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Merge pull request #216 from hakonanes/prep-for-0.6.0-release
Prepare for 0.6rc1 release
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‎.gitignore

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# Test files
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file_01.pickle
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]

‎.zenodo.json

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"orcid": "0000-0002-1213-2911",
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"affiliation": "Norwegian University of Science and Technology"
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},
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{
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"name":"Carter Francis",
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"orcid": "0000-0003-2564-1851",
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"affiliation": "University of Wisconsin Madison"
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},
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{
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"name":"Eric Prestat"
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},

‎CHANGELOG.rst

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

‎README.rst

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

‎diffsims/__init__.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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#

‎diffsims/conftest.py

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

‎diffsims/crystallography/__init__.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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#

‎diffsims/crystallography/get_hkl.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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#

‎diffsims/crystallography/reciprocal_lattice_vector.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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#

‎diffsims/generators/__init__.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/generators/diffraction_generator.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/generators/library_generator.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/generators/rotation_list_generators.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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from orix.sampling.sample_generators import get_sample_fundamental, get_sample_local
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from orix.vector.neo_euler import AxAngle
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from diffsims.utils.sim_utils import uvtw_to_uvw
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from diffsims.generators.sphere_mesh_generators import (
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np.arange(start=angular_range[0], stop=angular_range[1], step=resolution)
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)
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axes = np.repeat([[0, 0, 1]], angles.shape[0], axis=0)
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in_plane_rotation = Rotation.from_neo_euler(AxAngle.from_axes_angles(axes, angles))
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in_plane_rotation = Rotation.from_axes_angles(axes, angles)
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orix_grid = beam_rotation * in_plane_rotation
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rotation_list = get_list_from_orix(orix_grid, rounding=2)

‎diffsims/generators/sphere_mesh_generators.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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‎diffsims/generators/zap_map_generator.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/libraries/__init__.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/libraries/diffraction_library.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/libraries/structure_library.py

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

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/pattern/__init__.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/pattern/detector_functions.py

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# -*- coding: utf-8 -*-
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# Copyright 2017-2023 The diffsims developers
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# Copyright 2017-2024 The diffsims developers
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#
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# This file is part of diffsims.
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‎diffsims/release_info.py

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

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