Merge #191 from hakonanes/fix-allowed-vectors

Fix allowed vectors when (hkl) are slightly off integers

.github/workflows/build.yml

@@ -1,16 +1,27 @@
 name: build
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  workflow_dispatch:
+    workflow: '*'
+
+env:
+  MPLBACKEND: agg
 
 jobs:
   # Make sure all necessary files will be included in a release
   manifest:
     name: check manifest
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
 
       - name: Install dependencies
         run: pip install manifix
@@ -19,58 +30,58 @@ jobs:
         run: python setup.py manifix
 
   build-with-pip:
-    name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.label }}
+    name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
-    env:
-      MPLBACKEND: agg
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.9, '3.10']
         include:
           # Oldest supported version of main dependencies on Python 3.6
-          - os: ubuntu-latest
+          - os: ubuntu-20.04
             python-version: 3.6
             OLDEST_SUPPORTED_VERSION: true
             DEPENDENCIES: diffpy.structure==3.0.0 matplotlib==3.3 numpy==1.17 orix==0.9.0 scipy==1.0 tqdm==4.9
             LABEL: -oldest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Display Python and pip versions
-        run: |
-          python -V
-          pip -V
-
       - name: Install dependencies and package
         shell: bash
-        run: pip install -U -e .'[tests]'
+        run: |
+          pip install -U -e .'[tests]'
 
       - name: Install oldest supported version
         if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
-        run: pip install ${{ matrix.DEPENDENCIES }}
+        run: |
+          pip install ${{ matrix.DEPENDENCIES }}
 
-      - name: Display package versions
-        run: pip list
+      - name: Display Python, pip and package versions
+        run: |
+          python -V
+          pip -V
+          pip list
 
       - name: Run docstring tests
         if: ${{ matrix.os == 'ubuntu-latest' }}
         continue-on-error: true
-        run: pytest --doctest-modules --ignore-glob=diffsims/tests/*
+        run: |
+          pytest --doctest-modules --doctest-continue-on-failure --ignore-glob=diffsims/tests/*
 
       - name: Run tests
-        run: pytest --cov=diffsims --pyargs diffsims
+        run: pytest -n 2 --cov=diffsims --pyargs diffsims
 
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}
-        run: coverage report --show-missing
+        run: |
+          coverage report --show-missing
 
       - name: Upload coverage to Coveralls
         if: ${{ matrix.os == 'ubuntu-latest' }}

CHANGELOG.rst

@@ -8,6 +8,19 @@ The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0>`_
 and this project adheres to `Semantic Versioning
 <https://semver.org/spec/v2.0.0.html>`_.
 
+2023-01-25 - version 0.5.1
+==========================
+
+Fixed
+-----
+- ``ReciprocalLatticeVector.allowed`` rounds indices (hkl) internally to ensure correct
+  selection of which vectors are allowed or not given a lattice centering. Integer
+  indices are assumed.
+
+Deprecated
+----------
+- Support for Python 3.6 is deprecated and will be removed in v0.6.
+
 2022-06-10 - version 0.5.0
 ==========================
 
@@ -67,7 +80,7 @@ Fixed
 
 Added
 -----
-- API reference documentation via Read The Docs: https://diffsims.readthedocs.io
+- API reference documentation via Read The Docs: https://diffsims.readthedocs.io/en/latest/
 - New module: `sphere_mesh_generators`
 - New module: `detector_functions`
 - New module: `ring_pattern_utils`

CONTRIBUTING.rst

@@ -22,7 +22,7 @@ this guide boils down to using that platform well. so visit the following link a
 around the code, issues, and pull requests (PRs): `diffsims
 on GitHub <https://github.com/pyxem/diffsims>`_.
 
-It's probably also worth visiting the `GitHub guides <https://guides.github.com>`_ to
+It's probably also worth visiting the `GitHub guides <https://docs.github.com/en>`_ to
 get a feel for the terminology.
 
 In brief, to give you a hint on the terminology to search for, the contribution pattern
@@ -70,7 +70,7 @@ Git is an open source "version control" system that enables you to can separate
 modifications to the code into many versions (called branches) and switch between them
 easily. Later you can choose which version you want to have integrated into diffsims.
 
-You can learn all about Git `here <http://www.git-scm.com/about>`_!
+You can learn all about Git `here <https://www.git-scm.com/about>`_!
 
 The most important thing is to separate your contributions so that each branch is a
 small advancement on the "master" code or on another branch.
@@ -80,7 +80,7 @@ Get the style right
 
 diffsims closely follows the Style Guide for Python Code - these are just some rules for
 consistency that you can read all about in the `Python Style Guide
-<https://www.python.org/dev/peps/pep-0008/>`_.
+<https://peps.python.org/pep-0008/>`_.
 
 Please run the latest version of
 `black <https://black.readthedocs.io/en/stable/the_black_code_style/index.html>`_ on
@@ -89,18 +89,18 @@ your newly added and modified files prior to each PR.
 Run and write tests
 -------------------
 
-All functionality in diffsims is tested via the `pytest <https://docs.pytest.org>`_
-framework. The tests reside in the ``diffsims.tests`` module. Tests are short functions
-that call functions in diffsims and compare resulting output values with known answers.
-Good tests should depend on as few other features as possible so that when they break we
-know exactly what caused it.
+All functionality in diffsims is tested via the `pytest
+<https://docs.pytest.org/en/stable/>`_ framework. The tests reside in the
+``diffsims.tests`` module. Tests are short functions that call functions in diffsims and
+compare resulting output values with known answers. Good tests should depend on as few
+other features as possible so that when they break we know exactly what caused it.
 
 Install necessary dependencies to run the tests::
 
    pip install --editable .[tests]
 
-Some useful `fixtures <https://docs.pytest.org/en/latest/fixture.html>`_ are available
-in the ``conftest.py`` file.
+Some useful `fixtures <https://docs.pytest.org/en/latest/explanation/fixtures.html>`_
+are available in the ``conftest.py`` file.
 
 To run the tests::
 
@@ -122,16 +122,15 @@ Useful hints on testing:
 - ``@pytest.mark.parametrize()`` is a convenient decorator to test several parameters of
   the same function without having to write to much repetitive code, which is often
   error-prone. See `pytest documentation for more details
-  <http://doc.pytest.org/en/latest/parametrize.html>`_.
+  <https://doc.pytest.org/en/latest/how-to/parametrize.html>`_.
 
 Build and write documentation
 -----------------------------
 
 Docstrings -- written at the start of a function -- give essential information about how
 it should be used, such as which arguments can be passed to it and what the syntax
-should be. The docstrings follow the `NumPy specification
-<https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard>`_,
-as shown in `this example <https://github.com/numpy/numpy/blob/master/doc/example.py>`_.
+should be. The docstrings mostly follow the `numpydoc
+<https://numpydoc.readthedocs.io/en/latest/format.html>`_ standard.
 
 We use `Sphinx <https://www.sphinx-doc.org/en/master>`_ for documenting functionality.
 Install necessary dependencies to build the documentation::

README.rst

@@ -9,8 +9,8 @@
 .. |docs| image:: https://readthedocs.org/projects/diffsims/badge/?version=latest
 .. _docs: https://diffsims.readthedocs.io/en/latest
 
-.. |pypi_version| image:: http://img.shields.io/pypi/v/diffsims.svg?style=flat
-.. _pypi_version: https://pypi.python.org/pypi/diffsims
+.. |pypi_version| image:: https://img.shields.io/pypi/v/diffsims.svg?style=flat
+.. _pypi_version: https://pypi.org/project/diffsims/
 
 .. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
 .. _black: https://github.com/psf/black
@@ -23,7 +23,7 @@ diffsims is an open-source Python library for simulating diffraction.
 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>`_ for installation instructions, the API reference,
-the changelog and more.
+<https://diffsims.readthedocs.io/en/latest/>`_ for installation instructions, the API
+reference, the changelog and more.
 
 diffsims is released under the GPL v3 license.

diffsims/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/conftest.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/crystallography/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/crystallography/reciprocal_lattice_point.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/crystallography/reciprocal_lattice_vector.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2021 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #
@@ -59,8 +59,8 @@ class ReciprocalLatticeVector(Vector3d):
     Create a set of reciprocal lattice vectors from :math:`(hkl)` or
     :math:`(hkil)`.
 
-    The vectors are internally as cartesian coordinates in the ``data``
-    attribute.
+    The vectors are stored internally as cartesian coordinates in
+    :attr:`data`.
 
     Parameters
     ----------
@@ -583,6 +583,8 @@ def allowed(self):
         """Return whether vectors diffract according to diffraction
         selection rules assuming kinematic scattering theory.
 
+        Integer vectors are assumed.
+
         Returns
         -------
         allowed : numpy.ndarray
@@ -614,20 +616,22 @@ def allowed(self):
         # Translational symmetry
         centering = self.phase.space_group.short_name[0]
 
+        hkl = self.hkl.round().astype(int).reshape(-1, 3)
+
         if centering == "A":  # Centred on A faces only
-            return np.isclose(np.mod(self.k + self.l, 2), 0)
+            return np.isclose(np.mod(hkl[:, 1] + hkl[:, 2], 2), 0)
         elif centering == "B":  # Centred on B faces only
-            return np.isclose(np.mod(self.h + self.l, 2), 0)
+            return np.isclose(np.mod(hkl[:, 0] + hkl[:, 2], 2), 0)
         elif centering == "C":  # Centred on C faces only
-            return np.isclose(np.mod(self.h + self.k, 2), 0)
+            return np.isclose(np.mod(hkl[:, 0] + hkl[:, 1], 2), 0)
         elif centering == "F":  # Face-centred, hkl all odd/even
-            selection = np.sum(np.mod(self.hkl, 2), axis=-1)
+            selection = np.sum(np.mod(hkl, 2), axis=-1)
             return np.array([i not in [1, 2] for i in selection], dtype=bool)
         elif centering == "I":  # Body-centred, h + k + l = 2n (even)
-            return np.isclose(np.mod(np.sum(self.hkl, axis=-1), 2), 0)
+            return np.isclose(np.mod(np.sum(hkl, axis=-1), 2), 0)
         elif centering in ["R", "H"]:  # Rhombohedral obverse
             # Consider Rhombohedral reverse?
-            return np.isclose(np.mod(-self.h + self.k + self.l, 3), 0)
+            return np.isclose(np.mod(-hkl[:, 0] + hkl[:, 1] + hkl[:, 2], 3), 0)
         elif centering == "P":  # Primitive
             if self.has_hexagonal_lattice:
                 # TODO: See rules in e.g.

diffsims/generators/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/generators/diffraction_generator.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/generators/library_generator.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/generators/rotation_list_generators.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/generators/sphere_mesh_generators.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #
@@ -143,7 +143,7 @@ def get_cube_mesh_vertices(resolution, grid_type="spherified_corner"):
     References
     ----------
     .. [Cajaravelli2015] O. S. Cajaravelli, "Four Ways to Create a Mesh for a Sphere,"
-        https://medium.com/game-dev-daily/four-ways-to-create-a-mesh-for-a-sphere-d7956b825db4.
+        https://medium.com/@oscarsc/four-ways-to-create-a-mesh-for-a-sphere-d7956b825db4.
     """
     # the angle between 001 and 011
     max_angle = np.deg2rad(45)
@@ -385,8 +385,7 @@ def get_icosahedral_mesh_vertices(resolution):
 
     References
     ----------
-    .. [Meshzoo] The `meshzoo.sphere` module,
-        https://github.com/nschloe/meshzoo/blob/master/meshzoo/sphere.py.
+    .. [Meshzoo] The `meshzoo.sphere` module.
     """
     t = (1.0 + np.sqrt(5.0)) / 2.0
     corners = np.array(

diffsims/generators/zap_map_generator.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/libraries/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/libraries/diffraction_library.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #

diffsims/libraries/structure_library.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-# Copyright 2017-2022 The diffsims developers
+# Copyright 2017-2023 The diffsims developers
 #
 # This file is part of diffsims.
 #