dcnum 0.20.2__tar.gz → 0.20.3__tar.gz

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  1. {dcnum-0.20.2 → dcnum-0.20.3}/CHANGELOG +2 -0
  2. {dcnum-0.20.2/src/dcnum.egg-info → dcnum-0.20.3}/PKG-INFO +1 -1
  3. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/_version.py +2 -2
  4. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/event_extractor_manager_thread.py +7 -5
  5. {dcnum-0.20.2 → dcnum-0.20.3/src/dcnum.egg-info}/PKG-INFO +1 -1
  6. {dcnum-0.20.2 → dcnum-0.20.3}/.github/workflows/check.yml +0 -0
  7. {dcnum-0.20.2 → dcnum-0.20.3}/.github/workflows/deploy_pypi.yml +0 -0
  8. {dcnum-0.20.2 → dcnum-0.20.3}/.gitignore +0 -0
  9. {dcnum-0.20.2 → dcnum-0.20.3}/.readthedocs.yml +0 -0
  10. {dcnum-0.20.2 → dcnum-0.20.3}/LICENSE +0 -0
  11. {dcnum-0.20.2 → dcnum-0.20.3}/README.rst +0 -0
  12. {dcnum-0.20.2 → dcnum-0.20.3}/docs/conf.py +0 -0
  13. {dcnum-0.20.2 → dcnum-0.20.3}/docs/extensions/github_changelog.py +0 -0
  14. {dcnum-0.20.2 → dcnum-0.20.3}/docs/index.rst +0 -0
  15. {dcnum-0.20.2 → dcnum-0.20.3}/docs/requirements.txt +0 -0
  16. {dcnum-0.20.2 → dcnum-0.20.3}/pyproject.toml +0 -0
  17. {dcnum-0.20.2 → dcnum-0.20.3}/setup.cfg +0 -0
  18. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/__init__.py +0 -0
  19. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/__init__.py +0 -0
  20. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_background/__init__.py +0 -0
  21. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_background/base.py +0 -0
  22. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_background/bg_copy.py +0 -0
  23. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_background/bg_roll_median.py +0 -0
  24. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_background/bg_sparse_median.py +0 -0
  25. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_brightness/__init__.py +0 -0
  26. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_brightness/bright_all.py +0 -0
  27. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_brightness/common.py +0 -0
  28. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_contour/__init__.py +0 -0
  29. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_contour/contour.py +0 -0
  30. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_contour/moments.py +0 -0
  31. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_contour/volume.py +0 -0
  32. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_texture/__init__.py +0 -0
  33. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_texture/common.py +0 -0
  34. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/feat_texture/tex_all.py +0 -0
  35. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/gate.py +0 -0
  36. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/queue_event_extractor.py +0 -0
  37. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/logic/__init__.py +0 -0
  38. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/logic/ctrl.py +0 -0
  39. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/logic/job.py +0 -0
  40. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/logic/json_encoder.py +0 -0
  41. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/meta/__init__.py +0 -0
  42. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/meta/paths.py +0 -0
  43. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/meta/ppid.py +0 -0
  44. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/__init__.py +0 -0
  45. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/cache.py +0 -0
  46. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/const.py +0 -0
  47. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/hdf5_data.py +0 -0
  48. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/mapped.py +0 -0
  49. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/segm/__init__.py +0 -0
  50. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/segm/segm_thresh.py +0 -0
  51. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/segm/segmenter.py +0 -0
  52. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/segm/segmenter_cpu.py +0 -0
  53. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/segm/segmenter_gpu.py +0 -0
  54. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/segm/segmenter_manager_thread.py +0 -0
  55. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/write/__init__.py +0 -0
  56. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/write/deque_writer_thread.py +0 -0
  57. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/write/queue_collector_thread.py +0 -0
  58. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/write/writer.py +0 -0
  59. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum.egg-info/SOURCES.txt +0 -0
  60. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum.egg-info/dependency_links.txt +0 -0
  61. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum.egg-info/requires.txt +0 -0
  62. {dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum.egg-info/top_level.txt +0 -0
  63. {dcnum-0.20.2 → dcnum-0.20.3}/tests/conftest.py +0 -0
  64. {dcnum-0.20.2 → dcnum-0.20.3}/tests/data/fmt-hdf5_cytoshot_extended-moments-features.zip +0 -0
  65. {dcnum-0.20.2 → dcnum-0.20.3}/tests/data/fmt-hdf5_cytoshot_full-features_2023.zip +0 -0
  66. {dcnum-0.20.2 → dcnum-0.20.3}/tests/data/fmt-hdf5_cytoshot_full-features_2024.zip +0 -0
  67. {dcnum-0.20.2 → dcnum-0.20.3}/tests/data/fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip +0 -0
  68. {dcnum-0.20.2 → dcnum-0.20.3}/tests/data/fmt-hdf5_shapein_empty.zip +0 -0
  69. {dcnum-0.20.2 → dcnum-0.20.3}/tests/data/fmt-hdf5_shapein_raw-with-variable-length-logs.zip +0 -0
  70. {dcnum-0.20.2 → dcnum-0.20.3}/tests/helper_methods.py +0 -0
  71. {dcnum-0.20.2 → dcnum-0.20.3}/tests/requirements.txt +0 -0
  72. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_background_base.py +0 -0
  73. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_background_bg_copy.py +0 -0
  74. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_background_bg_roll_median.py +0 -0
  75. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_background_bg_sparsemed.py +0 -0
  76. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_brightness.py +0 -0
  77. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_event_extractor_manager.py +0 -0
  78. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_gate.py +0 -0
  79. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_haralick.py +0 -0
  80. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_moments_based.py +0 -0
  81. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_moments_based_extended.py +0 -0
  82. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_volume.py +0 -0
  83. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_init.py +0 -0
  84. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_job.py +0 -0
  85. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_join.py +0 -0
  86. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_json.py +0 -0
  87. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_pipeline.py +0 -0
  88. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_paths.py +0 -0
  89. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_ppid_base.py +0 -0
  90. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_ppid_bg.py +0 -0
  91. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_ppid_data.py +0 -0
  92. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_ppid_feat.py +0 -0
  93. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_ppid_gate.py +0 -0
  94. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_ppid_segm.py +0 -0
  95. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_basin.py +0 -0
  96. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_concat_hdf5.py +0 -0
  97. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_hdf5.py +0 -0
  98. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_hdf5_basins.py +0 -0
  99. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_hdf5_index_mapping.py +0 -0
  100. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_segm_base.py +0 -0
  101. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_segm_no_mask_proc.py +0 -0
  102. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_segm_thresh.py +0 -0
  103. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_write_deque_writer_thread.py +0 -0
  104. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_write_queue_collector_thread.py +0 -0
  105. {dcnum-0.20.2 → dcnum-0.20.3}/tests/test_write_writer.py +0 -0
{dcnum-0.20.2 → dcnum-0.20.3}/CHANGELOG RENAMED
@@ -1,3 +1,5 @@
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+ 0.20.3
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+ - enh: improve strategy for stalling for slow writer
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  0.20.2
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  - ref: remove __init__ from SegmentThresh
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  0.20.1
{dcnum-0.20.2/src/dcnum.egg-info → dcnum-0.20.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: dcnum
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- Version: 0.20.2
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+ Version: 0.20.3
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller
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  Maintainer-email: Paul Müller <dev@craban.de>
{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/_version.py RENAMED
@@ -12,5 +12,5 @@ __version__: str
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  __version_tuple__: VERSION_TUPLE
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  version_tuple: VERSION_TUPLE
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- __version__ = version = '0.20.2'
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- __version_tuple__ = version_tuple = (0, 20, 2)
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+ __version__ = version = '0.20.3'
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+ __version_tuple__ = version_tuple = (0, 20, 3)
{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/event_extractor_manager_thread.py RENAMED
@@ -95,12 +95,14 @@ class EventExtractorManagerThread(threading.Thread):
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  while True:
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  # If the writer_dq starts filling up, then this could lead to
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  # an oom-kill signal. Stall for the writer to prevent this.
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- ldq = len(self.writer_dq)
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- if ldq > 1000:
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- stallsec = ldq / 1000
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+ if (ldq := len(self.writer_dq)) > 1000:
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+ time.sleep(1)
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+ ldq2 = len(self.writer_dq)
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+ stall_time = (ldq2 - 200) / (ldq - ldq2) if ldq2 > 200 else 0
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+ time.sleep(stall_time)
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  self.logger.warning(
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- f"Stalling {stallsec:.1f}s for slow writer")
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- time.sleep(stallsec)
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+ f"Stalled {stall_time + 1:.1f}s for slow writer "
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+ f"({ldq} chunks queued)")
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  cur_slot = 0
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  unavailable_slots = 0
{dcnum-0.20.2 → dcnum-0.20.3/src/dcnum.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: dcnum
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- Version: 0.20.2
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+ Version: 0.20.3
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller
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  Maintainer-email: Paul Müller <dev@craban.de>
{dcnum-0.20.2 → dcnum-0.20.3}/.gitignore RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/.readthedocs.yml RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/LICENSE RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/README.rst RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/docs/conf.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/docs/index.rst RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/docs/requirements.txt RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/pyproject.toml RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/setup.cfg RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/__init__.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/feat/gate.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/logic/ctrl.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/logic/job.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/meta/paths.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/meta/ppid.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/cache.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/const.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/read/mapped.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/src/dcnum/write/writer.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/conftest.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/helper_methods.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/requirements.txt RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_gate.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_feat_volume.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_init.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_job.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_join.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_logic_json.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_meta_paths.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_basin.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_read_hdf5.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_segm_base.py RENAMED
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{dcnum-0.20.2 → dcnum-0.20.3}/tests/test_segm_thresh.py RENAMED
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