Release 0.2.2

.gitattributes

@@ -1,4 +1,5 @@
 dist/** -linguist-detectable
 examples/** -linguist-detectable
 tests/** -linguist-detectable
-xcoll/scattering_routines/k2/FORTRAN_src/** linguist-vendored
+dev/** linguist-vendored
+duckcoll/scattering_routines/k2/FORTRAN_src/** linguist-vendored

README.md

@@ -2,7 +2,14 @@
 
 <!---![PyPI - Python Version](https://img.shields.io/pypi/pyversions/xcoll?logo=PyPI?style=plastic) ![PyPI - Wheel](https://img.shields.io/pypi/wheel/xcoll?logo=PyPI?style=plastic)-->
 
-![GitHub release (latest by date)](https://img.shields.io/github/v/release/xsuite/xcoll?style=plastic) ![GitHub](https://img.shields.io/github/license/xsuite/xcoll?style=plastic) ![GitHub all releases](https://img.shields.io/github/downloads/xsuite/xcoll/total?logo=GitHub&style=plastic) ![GitHub issues](https://img.shields.io/github/issues/xsuite/xcoll?logo=GitHub&style=plastic) ![GitHub pull requests](https://img.shields.io/github/issues-pr/xsuite/xcoll?logo=GitHub&style=plastic) ![GitHub repo size](https://img.shields.io/github/repo-size/xsuite/xcoll?logo=GitHub&style=plastic)
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/xsuite/xcoll?style=plastic)
+![GitHub](https://img.shields.io/github/license/xsuite/xcoll?style=plastic)
+![PyPi](https://img.shields.io/pypi/dm/xcoll?logo=PyPI&style=plastic)
+![GitHub all releases](https://img.shields.io/github/downloads/xsuite/xcoll/total?logo=GitHub&style=plastic)
+
+![GitHub pull requests](https://img.shields.io/github/issues-pr/xsuite/xcoll?logo=GitHub&style=plastic)
+![GitHub issues](https://img.shields.io/github/issues/xsuite/xcoll?logo=GitHub&style=plastic)
+![GitHub repo size](https://img.shields.io/github/repo-size/xsuite/xcoll?logo=GitHub&style=plastic)
 
 Collimation in xtrack simulations
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xcoll"
-version = "0.2.1"
+version = "0.2.2"
 description = "Xsuite collimation package"
 homepage = "https://github.com/xsuite/xcoll"
 repository = "https://github.com/xsuite/xcoll"
@@ -17,16 +17,21 @@ include = [ "LICENSE", "NOTICE" ]
 
 [tool.poetry.dependencies]
 python = ">=3.8"
-#numpy
-#pandas
-#scipy
-#xobjects
-#xdeps
-#xpart
-#xtrack
+ruamel-yaml = { version = "^0.17.31", optional = true }
+numpy = ">=1.0"
+pandas = ">=1.4"
+xobjects = "^0.2.6"
+xdeps = "^0.1.1"
+xpart = "^0.15.0"
+xtrack = "^0.36.5"
+xfields = "^0.12.1"
+xcoll = "^0.2.1"
 
 [tool.poetry.dev-dependencies]
-pytest = "^5.2"
+pytest = ">=7.3"
+
+[tool.poetry.extras]
+tests = ["pytest", "ruamel-yaml"]
 
 [build-system]
 # Needed for pip install -e (BTW: need pip version 22)

tests/test_black_absorber.py

@@ -13,6 +13,7 @@ def test_horizontal_parallel(test_context):
     jaw_L, jaw_R, _, _, cox, _, L, coll = _make_absorber(_context=test_context)
     part, x, _, _, _ = _generate_particles(_context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # As the angles are zero, only particles that started in front of the jaw are lost
     mask_hit = (x >= jaw_L + cox) | (x <= jaw_R + cox)
@@ -32,6 +33,7 @@ def test_horizontal(test_context):
     jaw_L, jaw_R, _, _, cox, _, L, coll = _make_absorber(_context=test_context)
     part, x, _, xp, _ = _generate_particles(four_dim=True, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # Particles in front of the jaw are lost, ...
     mask_hit_front = (x >= jaw_L + cox) | (x <= jaw_R + cox)
@@ -62,6 +64,7 @@ def test_horizontal_with_tilts(test_context):
     jaw_L, jaw_R, jaw_LD, jaw_RD, cox, _, L, coll = _make_absorber(tilts=[0.0005, -0.00015], _context=test_context)
     part, x, _, xp, _ = _generate_particles(four_dim=True, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # Particles in front of the jaw are lost, ...
     mask_hit_front = (x >= jaw_L + cox) | (x <= jaw_R + cox)
@@ -92,6 +95,7 @@ def test_vertical_parallel(test_context):
     jaw_L, jaw_R, _, _, _, coy, L, coll = _make_absorber(angle=90, _context=test_context)
     part, _, y, _, _ = _generate_particles(_context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # As the angles are zero, only particles that started in front of the jaw are lost
     mask_hit = (y >= jaw_L + coy) | (y <= jaw_R + coy)
@@ -111,6 +115,7 @@ def test_vertical(test_context):
     jaw_L, jaw_R, _, _, _, coy, L, coll = _make_absorber(angle=90, _context=test_context)
     part, _, y, _, yp = _generate_particles(four_dim=True, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # Particles in front of the jaw are lost, ...
     mask_hit_front = (y >= jaw_L + coy) | (y <= jaw_R + coy)
@@ -141,6 +146,7 @@ def test_vertical_with_tilts(test_context):
     jaw_L, jaw_R, jaw_LD, jaw_RD, _, coy, L, coll = _make_absorber(angle=90, tilts=[0.0005, -0.00015], _context=test_context)
     part, _, y, _, yp = _generate_particles(four_dim=True, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # Particles in front of the jaw are lost, ...
     mask_hit_front = (y >= jaw_L + coy) | (y <= jaw_R + coy)
@@ -172,6 +178,7 @@ def test_angled_parallel(test_context):
     jaw_L, jaw_R, _, _, cox, _, L, coll = _make_absorber(angle=angle, rotate_co=True, _context=test_context)
     part, x, _, _, _ = _generate_particles(angle=angle, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # As the angles are zero, only particles that started in front of the jaw are lost
     mask_hit = (x >= jaw_L + cox) | (x <= jaw_R + cox)
@@ -193,6 +200,7 @@ def test_angled(test_context):
     jaw_L, jaw_R, _, _, cox, _, L, coll = _make_absorber(angle=angle, rotate_co=True, _context=test_context)
     part, x, _, xp, _ = _generate_particles(four_dim=True, angle=angle, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # Particles in front of the jaw are lost, ...
     mask_hit_front = (x >= jaw_L + cox) | (x <= jaw_R + cox)
@@ -225,6 +233,7 @@ def test_angled_with_tilts(test_context):
     jaw_L, jaw_R, jaw_LD, jaw_RD, cox, _, L, coll = _make_absorber(angle=angle, tilts=[0.0005, -0.00015], rotate_co=True, _context=test_context)
     part, x, _, xp, _ = _generate_particles(four_dim=True,angle=angle, _context=test_context)
     coll.track(part)
+    part.move(_context=xo.ContextCpu())
     part.sort(interleave_lost_particles=True)
     # Particles in front of the jaw are lost, ...
     mask_hit_front = (x >= jaw_L + cox) | (x <= jaw_R + cox)
@@ -251,8 +260,6 @@ def test_angled_with_tilts(test_context):
     assert np.allclose(part_x_rot[mask_hit_angle_R], jaw_R + cox + (jaw_RD-jaw_R)/L*s_hit_R, atol=1e-15, rtol=0)
 
 
-
-
 def _make_absorber(angle=0, tilts=[0,0], rotate_co=False, _context=None):
     if _context is None:
         _context = xo.ContextCpu()
@@ -291,6 +298,3 @@ def _generate_particles(four_dim=False, angle=0, _context=None):
     xp_rot = part_init.px * part_init.rpp * np.cos(angle/180.*np.pi) + part_init.py * part_init.rpp * np.sin(angle/180.*np.pi)
     yp_rot = part_init.px * part_init.rpp * np.sin(angle/180.*np.pi) + part_init.py * part_init.rpp * np.cos(angle/180.*np.pi)
     return part, x_rot, y_rot, xp_rot, yp_rot
-
-
-

tests/test_colldb.py

@@ -3,7 +3,7 @@
 import xcoll as xc
 
 
-path = Path.cwd() / 'data'
+path =  Path(__file__).parent / 'data'
 
 
 def test_loading():

tests/test_collimator_elements.py

@@ -244,7 +244,9 @@ def test_black_absorber_length_instantiation(test_context):
         elem = xc.BlackAbsorber(length=1.1, active_length=0.5, inactive_front=0.4, inactive_back=0.2, _context=test_context)
 
 
-@for_all_test_contexts
+@for_all_test_contexts(
+    excluding=('ContextCupy', 'ContextPyopencl')  # Rutherford RNG not on GPU
+)
 def test_everest(test_context):
     # Test instantiation
     elem = xc.EverestCollimator(length=1, material=xc.materials.Carbon, _context=test_context)
@@ -287,7 +289,9 @@ def test_everest(test_context):
             setattr(elem, field, 0.3)
 
 
-@for_all_test_contexts
+@for_all_test_contexts(
+    excluding=('ContextCupy', 'ContextPyopencl')  # Rutherford RNG not on GPU
+)
 def test_everest_crystal(test_context):
     # Test instantiation
     elem = xc.EverestCrystal(length=1, material=xc.materials.SiliconCrystal, _context=test_context)

tests/test_everest.py

@@ -81,7 +81,7 @@
 ]
 
 
-path = Path('./data_test_everest/')
+path = Path(__file__).parent / 'data_test_everest'
 
 def test_primaries():
     _track_collimator('tcp.c6l7.b1')
@@ -124,7 +124,7 @@ def test_crystals():
         _track_collimator(name)
 
 
-def _track_collimator(name, atolx=1e-11, atoly=1e-11, atolpx=1e-11, atolpy=1e-11, atolz=1e-11, atold=1e-10):
+def _track_collimator(name, atolx=3e-9, atoly=3e-10, atolpx=5e-9, atolpy=2e-9, atolz=1e-11, atold=2e-8):
     with open(Path(path, 'initial.json'), 'r') as fid:
         part = xp.Particles.from_dict(json.load(fid))
     with open(Path(path, 'Collimators', name+'.json'), 'r') as fid:

tests/test_lossmap.py

@@ -6,10 +6,10 @@
 import pytest
 from xpart.test_helpers import flaky_assertions, retry
 
-path = Path.cwd() / 'data'
+path = Path(__file__).parent / 'data'
 
 # https://github.com/xsuite/xtrack/blob/18b1ac33d6a9d87a156e87bfb71cb2c8011085f6/tests/test_radiation.py#LL138C5-L138C29
-@retry
+@retry()
 @pytest.mark.parametrize("beam, plane, npart, interpolation, ignore_crystals", [
                             [1, 'H', 25000, 0.2, True],
                             [2, 'V', 25000, 0.3, True],
@@ -36,7 +36,7 @@ def test_run_lossmap(beam, plane, npart, interpolation, ignore_crystals):
     with flaky_assertions():
         summ = coll_manager.summary(part, show_zeros=False)
         assert list(summ.columns) == ['collname', 'nabs', 'length', 's', 'type']
-        assert len(summ) == 10
+        assert len(summ[summ.type=='EverestCollimator']) == 10
         # We want at least 5% absorption on the primary
         assert summ.loc[summ.collname==tcp,'nabs'].values[0] > 0.05*npart
 
@@ -63,21 +63,6 @@ def test_run_lossmap(beam, plane, npart, interpolation, ignore_crystals):
         assert lm['reversed'] == line_is_reversed
 
 
-# @retry
-# def test_lossmap_B1H():
-#     _run_lossmap(1, 'H', 25000, 0.2)
-
-
-# def test_lossmap_B2V():
-#     _run_lossmap(2, 'V', 25000, 0.3)
-
-
-# def test_lossmap_crystals_B1V():
-#     _run_lossmap(1, 'V', 35000, 0.1, ignore_crystals=False)
-
-# def test_lossmap_crystals_B2H():
-#     _run_lossmap(2, 'H', 30000, 0.15, ignore_crystals=False)
-
 
 
 # def test_off_momentum_lossmap():

tests/test_version.py

@@ -1,5 +1,5 @@
 from xcoll import __version__
 
 def test_version():
-    assert __version__ == '0.2.1'
+    assert __version__ == '0.2.2'
 

version.sh

@@ -34,6 +34,7 @@ git switch main
 git pull
 PR=$( gh pr list --head $branch | tail -1 | awk '{print $1;}' )
 gh pr merge ${PR} --merge --admin --delete-branch
+git pull
 
 # Make a tag
 git tag v${new_ver}

xcoll/__init__.py

@@ -6,4 +6,4 @@
 from .manager import CollimatorManager
 from .colldb import CollimatorDatabase, load_SixTrack_colldb
 
-__version__ = '0.2.1'
+__version__ = '0.2.2'

xcoll/beam_elements/collimators_src/absorber.h

@@ -31,7 +31,7 @@ void BlackAbsorber_track_local_particle(BlackAbsorberData el, LocalParticle* par
     double const cos_zL = BlackAbsorberData_get_cos_zL(el);
     double const sin_zR = BlackAbsorberData_get_sin_zR(el);
     double const cos_zR = BlackAbsorberData_get_cos_zR(el);
-    if (abs(sin_zL-sin_zR) > 1.e-10 || abs(cos_zL-cos_zR) > 1.e-10 ){
+    if (fabs(sin_zL-sin_zR) > 1.e-10 || fabs(cos_zL-cos_zR) > 1.e-10 ){
         kill_all_particles(part0, XC_ERR_NOT_IMPLEMENTED);
     };
     double const dx = BlackAbsorberData_get_ref_x(el);

xcoll/beam_elements/collimators_src/everest_collimator.h

@@ -31,7 +31,7 @@ void EverestCollimator_track_local_particle(EverestCollimatorData el, LocalParti
     double const cos_zL     = EverestCollimatorData_get_cos_zL(el);
     double const sin_zR     = EverestCollimatorData_get_sin_zR(el);
     double const cos_zR     = EverestCollimatorData_get_cos_zR(el);
-    if (abs(sin_zL-sin_zR) > 1.e-10 || abs(cos_zL-cos_zR) > 1.e-10 ){
+    if (fabs(sin_zL-sin_zR) > 1.e-10 || fabs(cos_zL-cos_zR) > 1.e-10 ){
         kill_all_particles(part0, XC_ERR_NOT_IMPLEMENTED);
     };
     double const c_aperture = EverestCollimatorData_get_jaw_L(el) - EverestCollimatorData_get_jaw_R(el);

xcoll/beam_elements/collimators_src/everest_crystal.h

@@ -32,14 +32,14 @@ void EverestCrystal_track_local_particle(EverestCrystalData el, LocalParticle* p
     double const cos_zL     = EverestCrystalData_get_cos_zL(el);
     double const sin_zR     = EverestCrystalData_get_sin_zR(el);
     double const cos_zR     = EverestCrystalData_get_cos_zR(el);
-    if (abs(sin_zL-sin_zR) > 1.e-10 || abs(cos_zL-cos_zR) > 1.e-10 ){
+    if (fabs(sin_zL-sin_zR) > 1.e-10 || fabs(cos_zL-cos_zR) > 1.e-10 ){
         kill_all_particles(part0, XC_ERR_NOT_IMPLEMENTED);
     };
     double const c_aperture = EverestCrystalData_get_jaw_L(el) - EverestCrystalData_get_jaw_R(el);
     double const c_offset   = ( EverestCrystalData_get_jaw_L(el) + EverestCrystalData_get_jaw_R(el) ) /2;
     double const c_tilt0    = asin(EverestCrystalData_get_sin_yL(el));
     double const c_tilt1    = asin(EverestCrystalData_get_sin_yR(el));
-    if (abs(c_tilt1) > 1.e-10){
+    if (fabs(c_tilt1) > 1.e-10){
         kill_all_particles(part0, XC_ERR_INVALID_XOFIELD);
     };
     int    const side       = EverestCrystalData_get__side(el);