Merge pull request #694 from hakonanes/hs2-io-compat

Adopt RosettaSciIO's plugin design

CHANGELOG.rst

@@ -18,11 +18,13 @@ Unreleased
 
 Added
 -----
+- Dependency on RosettaSciIO for read/write of some file formats.
+  (`#? <https://github.com/pyxem/kikuchipy/pull/?>`_)
 
 Changed
 -------
 - Minimum Python version is now 3.10.
-  (`#? <https://github.com/pyxem/kikuchipy/pull/?>`_)
+  (`#689 <https://github.com/pyxem/kikuchipy/pull/689>`_)
 
 Removed
 -------

conftest.py

@@ -298,6 +298,11 @@ def save_path_hdf5(request, tmpdir) -> Generator[Path, None, None]:
     yield Path(tmpdir / f"patterns.{ext}")
 
 
+@pytest.fixture()
+def save_path_nordif(tmpdir) -> Generator[Path, None, None]:
+    yield Path(tmpdir / "nordif/save_temp.dat")
+
+
 @pytest.fixture
 def ni_small_axes_manager() -> Generator[dict, None, None]:
     """Axes manager for :func:`kikuchipy.data.nickel_ebsd_small`."""

doc/conf.py

@@ -79,6 +79,7 @@
     "pyvista": ("https://docs.pyvista.org", None),
     "pyxem": ("https://pyxem.readthedocs.io/en/latest", None),
     "readthedocs": ("https://docs.readthedocs.io/en/stable", None),
+    "rosettasciio": ("https://rosettasciio.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),

doc/environment.yml

@@ -3,4 +3,5 @@ channels:
 dependencies:
   - pip
   - python=3.11
-  - pandoc>=2.14.2, <4.0.0
+  - pandoc>=2.14.2, <4.0.0
+  - ipykernel

doc/user/installation.rst

@@ -106,11 +106,11 @@ This is a list of core package dependencies:
 * :doc:`orix <orix:index>`: Handling of rotations and vectors using crystal symmetry
 * :doc:`pooch <pooch:api/index>`: Downloading and caching of datasets
 * `pyyaml <https://pyyaml.org/>`__: Parcing of YAML files
-* `tqdm <https://tqdm.github.io/>`__: Progressbars
 * :doc:`scikit-image <skimage:index>`: Image processing like adaptive histogram
   equalization
 * `scikit-learn <https://scikit-learn.org/stable/>`__: Multivariate analysis
 * :doc:`scipy <scipy:index>`: Optimization algorithms, filtering and more
+* `tqdm <https://tqdm.github.io/>`__: Progressbars
 
 .. _lazy_loader: https://scientific-python.org/specs/spec-0001/#lazy_loader
 

examples/selecting_data/crop_signal_axes.py

@@ -5,7 +5,7 @@
 This example shows various ways to crop the signal axes of an
 :class:`~kikuchipy.signals.EBSD` signal using HyperSpy's ``isig`` slicer and the
 :meth:`~kikuchipy.signals.EBSD.crop` and
-:meth:`~hyperspy._signals.signal2d.Signal2D.crop_image` methods (see
+:meth:`~hyperspy._signals.signal2d.Signal2D.crop_signal` methods (see
 :ref:`hyperspy:signal.indexing` for details).
 """
 
@@ -49,10 +49,10 @@
 print(s3.detector)
 
 # %%
-# Do the same inplace using ``crop_image()``
+# Do the same inplace using ``crop_signal()``
 
 s4 = s.deepcopy()
-s4.crop_image(top=10, bottom=50, left=5, right=55)
+s4.crop_signal(top=10, bottom=50, left=5, right=55)
 
 _ = hs.plot.plot_images(s4, **plot_kwds)
 print(s4)

pyproject.toml

@@ -2,6 +2,8 @@
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
+# ----------------------------- Project ------------------------------ #
+
 [project]
 name = "kikuchipy"
 authors = [{name = "kikuchipy developers"}]
@@ -40,33 +42,23 @@ dependencies = [
     "dask[array]      >= 2021.8.1",
     "diffpy.structure >= 3",
     "diffsims         >= 0.5.2",
-    "hyperspy         >= 2",
+    # TODO: Replace with HyperSpy 2.2 once it's out
+    "hyperspy @ git+https://github.com/hyperspy/hyperspy.git@RELEASE_next_patch",
     "h5py             >= 2.10",
     "imageio",
     "lazy_loader",
     "matplotlib       >= 3.5",
     "numba            >= 0.57",
-    # TODO: Remove pinning of NumPy <2 once HyperSpy 2.0 is supported
-    "numpy            >= 1.23.0, <2",
+    "numpy            >= 1.23.0",
     "orix             >= 0.12.1",
     "pooch            >= 1.3.0",
     "pyyaml",
-    "tqdm             >= 0.5.2",
     "scikit-image     >= 0.16.2",
     "scikit-learn",
     "scipy            >= 1.7",
+    "tqdm             >= 0.5.2",
 ]
 
-[project.entry-points."hyperspy.extensions"]
-kikuchipy = "kikuchipy"
-
-[project.urls]
-Documentation = "https://kikuchipy.org"
-Download = "https://pypi.python.org/pypi/kikuchipy"
-"Bug Tracker" = "https://github.com/pyxem/kikuchipy/issues"
-"Source Code" = "https://github.com/pyxem/kikuchipy"
-Changelog = "https://kikuchipy.org/en/stable/changelog.html"
-
 [project.optional-dependencies]
 all = [
     "nlopt",
@@ -108,22 +100,34 @@ dev = [
     "kikuchipy[doc,tests,coverage]",
 ]
 
+[project.entry-points."hyperspy.extensions"]
+kikuchipy = "kikuchipy"
+
+[project.urls]
+Documentation = "https://kikuchipy.org"
+Download = "https://pypi.python.org/pypi/kikuchipy"
+"Bug Tracker" = "https://github.com/pyxem/kikuchipy/issues"
+"Source Code" = "https://github.com/pyxem/kikuchipy"
+Changelog = "https://kikuchipy.org/en/stable/changelog.html"
+
+# ------------------------------- Tool ------------------------------- #
+
 [tool.hatch.version]
 path = "src/kikuchipy/__init__.py"
 
-# TODO: Remove this section and the duplicated file when HS 2.0 is
-# supported
-[tool.hatch.build.force-include]
-"hyperspy_extension.yaml" = "hyperspy_extension.yaml"
-
 # https://github.com/pypa/hatch/discussions/427
 # https://github.com/pypa/hatch/issues/492
+[tool.hatch.build.targets.wheel.sources]
+src = ""
+
 [tool.hatch.build.targets.wheel]
 include = [
     "src/kikuchipy",
 ]
-[tool.hatch.build.targets.wheel.sources]
-"src" = ""
+
+# TODO: Remove once HyperSpy is not installed from a direct reference (GitHub)
+[tool.hatch.metadata]
+allow-direct-references = true
 
 [tool.coverage.report]
 precision = 2

src/kikuchipy/_util/_deprecated.py

@@ -31,7 +31,7 @@
 from typing import Callable
 import warnings
 
-import numpy as np
+from kikuchipy.constants import VisibleDeprecationWarning
 
 
 class deprecated:
@@ -93,12 +93,12 @@ def __call__(self, func: Callable) -> None:
         @functools.wraps(func)
         def wrapped(*args, **kwargs) -> Callable:
             warnings.simplefilter(
-                action="always", category=np.VisibleDeprecationWarning, append=True
+                action="always", category=VisibleDeprecationWarning, append=True
             )
             func_code = func.__code__
             warnings.warn_explicit(
                 message=msg,
-                category=np.VisibleDeprecationWarning,
+                category=VisibleDeprecationWarning,
                 filename=func_code.co_filename,
                 lineno=func_code.co_firstlineno + 1,
             )
@@ -151,12 +151,12 @@ def wrapped(*args, **kwargs):
                     msg += f"Use `{self.alternative}` instead. "
                 msg += f"See the documentation of `{func.__name__}()` for more details."
                 warnings.simplefilter(
-                    action="always", category=np.VisibleDeprecationWarning
+                    action="always", category=VisibleDeprecationWarning
                 )
                 func_code = func.__code__
                 warnings.warn_explicit(
                     message=msg,
-                    category=np.VisibleDeprecationWarning,
+                    category=VisibleDeprecationWarning,
                     filename=func_code.co_filename,
                     lineno=func_code.co_firstlineno + 1,
                 )

src/kikuchipy/constants.py

@@ -51,3 +51,15 @@
     # Have to use bare except because PyOpenCL might raise its own
     # LogicError, but we also want to catch import errors here
     pyopencl_context_available = False
+
+
+# TODO: Remove and use numpy.exceptions.VisibleDeprecationWarning once
+# NumPy 1.25 is minimal supported version
+try:
+    # Added in NumPy 1.25.0
+    from numpy.exceptions import VisibleDeprecationWarning
+except ImportError:  # pragma: no cover
+    # Removed in NumPy 2.0.0
+    from numpy import VisibleDeprecationWarning
+
+del optional_deps, version

src/kikuchipy/detectors/ebsd_detector.py

@@ -226,15 +226,15 @@ def __init__(
 
     def __repr__(self) -> str:
         decimals = 3
-        pc_average = tuple(self.pc_average.round(decimals))
+        pc_average = tuple(map(float, self.pc_average.round(decimals)))
         sample_tilt = np.round(self.sample_tilt, decimals)
         tilt = np.round(self.tilt, decimals)
         azimuthal = np.round(self.azimuthal, decimals)
         px_size = np.round(self.px_size, decimals)
         return (
             f"{type(self).__name__}"
             f"(shape={self.shape}, "
-            f"pc={pc_average!r}, "
+            f"pc={pc_average}, "
             f"sample_tilt={sample_tilt}, "
             f"tilt={tilt}, "
             f"azimuthal={azimuthal}, "