phaserEM 0.3.0__tar.gz → 0.3.1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (119) hide show
  1. {phaserem-0.3.0 → phaserem-0.3.1}/PKG-INFO +1 -1
  2. phaserem-0.3.1/phaser/__init__.py +1 -0
  3. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/regularizers.py +1 -1
  4. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/slurm.py +9 -3
  5. {phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/PKG-INFO +1 -1
  6. phaserem-0.3.0/phaser/__init__.py +0 -1
  7. {phaserem-0.3.0 → phaserem-0.3.1}/LICENSE.txt +0 -0
  8. {phaserem-0.3.0 → phaserem-0.3.1}/README.md +0 -0
  9. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/__main__.py +0 -0
  10. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/cli/__init__.py +0 -0
  11. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/cli/calc_drift.py +0 -0
  12. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/cli/process_empad.py +0 -0
  13. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/cli/validate.py +0 -0
  14. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/__init__.py +0 -0
  15. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/noise_models.py +0 -0
  16. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/output.py +0 -0
  17. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/position_correction.py +0 -0
  18. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/simulation.py +0 -0
  19. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/conventional/__init__.py +0 -0
  20. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/conventional/run.py +0 -0
  21. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/conventional/solvers.py +0 -0
  22. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/gradient/run.py +0 -0
  23. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/gradient/solvers.py +0 -0
  24. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/gradient/synthetic.py +0 -0
  25. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/execute.py +0 -0
  26. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/__init__.py +0 -0
  27. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/_dependencies.py +0 -0
  28. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/filter.py +0 -0
  29. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/hook.py +0 -0
  30. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/io/empad.py +0 -0
  31. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/io/gatan.py +0 -0
  32. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/io/manual.py +0 -0
  33. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/io/nion.py +0 -0
  34. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/object.py +0 -0
  35. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/preprocessing.py +0 -0
  36. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/probe.py +0 -0
  37. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/regularization.py +0 -0
  38. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/scan.py +0 -0
  39. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/schedule.py +0 -0
  40. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/solver.py +0 -0
  41. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/tilt.py +0 -0
  42. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/__init__.py +0 -0
  43. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/empad.py +0 -0
  44. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/gatan.py +0 -0
  45. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/nion.py +0 -0
  46. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/main.py +0 -0
  47. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/observer.py +0 -0
  48. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/plan.py +0 -0
  49. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/py.typed +0 -0
  50. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/state.py +0 -0
  51. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/types.py +0 -0
  52. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/__init__.py +0 -0
  53. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/_cuda_kernels.py +0 -0
  54. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/_jax_kernels.py +0 -0
  55. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/_torch_kernels.py +0 -0
  56. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/analysis.py +0 -0
  57. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/config.py +0 -0
  58. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/image.py +0 -0
  59. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/io.py +0 -0
  60. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/misc.py +0 -0
  61. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/num.py +0 -0
  62. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/object.py +0 -0
  63. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/optics.py +0 -0
  64. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/physics.py +0 -0
  65. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/plotting.py +0 -0
  66. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/scan.py +0 -0
  67. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/tree.py +0 -0
  68. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/version.py +0 -0
  69. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/__init__.py +0 -0
  70. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/debug.py +0 -0
  71. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/notebook.py +0 -0
  72. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/pubsub.py +0 -0
  73. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/routes.py +0 -0
  74. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/server.py +0 -0
  75. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/apple-touch-icon.png +0 -0
  76. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/dashboard.js +0 -0
  77. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/dashboard.js.LICENSE.txt +0 -0
  78. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/dashboard.js.map +0 -0
  79. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/error.js +0 -0
  80. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/error.js.map +0 -0
  81. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/manager.js +0 -0
  82. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/manager.js.LICENSE.txt +0 -0
  83. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/manager.js.map +0 -0
  84. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/runtime.js +0 -0
  85. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/runtime.js.map +0 -0
  86. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/shared.js +0 -0
  87. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/shared.js.LICENSE.txt +0 -0
  88. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/dist/shared.js.map +0 -0
  89. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/favicon.ico +0 -0
  90. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/icon.svg +0 -0
  91. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/logo-text.svg +0 -0
  92. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/static/logo.svg +0 -0
  93. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/templates/base.html +0 -0
  94. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/templates/dashboard.html +0 -0
  95. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/templates/error.html +0 -0
  96. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/templates/manager.html +0 -0
  97. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/types.py +0 -0
  98. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/util.py +0 -0
  99. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/views.py +0 -0
  100. {phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/worker.py +0 -0
  101. {phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/SOURCES.txt +0 -0
  102. {phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/dependency_links.txt +0 -0
  103. {phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/entry_points.txt +0 -0
  104. {phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/requires.txt +0 -0
  105. {phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/top_level.txt +0 -0
  106. {phaserem-0.3.0 → phaserem-0.3.1}/pyproject.toml +0 -0
  107. {phaserem-0.3.0 → phaserem-0.3.1}/setup.cfg +0 -0
  108. {phaserem-0.3.0 → phaserem-0.3.1}/setup.py +0 -0
  109. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_empad.py +0 -0
  110. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_engines.py +0 -0
  111. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_image.py +0 -0
  112. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_initialization.py +0 -0
  113. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_load.py +0 -0
  114. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_misc.py +0 -0
  115. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_num.py +0 -0
  116. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_object.py +0 -0
  117. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_optics.py +0 -0
  118. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_physics.py +0 -0
  119. {phaserem-0.3.0 → phaserem-0.3.1}/tests/test_state.py +0 -0
{phaserem-0.3.0 → phaserem-0.3.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: phaserEM
3
- Version: 0.3.0
3
+ Version: 0.3.1
4
4
  Summary: Weapon of choice for electron ptychographic reconstructions
5
5
  Author-email: Colin Gilgenbach <hexane@mit.edu>
6
6
  License-Expression: MPL-2.0
phaserem-0.3.1/phaser/__init__.py ADDED
@@ -0,0 +1 @@
1
+ __version__ = '0.3.1'
{phaserem-0.3.0 → phaserem-0.3.1}/phaser/engines/common/regularizers.py RENAMED
@@ -143,7 +143,7 @@ class RegularizeLayers:
143
143
 
144
144
  def apply_iter(self, sim: ReconsState, state: None) -> t.Tuple[ReconsState, None]:
145
145
  xp = get_array_module(sim.object.data)
146
- dtype = to_real_dtype(sim.object.data)
146
+ dtype = to_real_dtype(sim.object.data.dtype)
147
147
 
148
148
  if len(sim.object.thicknesses) < 2:
149
149
  return (sim, None)
{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/slurm.py RENAMED
@@ -151,14 +151,20 @@ class SlurmManager:
151
151
 
152
152
  for job in d["jobs"]:
153
153
  try:
154
- worker = self._slurm_workers[job["job_id"]]
154
+ job_id = job['job_id']
155
+ job_state = job['job_state']
156
+ worker = self._slurm_workers[job_id]
155
157
  except KeyError:
156
158
  continue
157
159
 
158
- if job['job_state'] in ('CONFIGURING', 'RUNNING'):
160
+ if isinstance(job_state, str):
161
+ job_state = [job_state]
162
+
163
+ if any(j in ('CONFIGURING', 'RUNNING') for j in job_state):
159
164
  if worker.status == 'queued':
160
165
  await worker.set_status('starting')
161
- elif job['job_state'] != 'PENDING':
166
+ elif not any(j == 'PENDING' for j in job_state):
167
+ self.logger.debug(f"Stopping worker {job_id}, squeue got job_state: {job_state}")
162
168
  if worker.status != 'stopped':
163
169
  # TODO grab some exit information here
164
170
  await worker.set_status('stopped')
{phaserem-0.3.0 → phaserem-0.3.1}/phaserEM.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: phaserEM
3
- Version: 0.3.0
3
+ Version: 0.3.1
4
4
  Summary: Weapon of choice for electron ptychographic reconstructions
5
5
  Author-email: Colin Gilgenbach <hexane@mit.edu>
6
6
  License-Expression: MPL-2.0
phaserem-0.3.0/phaser/__init__.py DELETED
@@ -1 +0,0 @@
1
- __version__ = '0.3.0'
{phaserem-0.3.0 → phaserem-0.3.1}/LICENSE.txt RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/README.md RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/__main__.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/execute.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/hook.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/probe.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/scan.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/hooks/tilt.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/__init__.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/empad.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/gatan.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/io/nion.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/main.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/observer.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/plan.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/py.typed RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/state.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/types.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/image.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/io.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/misc.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/num.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/scan.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/utils/tree.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/version.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/debug.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/pubsub.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/routes.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/server.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/types.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/util.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/views.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/phaser/web/worker.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/pyproject.toml RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/setup.cfg RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/setup.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_empad.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_engines.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_image.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_load.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_misc.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_num.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_object.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_optics.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_physics.py RENAMED
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{phaserem-0.3.0 → phaserem-0.3.1}/tests/test_state.py RENAMED
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