Merge pull request #216 from hakonanes/prep-for-0.6.0-release

Prepare for 0.6rc1 release
pyxem · May 13, 2024 · 870d632 · 870d632
2 parents cc8b0a7 + 5bbd6f2
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diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,3 @@
-# Test files
-file_01.pickle
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

diff --git a/.zenodo.json b/.zenodo.json
@@ -12,6 +12,11 @@
       "orcid": "0000-0002-1213-2911",
       "affiliation": "Norwegian University of Science and Technology"
     },
+    {
+      "name":"Carter Francis",
+      "orcid": "0000-0003-2564-1851",
+      "affiliation": "University of Wisconsin Madison"
+    },
     {
       "name":"Eric Prestat"
     },

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,14 +7,15 @@ The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0>`_
 this project tries its best to adhere to
 `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
-Unreleased
-==========
+2024-05-12 - version 0.6.0
+==========================
 
 Added
 -----
 - Explicit support for Python 3.11.
 - Added Pre-Commit for code formatting.
-- Added deprecation tools for deprecating functions, parameters, methods, and properties.
+- Added deprecation tools for deprecating functions, parameters, methods, and
+  properties.
 
 Changed
 -------
@@ -23,16 +24,19 @@ Changed
 
 Deprecated
 ----------
+- ``get_hkl()``, ``get_highest_hkl()``, and ``get_equivalent_hkl()`` methods in the
+  crystallography module. Please use the following corresponding methods in the
+  ``ReciprocalLatticeVector`` class instead: ``from_highest_hkl()``,
+  ``from_min_dspacing()``, and ``symmetrise()``.
 
 Removed
 -------
 - Removed support for Python 3.6 and Python 3.7, leaving 3.8 as the oldest supported
   version.
 - ``ReciprocalLatticePoint`` class; Use the ``ReciprocalLatticeVector`` class instead,
   which is an improved replacement.
-
-Fixed
------
+- ``StructureLibrary.from_crystal_systems()`` class method, which previously raised a
+  ``NotImplementedError``, but now will throw an ``AttributeError`` instead.
 
 2023-05-22 - version 0.5.2
 ==========================

diff --git a/README.rst b/README.rst
@@ -1,29 +1,89 @@
-|build_status|_ |Coveralls|_ |docs|_ |pypi_version|_ |black|_ |doi|_
+diffsims is an open-source Python library for simulating diffraction.
+
+The package is released under the GPL v3 license.
+
+.. |pypi_version| image:: https://img.shields.io/pypi/v/diffsims.svg?style=flat
+   :target: https://pypi.python.org/pypi/diffsims
+
+.. |conda| image:: https://img.shields.io/conda/vn/conda-forge/diffsims.svg?logo=conda-forge&logoColor=white
+   :target: https://anaconda.org/conda-forge/diffsims
 
 .. |build_status| image:: https://github.com/pyxem/diffsims/workflows/build/badge.svg
-.. _build_status: https://github.com/pyxem/diffsims/actions
+   :target: https://github.com/pyxem/diffsims/actions/workflows/build.yml
 
-.. |Coveralls| image:: https://coveralls.io/repos/github/pyxem/diffsims/badge.svg?branch=master
-.. _Coveralls: https://coveralls.io/github/pyxem/diffsims?branch=master
+.. |python| image:: https://img.shields.io/badge/python-3.8+-blue.svg
+   :target: https://www.python.org/downloads/
 
-.. |docs| image:: https://readthedocs.org/projects/diffsims/badge/?version=latest
-.. _docs: https://diffsims.readthedocs.io/en/latest
+.. |Coveralls| image:: https://coveralls.io/repos/github/pyxem/diffsims/badge.svg?branch=main
+   :target: https://coveralls.io/github/pyxem/diffsims?branch=main
 
-.. |pypi_version| image:: https://img.shields.io/pypi/v/diffsims.svg?style=flat
-.. _pypi_version: https://pypi.org/project/diffsims/
+.. |pypi_downloads| image:: https://img.shields.io/pypi/dm/diffsims.svg?label=PyPI%20downloads
+   :target: https://pypi.org/project/diffsims/
 
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-.. _black: https://github.com/psf/black
+.. |conda_downloads| image:: https://img.shields.io/conda/dn/conda-forge/diffsims.svg?label=Conda%20downloads
+   :target: https://anaconda.org/conda-forge/diffsims
 
 .. |doi| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3337900.svg
-.. _doi: https://doi.org/10.5281/zenodo.3337900
+   :target: https://doi.org/10.5281/zenodo.3337900
 
-diffsims is an open-source Python library for simulating diffraction.
+.. |GPLv3| image:: https://img.shields.io/github/license/pyxem/diffsims
+   :target: https://opensource.org/license/GPL-3.0
 
-If simulations performed using diffsims form a part of published work please
-cite the DOI at the top of this page. You can find demos in the `diffsims-demos
-<https://github.com/pyxem/diffsims-demos>`_ repository. See the `documentation
-<https://diffsims.readthedocs.io/en/latest/>`_ for installation instructions, the API
-reference, the changelog and more.
+.. |GH-issues| image:: https://img.shields.io/badge/GitHub-Issues-green?logo=github
+   :target: https://github.com/pyxem/diffsims/issues
+
+.. |docs| image:: https://readthedocs.org/projects/diffsims/badge/?version=latest
+   :target: https://diffsims.readthedocs.io/en/latest
+
+.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
+   :target: https://github.com/psf/black
+
++----------------------+------------------------------------------------+
+| Deployment           | |pypi_version| |conda|                         |
++----------------------+------------------------------------------------+
+| Build status         | |build_status| |docs| |python|                 |
++----------------------+------------------------------------------------+
+| Metrics              | |Coveralls|                                    |
++----------------------+------------------------------------------------+
+| Activity             | |pypi_downloads| |conda_downloads|             |
++----------------------+------------------------------------------------+
+| Citation             | |doi|                                          |
++----------------------+------------------------------------------------+
+| License              | |GPLv3|                                        |
++----------------------+------------------------------------------------+
+| Community            | |GH-issues|                                    |
++----------------------+------------------------------------------------+
+| Formatter            | |black|                                        |
++----------------------+------------------------------------------------+
+
+Documentation
+-------------
+
+Refer to the `documentation <https://diffsims.readthedocs.io>`__ for detailed
+installation instructions, a user guide, a technical (API) reference, and the `changelog
+<https://diffsims.readthedocs.io/en/latest/changelog.html>`_.
+
+Installation
+------------
+
+diffsims can be installed with ``pip``::
+
+    pip install diffsims
 
-diffsims is released under the GPL v3 license.
+or ``conda``::
+
+    conda install diffsims -c conda-forge
+
+The source code is hosted in `GitHub <https://github.com/pyxem/diffsims>`_, and can also
+be downloaded from `PyPI <https://pypi.org/project/diffsims>`_ and
+`Anaconda <https://anaconda.org/conda-forge/diffsims>`_.
+
+Further details are available in the
+`installation guide
+<https://diffsims.readthedocs.io/en/latest/user/installation.html>`_.
+
+Citing diffsims
+---------------
+
+If simulations performed using diffsims form a part of published work please
+cite the DOI at the top of this page.
diff --git a/diffsims/__init__.py b/diffsims/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/conftest.py b/diffsims/conftest.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #
@@ -17,16 +17,21 @@
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
 from diffpy.structure import Atom, Lattice, Structure
+import matplotlib.pyplot as plt
 from orix.crystal_map import Phase
 import pytest
 
 from diffsims.crystallography import ReciprocalLatticeVector
 from diffsims.generators.diffraction_generator import DiffractionGenerator
 
 
+def pytest_sessionstart(session):
+    plt.rcParams["backend"] = "agg"
+
+
 @pytest.fixture
 def default_structure():
-    """An atomic structure represented using diffpy"""
+    """An atomic structure represented using diffpy."""
     latt = Lattice(3, 3, 5, 90, 90, 120)
     atom = Atom(atype="Ni", xyz=[0, 0, 0], lattice=latt)
     hexagonal_structure = Structure(atoms=[atom], lattice=latt)
@@ -109,3 +114,10 @@ def add_reciprocal_lattice_vector_al(doctest_namespace):
     )
     rlv = ReciprocalLatticeVector(phase, hkl=[[1, 1, 1], [2, 0, 0]])
     doctest_namespace["rlv"] = rlv
+
+
+@pytest.fixture(params=[("file_01")])
+def pickle_temp_file(tmpdir, request):
+    name = request.param
+    fname = tmpdir.join(name + ".pickle")
+    yield fname
diff --git a/diffsims/crystallography/__init__.py b/diffsims/crystallography/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/crystallography/get_hkl.py b/diffsims/crystallography/get_hkl.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/crystallography/reciprocal_lattice_vector.py b/diffsims/crystallography/reciprocal_lattice_vector.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/generators/__init__.py b/diffsims/generators/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/generators/diffraction_generator.py b/diffsims/generators/diffraction_generator.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/generators/library_generator.py b/diffsims/generators/library_generator.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/generators/rotation_list_generators.py b/diffsims/generators/rotation_list_generators.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #
@@ -22,7 +22,6 @@
 
 from orix.sampling.sample_generators import get_sample_fundamental, get_sample_local
 from orix.quaternion.rotation import Rotation
-from orix.vector.neo_euler import AxAngle
 
 from diffsims.utils.sim_utils import uvtw_to_uvw
 from diffsims.generators.sphere_mesh_generators import (
@@ -168,7 +167,7 @@ def get_grid_around_beam_direction(beam_rotation, resolution, angular_range=(0,
         np.arange(start=angular_range[0], stop=angular_range[1], step=resolution)
     )
     axes = np.repeat([[0, 0, 1]], angles.shape[0], axis=0)
-    in_plane_rotation = Rotation.from_neo_euler(AxAngle.from_axes_angles(axes, angles))
+    in_plane_rotation = Rotation.from_axes_angles(axes, angles)
 
     orix_grid = beam_rotation * in_plane_rotation
     rotation_list = get_list_from_orix(orix_grid, rounding=2)

diff --git a/diffsims/generators/sphere_mesh_generators.py b/diffsims/generators/sphere_mesh_generators.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/generators/zap_map_generator.py b/diffsims/generators/zap_map_generator.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/libraries/__init__.py b/diffsims/libraries/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/libraries/diffraction_library.py b/diffsims/libraries/diffraction_library.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/libraries/structure_library.py b/diffsims/libraries/structure_library.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #
@@ -81,36 +81,6 @@ def from_orientation_lists(cls, identifiers, structures, orientations):
         """
         return cls(identifiers, structures, orientations)
 
-    @classmethod
-    def from_crystal_systems(
-        cls, identifiers, structures, systems, resolution, equal="angle"
-    ):
-        """
-        Creates a structure library from crystal system derived orientation lists
-
-        Parameters
-        ----------
-        identifiers : list of strings/ints
-            A list of phase identifiers referring to different atomic structures.
-        structures : list of diffpy.structure.Structure objects.
-            A list of diffpy.structure.Structure objects describing the atomic
-            structure associated with each phase in the library.
-        systems : list
-            A list over indentifiers of crystal systems
-        resolution : float
-            resolution in degrees
-        equal : str
-            Default is 'angle'
-
-        Raises
-        ------
-        NotImplementedError:
-            "This function has been removed in version 0.3.0, in favour of creation from orientation lists"
-        """
-        raise NotImplementedError(
-            "This function has been removed in version 0.3.0, in favour of creation from orientation lists"
-        )
-
     def get_library_size(self, to_print=False):
         """
         Returns the the total number of orientations in the

diff --git a/diffsims/libraries/vector_library.py b/diffsims/libraries/vector_library.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/pattern/__init__.py b/diffsims/pattern/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/pattern/detector_functions.py b/diffsims/pattern/detector_functions.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2023 The diffsims developers
+# Copyright 2017-2024 The diffsims developers
 #
 # This file is part of diffsims.
 #

diff --git a/diffsims/release_info.py b/diffsims/release_info.py
@@ -1,12 +1,13 @@
 name = "diffsims"
-version = "0.6.dev0"
+version = "0.6rc1"
 author = "Duncan Johnstone, Phillip Crout"
-copyright = "Copyright 2017-2023, The diffsims developers"
+copyright = "Copyright 2017-2024, The diffsims developers"
 # Initial committer first, then listed by line additions
 credits = [
     "Duncan Johnstone",
     "Phillip Crout",
     "Håkon Wiik Ånes",
+    "Carter Francis",
     "Eric Prestat",
     "Rob Tovey",
     "Simon Høgås",
@@ -25,6 +26,6 @@
     "Eirik Opheim",
 ]
 license = "GPLv3+"
-maintainer = "Duncan Johnstone, Phillip Crout, Håkon Wiik Ånes"
+maintainer = "Duncan Johnstone, Phillip Crout, Håkon Wiik Ånes, Carter Francis"
 email = "pyxem.team@gmail.com"
 status = "Development"