Changed references to amplus

MANIFEST.in

@@ -1,9 +1,9 @@
 include CMakeLists.txt
 recursive-include src *
 recursive-include pybind11 *
-include amplus/data/files/4v5d.cif
-include amplus/data/files/4v1w.cif
-include amplus/data/files/3jb9.cif
-include amplus/data/files/6qt9.cif
-include amplus/data/files/6z6u.pdb
-include amplus/data/files/water.cif
+include parakeet/data/files/4v5d.cif
+include parakeet/data/files/4v1w.cif
+include parakeet/data/files/3jb9.cif
+include parakeet/data/files/6qt9.cif
+include parakeet/data/files/6z6u.pdb
+include parakeet/data/files/water.cif

src/parakeet/simulation.py

@@ -956,14 +956,14 @@ def compute_image(psi, microscope, simulation, x_fov, y_fov, offset, device):
             # )
 
             # # Compute the fraction of electrons in the plasmon peak
-            # electron_fraction = amplus.inelastic.mp_loss_fraction(shape, angle)
+            # electron_fraction = parakeet.inelastic.mp_loss_fraction(shape, angle)
             # electron_fraction *= inelastic_fraction
 
             # # Scale the image by the fraction of electrons
             # image *= electron_fraction
 
             # Compute the energy and spread of the plasmon peak
-            # peak, sigma = amplus.inelastic.most_probable_loss(
+            # peak, sigma = parakeet.inelastic.most_probable_loss(
             #     microscope.beam.energy, shape, angle
             # )
             # peak /= 1000.0
@@ -1034,8 +1034,8 @@ def compute_image(psi, microscope, simulation, x_fov, y_fov, offset, device):
 
             # Compute the zero loss and mpl image fraction
             print(shape, angle)
-            zero_loss_fraction = amplus.inelastic.zero_loss_fraction(shape, angle)
-            mp_loss_fraction = amplus.inelastic.mp_loss_fraction(shape, angle)
+            zero_loss_fraction = parakeet.inelastic.zero_loss_fraction(shape, angle)
+            mp_loss_fraction = parakeet.inelastic.mp_loss_fraction(shape, angle)
             electron_fraction = (
                 elastic_filtered_fraction * zero_loss_fraction
                 + inelastic_filtered_fraction * mp_loss_fraction