Merge pull request #100 from xsuite/release/v0.5.2

Release 0.5.2

Author: freddieknets

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xcoll"
-version = "0.5.1"
+version = "0.5.2"
 description = "Xsuite collimation package"
 homepage = "https://github.com/xsuite/xcoll"
 repository = "https://github.com/xsuite/xcoll"

tests/test_install.py

@@ -35,7 +35,7 @@ def test_install_single_existing_marker(beam, test_context):
     assert np.isclose(pos_centre - line[name].length/2, line.get_s_position(name))
     assert isinstance(line[name], xc.BlackAbsorber)
     tab = line.get_table()
-    idx = tab.mask[[name]][0]
+    idx = tab.rows.indices[[name]][0]
     assert xt.line._is_aperture(line[idx-1], line)
     assert xt.line._is_aperture(line[idx+1], line)
 
@@ -47,14 +47,14 @@ def test_install_single_existing_marker(beam, test_context):
     tab = line.get_table()
     existing_length = 0.12
     line[name].length += existing_length
-    idx = tab.mask[[name]][0]
+    idx = tab.rows.indices[[name]][0]
     while True:
         idx -= 1
         if tab.element_type[idx].startswith('Drift'):
             assert line[idx].length > existing_length/2
             line[idx].length -= existing_length/2
             break
-    idx = tab.mask[[name]][0]
+    idx = tab.rows.indices[[name]][0]
     while True:
         idx += 1
         if tab.element_type[idx].startswith('Drift'):
@@ -68,7 +68,7 @@ def test_install_single_existing_marker(beam, test_context):
     assert np.isclose(pos_centre - line[name].length/2, line.get_s_position(name))
     assert isinstance(line[name], xc.EverestCollimator)
     tab = line.get_table()
-    idx = tab.mask[[name]][0]
+    idx = tab.rows.indices[[name]][0]
     assert xt.line._is_aperture(line[idx-1], line)
     assert xt.line._is_aperture(line[idx+1], line)
 
@@ -84,7 +84,7 @@ def test_install_single_existing_marker(beam, test_context):
     assert np.isclose(pos_centre - line[name].length/2, line.get_s_position(name))
     assert isinstance(line[name], xc.EverestCrystal)
     tab = line.get_table()
-    idx = tab.mask[[name]][0]
+    idx = tab.rows.indices[[name]][0]
     assert xt.line._is_aperture(line[idx-1], line)
     assert xt.line._is_aperture(line[idx+1], line)
 
@@ -121,7 +121,7 @@ def test_install_single_no_marker(beam, test_context):
     assert np.isclose(line.get_s_position(name), 12.4)
     assert isinstance(line[name], xc.BlackAbsorber)
     tab = line.get_table()
-    idx = tab.mask[[name]][0]
+    idx = tab.rows.indices[[name]][0]
     assert xt.line._is_aperture(line[idx-1], line)
     assert isinstance(line[idx-1], xt.LimitEllipse)
     assert np.isclose(line[idx-1].a_squ, 0.16)

tests/test_version.py

@@ -6,5 +6,5 @@
 from xcoll import __version__
 
 def test_version():
-    assert __version__ == '0.5.1'
+    assert __version__ == '0.5.2'
 

xcoll/beam_elements/base.py

@@ -629,7 +629,7 @@ def assign_optics(self, *, nemitt_x=None, nemitt_y=None, beta_gamma_rel=None, na
             raise ValueError("When using `twiss`, need to provide the name as well.")
         else:
             tw_up   = twiss.rows[name]
-            tw_down = twiss.rows[twiss.mask[[name]]+1]
+            tw_down = twiss.rows[twiss.rows.indices[[name]]+1]
         if not np.isclose(tw_up.s[0] + self.length, tw_down.s[0]):
             raise ValueError(f"Downstream twiss not compatible with length {self.length}m.")
         self._optics = {

xcoll/general.py

@@ -12,5 +12,5 @@
 # ======================
 # Do not change
 # ======================
-__version__ = '0.5.1'
+__version__ = '0.5.2'
 # ======================

xcoll/initial_distribution.py

@@ -61,13 +61,13 @@ def generate_pencil_on_collimator(line, name, num_particles, *, side='+-', penci
     if is_converging:
         # pencil at front of jaw
         match_at_s = s_front
-        sigma = beam_sizes.rows[name:f'{name}%%1'][f'sigma_{plane}'][0]
-        sigma_transv = beam_sizes.rows[name:f'{name}%%1'][f'sigma_{transv_plane}'][0]
+        sigma = beam_sizes.rows[name:f'{name}>>1'][f'sigma_{plane}'][0]
+        sigma_transv = beam_sizes.rows[name:f'{name}>>1'][f'sigma_{transv_plane}'][0]
     else:
         # pencil at back of jaw
         match_at_s = s_back
-        sigma = beam_sizes.rows[name:f'{name}%%1'][f'sigma_{plane}'][1]
-        sigma_transv = beam_sizes.rows[name:f'{name}%%1'][f'sigma_{transv_plane}'][1]
+        sigma = beam_sizes.rows[name:f'{name}>>1'][f'sigma_{plane}'][1]
+        sigma_transv = beam_sizes.rows[name:f'{name}>>1'][f'sigma_{transv_plane}'][1]
     dr_sigmas = pencil_spread/sigma
 
     # Generate 4D coordinates
@@ -157,7 +157,7 @@ def generate_delta_from_dispersion(line, at_element, *, plane, position_mm, nemi
         twiss = line.twiss()
 
     beam_sizes = twiss.get_beam_covariance(nemitt_x=nemitt_x, nemitt_y=nemitt_y)
-    beam_sizes = beam_sizes.rows[at_element:f'{at_element}%%1'][f'sigma_{plane}']
+    beam_sizes = beam_sizes.rows[at_element:f'{at_element}>>1'][f'sigma_{plane}']
     sigma = beam_sizes[0] if match_at_front else beam_sizes[1]
     delta  = (position_mm - betatron_cut*sigma - twiss.rows[at_element][plane])
     delta /= twiss.rows[at_element][f'd{plane}']

xcoll/line_tools.py

@@ -26,9 +26,9 @@ def get_optics_at(names, *, twiss=None, line=None):
         twiss = line.twiss()
     if not hasattr(names, '__iter__') and not isinstance(names, str):
         names = [names]
-    coll_entry_mask = twiss.mask[names]
-    tw_entry = twiss.rows[coll_entry_mask]
-    tw_exit = twiss.rows[coll_entry_mask+1]
+    coll_entry_indices = twiss.rows.indices[names]
+    tw_entry = twiss.rows[coll_entry_indices]
+    tw_exit = twiss.rows[coll_entry_indices+1]
     tw_exit.name = tw_entry.name
     return tw_entry, tw_exit