Merge 8aa1c88 into 200c26f

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# 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
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+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 }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

diffsims/generators/diffraction_generator.py

@@ -192,8 +192,7 @@ def calculate_profile_data(
         self,
         structure,
         reciprocal_radius=1.0,
-        magnitude_tolerance=1e-5,
-        minimum_intensity=1e-3,
+        minimum_intensity=1e-3
     ):
         """
         Calculates a one dimensional diffraction profile for a structure.
@@ -205,9 +204,6 @@ def calculate_profile_data(
         reciprocal_radius : float
             The maximum radius of the sphere of reciprocal space to sample, in
             reciprocal angstroms.
-        magnitude_tolerance : float
-            The minimum difference between diffraction magnitudes in reciprocal
-            angstroms for two peaks to be considered different.
         minimum_intensity : float
             The minimum intensity required for a diffraction peak to be
             considered real. Deals with numerical precision issues.
@@ -269,7 +265,7 @@ def calculate_profile_data(
                 y.append(v[0])
                 hkls.append(k)
 
-        y = y / max(y) * 100
+        y = np.asarray(y) / max(y) * 100
 
         return ProfileSimulation(x, y, hkls)
 

diffsims/libraries/diffraction_library.py

@@ -135,17 +135,14 @@ def get_library_entry(self, phase=None, angle=None):
         if phase is not None:
             phase_entry = self[phase]
             if angle is not None:
-                orientations = phase_entry["orientations"]
-                if isinstance(orientations, np.ndarray):
-                    orientations = orientations.tolist()
                 orientation_index = _get_library_entry_from_angles(self, phase, angle)
             else:
                 orientation_index = 0
-        else:
-            if angle is not None:
-                raise ValueError(
-                    "To select a certain angle you must first specify a phase"
+        elif angle is not None:
+            raise ValueError(
+                "To select a certain angle you must first specify a phase"
                 )
+        else:
             phase_entry = next(iter(self.values()))
             orientation_index = 0
 

diffsims/release_info.py

@@ -1,5 +1,5 @@
 name = "diffsims"
-version = "0.2.3"
+version = "0.3.0"
 author = "Duncan Johnstone, Phillip Crout"
 copyright = "Copyright 2017-2020, The pyXem Developers"
 credits = [

diffsims/sims/diffraction_simulation.py

@@ -175,31 +175,22 @@ class ProfileSimulation:
         Magnitudes of scattering vectors.
     intensities : array-like, shape [n_peaks, 1]
         The kinematic intensity of the diffraction peaks.
-
-    Returns
-    -------
     hkls: [{(h, k, l): mult}] {(h, k, l): mult} is a dict of Miller
         indices for all diffracted lattice facets contributing to each
         intensity.
     """
 
     def __init__(self, magnitudes, intensities, hkls):
-        """Initializes the ProfileSimulation object with data values for the
-        magnitudes, intensities, and hkls.
-        """
         self.magnitudes = magnitudes
         self.intensities = intensities
         self.hkls = hkls
 
-    def get_plot(self, g_max, annotate_peaks=True, with_labels=True, fontsize=12):
-
+    def get_plot(self,annotate_peaks=True, with_labels=True, fontsize=12):
         """Plots the diffraction profile simulation for the
            calculate_profile_data method in DiffractionGenerator.
 
         Parameters
         ----------
-        g_max : float
-            Maximum g-vector magnitude to plot.
         annotate_peaks : boolean
             If True, peaks are annotaed with hkl information.
         with_labels : boolean

diffsims/tests/test_generators/test_rotation_list_generator.py

@@ -30,8 +30,7 @@
     "grid",
     [
         pytest.param(
-            get_local_grid(resolution=30, center=(0, 1, 0), grid_width=35),
-            marks=pytest.mark.xfail(reason="Downstream bug"),
+            get_local_grid(resolution=30, center=(0,1,0), grid_width=35)
         ),
         get_fundamental_zone_grid(space_group=20, resolution=20),
     ],

diffsims/tests/test_sims/test_diffraction_simulation.py

@@ -82,7 +82,7 @@ def profile_simulation():
 
 
 def test_plot_profile_simulation(profile_simulation):
-    profile_simulation.get_plot(g_max=1)
+    profile_simulation.get_plot()
 
 
 class TestDiffractionSimulation:

setup.py

@@ -51,7 +51,7 @@
         "tqdm>=0.4.9",
         "transforms3d",
         "diffpy.structure>=3.0.0",  # First Python 3 support
-        "orix>=0.4.0",
+        "orix>=0.5.0",
         "numba",
         "psutil",
     ],