Minor preparations for a 0.5 release

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,3 +19,5 @@
 - [ ] New functions are imported in corresponding `__init__.py`.
 - [ ] New features, API changes, and deprecations are mentioned in the
       unreleased section in `CHANGELOG.rst`.
+- [ ] Contributor(s) are listed correctly in `credits` in `diffsims/release_info.py` and
+      in `.zenodo.json`.

.github/workflows/build.yml

@@ -9,9 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
+
       - uses: actions/setup-python@v2
+
       - name: Install dependencies
         run: pip install manifix
+
       - name: Check MANIFEST.in file
         run: python setup.py manifix
 
@@ -31,31 +34,39 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.6
             OLDEST_SUPPORTED_VERSION: true
-            # orix requires matplotlib 3.3, matplotlib 3.3 requires numpy 1.15
-            # numba requires scipy==1.0
             DEPENDENCIES: diffpy.structure==3.0.0 matplotlib==3.3 numpy==1.17 orix==0.5.0 scipy==1.0 tqdm==4.9
             LABEL: -oldest
     steps:
       - uses: actions/checkout@v2
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Display Python and pip versions
-        run: python -V; pip -V
-      - name: Install depedencies and package
+        run: |
+          python -V
+          pip -V
+
+      - name: Install dependencies and package
         shell: bash
         run: pip install -U -e .'[tests]'
+
       - name: Install oldest supported version
         if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
         run: pip install ${{ matrix.DEPENDENCIES }}
+
       - name: Display package versions
         run: pip list
+
       - name: Run tests
         run: pytest --cov=diffsims --pyargs diffsims
+
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}
         run: coverage report --show-missing
+
       - name: Upload coverage to Coveralls
         if: ${{ matrix.os == 'ubuntu-latest' }}
         uses: AndreMiras/coveralls-python-action@develop

.github/workflows/python-publish.yml

@@ -1,31 +1,49 @@
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+# This workflow runs when a tagged release is created or it is triggered manually.
+# For more information see:
+# - Python docs: https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+# - GitHub action: https://github.com/marketplace/actions/pypi-publish
+# - GitHub docs: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+# The source distribution (sdist) is built with the `build` package
+# (https://pypa-build.readthedocs.io/en/stable/index.html).
+# The sdist is attempted uploaded to TestPyPI and PyPI whenever the workflow is run
 
-name: Upload Python Package
+name: Upload to PyPI
 
 on:
   release:
     types: [published]
+  workflow_dispatch:
+    workflow: "*"
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
-
     steps:
     - uses: actions/checkout@v2
+
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: '3.x'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        pip install build
+
+    - name: Build package
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python -m build
+
+    - name: Publish package to TestPyPI
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_url: https://test.pypi.org/legacy/
+
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.zenodo.json

@@ -0,0 +1,65 @@
+{
+  "creators": [
+    {
+      "name": "Duncan Johnstone"
+    },
+    {
+      "name":"Phillip Crout",
+      "orcid": "0000-0001-5754-0938"
+    },
+    {
+      "name":"Håkon Wiik Ånes",
+      "orcid": "0000-0002-1213-2911",
+      "affiliation": "Norwegian University of Science and Technology"
+    },
+    {
+      "name":"Eric Prestat"
+    },
+    {
+      "name":"Rob Tovey"
+    },
+    {
+      "name":"Simon Høgås"
+    },
+    {
+      "name":"Ben Martineau"
+    },
+    {
+      "name":"Joonatan Laulainen"
+    },
+    {
+      "name":"Niels Cautaerts",
+      "orcid": "0000-0002-6402-9879"
+    },
+    {
+      "name":"Isabel Wood"
+    },
+    {
+      "name":"Sean Collins"
+    },
+    {
+      "name":"Stef Smeets"
+    },
+    {
+      "name":"Alex Borrelli"
+    },
+    {
+      "name": "Tiarnan Doherty"
+    },
+    {
+      "name":"Jedrzej Morzy"
+    },
+    {
+      "name":"Endre Jacobsen"
+    },
+    {
+      "name":"Tina Bergh"
+    },
+    {
+      "name":"Tomas Ostasevicius"
+    },
+    {
+      "name":"Eirik Opheim"
+    }
+  ]
+}

CHANGELOG.rst

@@ -8,8 +8,8 @@ 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>`_.
 
-Unreleased
-==========
+2022-05-30 - version 0.5.0
+==========================
 
 Added
 -----
@@ -20,7 +20,7 @@ Added
 
 Changed
 -------
-- Minimal version of dependencies numpy >= 1.17 and tqdm >= 4.9.
+- Minimal version of dependencies orix >= 0.9, numpy >= 1.17 and tqdm >= 4.9.
 - The Laue group representing the rotation list sampling of "hexagonal" from 6/m to
   6/mmm.
 - Loosened the angle tolerance in ``DiffractionLibrary.get_library_entry()`` from

diffsims/crystallography/reciprocal_lattice_point.py

@@ -29,7 +29,7 @@
 )
 
 
-_FLOAT_EPS = np.finfo(np.float).eps  # Used to round values below 1e-16 to zero
+_FLOAT_EPS = np.finfo(float).eps  # Used to round values below 1e-16 to zero
 
 
 class ReciprocalLatticePoint:

diffsims/generators/rotation_list_generators.py

@@ -67,7 +67,7 @@ def get_list_from_orix(grid, rounding=2):
     rotation_list : list of tuples
         A rotation list
     """
-    z = grid.to_euler(convention="bunge")
+    z = grid.to_euler()
     rotation_list = z.data.tolist()
     i = 0
     while i < len(rotation_list):
@@ -122,7 +122,7 @@ def get_local_grid(resolution=2, center=None, grid_width=10):
     """
     if isinstance(center, tuple):
         z = np.deg2rad(np.asarray(center))
-        center = Rotation.from_euler(z, convention="bunge", direction="crystal2lab")
+        center = Rotation.from_euler(z)
 
     orix_grid = get_sample_local(
         resolution=resolution, center=center, grid_width=grid_width
@@ -153,11 +153,11 @@ def get_grid_around_beam_direction(beam_rotation, resolution, angular_range=(0,
     Examples
     --------
     >>> from diffsims.generators.zap_map_generator import get_rotation_from_z_to_direction
-    >>> beam_rotation = get_rotation_from_z_to_direction(structure,[1,1,1])
-    >>> grid = get_grid_around_beam_direction(beam_rotation,1)
+    >>> beam_rotation = get_rotation_from_z_to_direction(structure, [1, 1, 1])
+    >>> grid = get_grid_around_beam_direction(beam_rotation, 1)
     """
     z = np.deg2rad(np.asarray(beam_rotation))
-    beam_rotation = Rotation.from_euler(z, convention="bunge", direction="crystal2lab")
+    beam_rotation = Rotation.from_euler(z)
 
     angles = np.deg2rad(
         np.arange(start=angular_range[0], stop=angular_range[1], step=resolution)

diffsims/release_info.py

@@ -1,27 +1,30 @@
 name = "diffsims"
-version = "0.5.dev0"
+version = "0.5.0rc1"
 author = "Duncan Johnstone, Phillip Crout"
-copyright = "Copyright 2017-2022, The pyXem developers"
+copyright = "Copyright 2017-2022, The diffsims developers"
+# Initial committer first, then listed by line additions
 credits = [
     "Duncan Johnstone",
     "Phillip Crout",
+    "Håkon Wiik Ånes",
+    "Eric Prestat",
+    "Rob Tovey",
     "Simon Høgås",
     "Ben Martineau",
-    "Isabel Wood",
-    "Håkon Wiik Ånes",
+    "Niels Cautaerts",
     "Joonatan Laulainen",
-    "Stef Smeets",
+    "Isabel Wood",
     "Sean Collins",
-    "Endre Jacobsen",
-    "Niels Cautaerts",
-    "Eric Prestat",
+    "Stef Smeets",
+    "Alex Borrelli",
     "Tiarnan Doherty",
     "Jedrzej Morzy",
-    "Tomas Ostasevicius",
-    "Alex Borrelli",
+    "Endre Jacobsen",
     "Tina Bergh",
+    "Tomas Ostasevicius",
+    "Eirik Opheim",
 ]
-license = "GPLv3"
+license = "GPLv3+"
 maintainer = "Duncan Johnstone, Phillip Crout, Håkon Wiik Ånes"
 email = "pyxem.team@gmail.com"
 status = "Development"

diffsims/tests/generators/test_rotation_list_generator.py

@@ -16,8 +16,9 @@
 # You should have received a copy of the GNU General Public License
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
 
-import pytest
 import numpy as np
+import pytest
+
 from diffsims.generators.rotation_list_generators import (
     get_local_grid,
     get_grid_around_beam_direction,
@@ -73,7 +74,7 @@ def test_get_grid_around_beam_direction():
     ],
 )
 def test_get_beam_directions_grid(crystal_system, mesh):
-    grid = get_beam_directions_grid(crystal_system, 5, mesh=mesh)
+    _ = get_beam_directions_grid(crystal_system, 5, mesh=mesh)
 
 
 @pytest.mark.parametrize(

diffsims/tests/sims/test_diffraction_simulation.py

@@ -18,8 +18,10 @@
 
 import numpy as np
 import pytest
-from diffsims.sims.diffraction_simulation import DiffractionSimulation
-from diffsims.sims.diffraction_simulation import ProfileSimulation
+
+from diffsims.sims.diffraction_simulation import (
+    DiffractionSimulation, ProfileSimulation
+)
 
 
 def test_wrong_calibration_setting():
@@ -140,6 +142,7 @@ def test_addition(self, diffraction_simulation):
                 ]
             ),
         )
+        assert sim.size == 4
 
     def test_extend(self, diffraction_simulation):
         diffraction_simulation.extend(diffraction_simulation)

doc/conf.py

@@ -21,7 +21,7 @@
 import re
 import sys
 
-from diffsims import __author__, __version__, __file__
+from diffsims import __author__, __file__, __version__
 
 # -- Project information -----------------------------------------------------
 
@@ -50,11 +50,11 @@
 # Create links to references within diffsims' documentation to these packages
 intersphinx_mapping = {
     "diffpy.structure": ("https://www.diffpy.org/diffpy.structure", None),
-    "matplotlib": ("https://matplotlib.org", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "orix": ("https://orix.readthedocs.io/en/stable", None),
     "python": ("https://docs.python.org/3", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -86,7 +86,7 @@ def linkcode_resolve(domain, info):
     """Determine the URL corresponding to Python object.
 
     This is taken from SciPy's conf.py:
-    https://github.com/scipy/scipy/blob/master/doc/source/conf.py.
+    https://github.com/scipy/scipy/blob/develop/doc/source/conf.py.
     """
     if domain != "py":
         return None
@@ -131,12 +131,12 @@ def linkcode_resolve(domain, info):
     fn = relpath(fn, start=startdir).replace(os.path.sep, "/")
 
     if fn.startswith("diffsims/"):
-        m = re.match(r"^.*dev0\+([a-f0-9]+)$", __version__)
+        m = re.match(r"^.*dev0\+([a-f\d]+)$", __version__)
         pre_link = "https://github.com/pyxem/diffsims/blob/"
         if m:
             return pre_link + "%s/%s%s" % (m.group(1), fn, linespec)
         elif "dev" in __version__:
-            return pre_link + "master/%s%s" % (fn, linespec)
+            return pre_link + "develop/%s%s" % (fn, linespec)
         else:
             return pre_link + "v%s/%s%s" % (__version__, fn, linespec)
     else: