.0, as they are unused internally. If you depend on this module, please open an

doc/conf.py

@@ -54,7 +54,11 @@
 # packages
 intersphinx_mapping = {
     # Package
+    "black": ("https://black.readthedocs.io/en/stable", None),
+    "conda": ("https://conda.io/projects/conda/en/latest", None),
+    "coverage": ("https://coverage.readthedocs.io/en/latest", None),
     "dask": ("https://docs.dask.org/en/stable", None),
+    "defdap": ("https://defdap.readthedocs.io/en/latest", None),
     "diffpy.structure": ("https://www.diffpy.org/diffpy.structure", None),
     "diffsims": ("https://diffsims.readthedocs.io/en/latest", None),
     "hyperspy": ("https://hyperspy.org/hyperspy-doc/current", None),
@@ -63,27 +67,23 @@
     "matplotlib": ("https://matplotlib.org/stable", None),
     "numba": ("https://numba.pydata.org/numba-doc/latest", None),
     "numpy": ("https://numpy.org/doc/stable", None),
+    "nbsphinx": ("https://nbsphinx.readthedocs.io/en/latest", None),
+    "nbval": ("https://nbval.readthedocs.io/en/latest", None),
+    "numpydoc": ("https://numpydoc.readthedocs.io/en/latest", None),
     "orix": ("https://orix.readthedocs.io/en/stable", None),
+    "panel": ("https://panel.holoviz.org", None),
     "pooch": ("https://www.fatiando.org/pooch/latest", None),
     "pyebsdindex": ("https://pyebsdindex.readthedocs.io/en/stable", None),
+    "pyopencl": ("https://documen.tician.de/pyopencl/", None),
+    "pytest": ("https://docs.pytest.org/en/stable", None),
+    #    "pythreejs": ("https://pythreejs.readthedocs.io/en/stable", None),
     "python": ("https://docs.python.org/3", None),
     "pyvista": ("https://docs.pyvista.org", None),
+    "pyxem": ("https://pyxem.readthedocs.io/en/latest", None),
+    "readthedocs": ("https://docs.readthedocs.io/en/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
     "skimage": ("https://scikit-image.org/docs/stable", None),
     "sklearn": ("https://scikit-learn.org/stable", None),
-    # Docs
-    "black": ("https://black.readthedocs.io/en/stable", None),
-    "conda": ("https://conda.io/projects/conda/en/latest", None),
-    "coverage": ("https://coverage.readthedocs.io/en/latest", None),
-    "defdap": ("https://defdap.readthedocs.io/en/latest", None),
-    "nbsphinx": ("https://nbsphinx.readthedocs.io/en/latest", None),
-    "nbval": ("https://nbval.readthedocs.io/en/latest", None),
-    "numpydoc": ("https://numpydoc.readthedocs.io/en/latest", None),
-    "panel": ("https://panel.holoviz.org", None),
-    #    "pythreejs": ("https://pythreejs.readthedocs.io/en/stable", None),
-    "pytest": ("https://docs.pytest.org/en/stable", None),
-    "pyxem": ("https://pyxem.readthedocs.io/en/latest", None),
-    "readthedocs": ("https://docs.readthedocs.io/en/stable", None),
     "sphinx": ("https://www.sphinx-doc.org/en/master", None),
     "sphinx-gallery": ("https://sphinx-gallery.github.io/stable", None),
     "xcdskd": ("https://xcdskd.readthedocs.io/en/latest", None),

doc/dev/adding_to_data_module.rst

@@ -6,10 +6,10 @@ Adding data to the data module
 Example datasets used in the documentation and tests are included in the
 :mod:`kikuchipy.data` module via the `pooch <https://www.fatiando.org/pooch/latest/>`__
 Python library. These are listed in a file registry (``kikuchipy.data._registry.py``)
-with their file verification string (hash, SHA256, obtain with e.g.
-``sha256sum <file>``) and location, the latter potentially not within the package but
-from the `kikuchipy-data <https://github.com/pyxem/kikuchipy-data>`__ repository or
-elsewhere, since some files are considered too large to include in the package.
+with their file verification string (hash, MD5, obtain with e.g. ``md5sum <file>``) and
+location, the latter potentially not within the package but from the `kikuchipy-data
+<https://github.com/pyxem/kikuchipy-data>`__ repository or elsewhere, since some files
+are considered too large to include in the package.
 
 If a required dataset isn't in the package, but is in the registry, it can be downloaded
 from the repository when the user passes ``allow_download=True`` to e.g.