Patches for GAMP parsing and Particle display

The memory module of GAMP would use a dictionary to store the particle
data as an intermediate step, using the particle IDs as the key in the
dictionary. This worked great, until there were multiple particles with
the same ID. This patches that out by using the index of the particle
instead. This assumes that each event will have particles appear in the
same order consistently throughout the file, which _should_ be a safe
bet.

There was also an issue with some rushed out code involving the how
Particles are visually represented in iPython and Jupyter. The
underlying data structures were safe, but when the user would try to
view the values, errors would occur. This should also patch those
issues. However, there are no improvements in Testing with these sort of
functions since at this time I have not found a reliable way to test
that the display function is operating correctly.

CHANGELOG.md

@@ -5,6 +5,11 @@ All changes important to the user will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/)
 
+## [3.2.1] - 2021-6-10
+### Fixed
+- Gamp no longer combines particles with the same ID
+- Fixed issue where display_raw would fail in Jupyter with Particles
+
 ## [3.2.0] - 2021-6-1
 ### Added
 - Vectors now support iPython and Jupyter Pretty printing
@@ -189,7 +194,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/)
 - PySim plugin
 - Packaging
 
-[Unreleased]: https://github.com/JeffersonLab/PyPWA/compare/v3.2.0...main
+[Unreleased]: https://github.com/JeffersonLab/PyPWA/compare/v3.2.1...main
+[3.2.1]: https://github.com/JeffersonLab/PyPWA/compare/v3.2.0...v3.2.1
 [3.2.0]: https://github.com/JeffersonLab/PyPWA/compare/v3.1.0...v3.2.0
 [3.1.0]: https://github.com/JeffersonLab/PyPWA/compare/v3.0.0...v3.1.0
 [3.0.0]: https://github.com/JeffersonLab/PyPWA/compare/v3.0.0a1...v3.0.0

PyPWA/info.py

@@ -91,7 +91,7 @@
 __credits__ = ["Mark Jones"]
 
 AUTHOR = "PyPWA Team and Contributors"
-VERSION = "3.2.0"
+VERSION = "3.2.1"
 RELEASE = f"{VERSION}"
 LICENSE = "GPLv3"
 STATUS = "development"

PyPWA/libs/vectors/particle.py

@@ -149,9 +149,8 @@ def display_raw(self):
         df = pd.DataFrame()
         df['e'], df['x'], df['y'], df['z'] = self.e, self.x, self.y, self.z
 
-        display(
-            f'{self.__particle_id}: {self.__particle_name}', raw=True
-        )
+        name = f"{self.__particle_id}: {self.__particle_name}"
+        display(name)
         display(df)
 
     def __getitem__(
@@ -311,6 +310,7 @@ def _repr_pretty_(self, p, cycle):
         else:
             for particle in self.__particle_list:
                 particle._repr_pretty_(p, cycle)
+                p.text('\n')
 
     def _repr_html_(self):
         html = ""
@@ -320,6 +320,7 @@ def _repr_html_(self):
 
     def display_raw(self):
         for p in self.__particle_list:
+            print('\n')
             p.display_raw()
 
     def __len__(self):

PyPWA/plugins/data/gamp.py

@@ -30,7 +30,7 @@
 """
 
 from pathlib import Path
-from typing import Dict, List
+from typing import Dict, List, Tuple
 
 import numpy as np
 
@@ -223,16 +223,16 @@ def parse(self, filename: Path) -> vectors.ParticlePool:
 
             for event_index, line in enumerate(stream):
                 particle_num = int(line)
-                for i in range(particle_num):
+                for index in range(particle_num):
                     line = stream.readline()
                     p_id, charge, x, y, z, e = line.strip("\n").split()
-                    particle_dict[int(p_id)][event_index]["x"] = x
-                    particle_dict[int(p_id)][event_index]["y"] = y
-                    particle_dict[int(p_id)][event_index]["z"] = z
-                    particle_dict[int(p_id)][event_index]["e"] = e
+                    particle_dict[index][1][event_index]["x"] = x
+                    particle_dict[index][1][event_index]["y"] = y
+                    particle_dict[index][1][event_index]["z"] = z
+                    particle_dict[index][1][event_index]["e"] = e
 
         particles = []
-        for p_id, momenta in particle_dict.items():
+        for index, (p_id, momenta) in particle_dict.items():
             particles.append(
                 vectors.Particle(p_id, momenta)
             )
@@ -242,19 +242,22 @@ def parse(self, filename: Path) -> vectors.ParticlePool:
     @staticmethod
     def _make_particle_dict(
             filename: Path, particle_length: int = 1
-    ) -> Dict[int, np.ndarray]:
+    ) -> Dict[int, Tuple[int, np.ndarray]]:
         with filename.open() as stream:
             count = int(stream.readline())
             lines = [stream.readline() for i in range(count)]
 
         particles = dict()
-        for line in lines:
+        for index, line in enumerate(lines):
             p_id, charge, x, y, z, e = line.strip("\n").split()
-            particles[int(p_id)] = np.empty(
-                particle_length,
-                dtype=np.dtype(
-                    [("x", "f8"), ("y", "f8"), ("z", "f8"), ("e", "f8")],
-                    align=True
+            particles[index] = (
+                int(p_id),
+                np.empty(
+                    particle_length,
+                    dtype=np.dtype(
+                        [("x", "f8"), ("y", "f8"), ("z", "f8"), ("e", "f8")],
+                        align=True
+                    )
                 )
             )
         return particles

setup.py

@@ -20,7 +20,7 @@
 
 __author__ = "PyPWA Team and Contributors"
 __license__ = "GPLv3"
-__version__ = "3.2.0"
+__version__ = "3.2.1"
 __email__ = "[email protected]"
 __status__ = "development"
 

tests/libs/vectors/test_particle.py

@@ -52,3 +52,7 @@ def test_particle_can_do_math():
     assert c.x == 8.2
     assert c.y == 12.2
     assert c.z == 16.2
+
+
+def test_particle_raw_display(random_particle_pool):
+    random_particle_pool.display_raw()

tests/plugins/data/test_gamp.py

@@ -0,0 +1,41 @@
+import pytest
+
+from PyPWA.plugins.data import gamp
+from PyPWA.libs.vectors import particle
+
+from pathlib import Path
+
+ROOT = (Path(__file__).parent / "../../test_data/docs").resolve()
+LARGE = ROOT / "large.gamp"
+MULTI = ROOT / "multiple.gamp"
+
+
+@pytest.fixture()
+def gamp_mem():
+    return gamp._GampMemory()
+
+
+@pytest.fixture()
+def large_gamp(gamp_mem):
+    return gamp_mem.parse(LARGE)
+
+
+@pytest.fixture()
+def multi_gamp(gamp_mem):
+    return gamp_mem.parse(MULTI)
+
+
+def test_large_has_all_events(large_gamp):
+    assert 1000 == large_gamp.event_count
+
+
+def test_multi_has_all_events(multi_gamp):
+    assert 5 == multi_gamp.event_count
+
+
+def test_large_has_four_particles(large_gamp):
+    assert 4 == len(large_gamp)
+
+
+def test_multi_has_six_particles(multi_gamp):
+    assert 6 == len(multi_gamp)

tests/test_data/docs/multiple.gamp

@@ -0,0 +1,35 @@
+6
+1 0 0 0 9 9
+14 1 0.489366 1.16687 1.53077 2.19651
+11 1 -0.120747 -0.252622 1.82881 1.91485
+12 -1 -0.0471136 -0.468373 2.86627 2.94632
+1 0 0.144554 -0.0924801 0.396306 0.431864
+1 0 -0.46606 -0.353392 2.37784 2.44872
+6
+1 0 0 0 9 9
+14 1 0.0482325 0.574326 0.588864 1.24871
+11 1 0.147839 0.175565 3.20347 3.2494
+12 -1 0.113935 0.0947125 1.91567 1.9838
+1 0 0.116443 -0.468739 1.61144 1.68227
+1 0 -0.426449 -0.375865 1.68055 1.77409
+6
+1 0 0 0 9 9
+14 1 -0.603583 0.264803 7.6721 7.75731
+11 1 0.277164 -0.0236316 0.372865 0.678319
+12 -1 0.0582607 -0.150773 0.285835 0.592907
+1 0 0.0214529 0.210537 0.337733 0.39856
+1 0 0.246705 -0.300936 0.331466 0.511171
+6
+1 0 0 0 9 9
+14 1 -0.6922 -0.280769 4.1272 4.29791
+11 1 0.59143 0.0433621 2.47691 2.59431
+12 -1 0.56086 0.262788 2.14699 2.28843
+1 0 -0.220055 0.120091 0.374064 0.450299
+1 0 -0.240035 -0.145471 -0.125159 0.307316
+6
+1 0 0 0 9 9
+14 1 -1.08832 -0.149006 2.61188 2.98478
+11 1 0.620169 -0.015586 2.69034 2.80472
+12 -1 0.534044 -0.126931 3.35861 3.43879
+1 0 -0.00930206 -0.143393 0.206859 0.251871
+1 0 -0.0565951 0.434916 0.132317 0.458108