dcnum 0.21.0__tar.gz → 0.21.2__tar.gz

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  1. {dcnum-0.21.0 → dcnum-0.21.2}/CHANGELOG +4 -0
  2. {dcnum-0.21.0/src/dcnum.egg-info → dcnum-0.21.2}/PKG-INFO +1 -1
  3. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/_version.py +2 -2
  4. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/event_extractor_manager_thread.py +2 -2
  5. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/segmenter.py +8 -2
  6. {dcnum-0.21.0 → dcnum-0.21.2/src/dcnum.egg-info}/PKG-INFO +1 -1
  7. {dcnum-0.21.0 → dcnum-0.21.2}/.github/workflows/check.yml +0 -0
  8. {dcnum-0.21.0 → dcnum-0.21.2}/.github/workflows/deploy_pypi.yml +0 -0
  9. {dcnum-0.21.0 → dcnum-0.21.2}/.gitignore +0 -0
  10. {dcnum-0.21.0 → dcnum-0.21.2}/.readthedocs.yml +0 -0
  11. {dcnum-0.21.0 → dcnum-0.21.2}/LICENSE +0 -0
  12. {dcnum-0.21.0 → dcnum-0.21.2}/README.rst +0 -0
  13. {dcnum-0.21.0 → dcnum-0.21.2}/docs/conf.py +0 -0
  14. {dcnum-0.21.0 → dcnum-0.21.2}/docs/extensions/github_changelog.py +0 -0
  15. {dcnum-0.21.0 → dcnum-0.21.2}/docs/index.rst +0 -0
  16. {dcnum-0.21.0 → dcnum-0.21.2}/docs/requirements.txt +0 -0
  17. {dcnum-0.21.0 → dcnum-0.21.2}/pyproject.toml +0 -0
  18. {dcnum-0.21.0 → dcnum-0.21.2}/setup.cfg +0 -0
  19. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/__init__.py +0 -0
  20. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/__init__.py +0 -0
  21. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_background/__init__.py +0 -0
  22. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_background/base.py +0 -0
  23. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_background/bg_copy.py +0 -0
  24. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_background/bg_roll_median.py +0 -0
  25. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_background/bg_sparse_median.py +0 -0
  26. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_brightness/__init__.py +0 -0
  27. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_brightness/bright_all.py +0 -0
  28. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_brightness/common.py +0 -0
  29. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_contour/__init__.py +0 -0
  30. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_contour/contour.py +0 -0
  31. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_contour/moments.py +0 -0
  32. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_contour/volume.py +0 -0
  33. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_texture/__init__.py +0 -0
  34. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_texture/common.py +0 -0
  35. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/feat_texture/tex_all.py +0 -0
  36. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/gate.py +0 -0
  37. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/queue_event_extractor.py +0 -0
  38. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/logic/__init__.py +0 -0
  39. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/logic/ctrl.py +0 -0
  40. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/logic/job.py +0 -0
  41. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/logic/json_encoder.py +0 -0
  42. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/meta/__init__.py +0 -0
  43. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/meta/paths.py +0 -0
  44. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/meta/ppid.py +0 -0
  45. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/__init__.py +0 -0
  46. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/cache.py +0 -0
  47. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/const.py +0 -0
  48. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/hdf5_data.py +0 -0
  49. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/mapped.py +0 -0
  50. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/__init__.py +0 -0
  51. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/segm_thresh.py +0 -0
  52. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/segmenter_cpu.py +0 -0
  53. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/segmenter_gpu.py +0 -0
  54. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/segmenter_manager_thread.py +0 -0
  55. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/write/__init__.py +0 -0
  56. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/write/deque_writer_thread.py +0 -0
  57. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/write/queue_collector_thread.py +0 -0
  58. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/write/writer.py +0 -0
  59. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum.egg-info/SOURCES.txt +0 -0
  60. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum.egg-info/dependency_links.txt +0 -0
  61. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum.egg-info/requires.txt +0 -0
  62. {dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum.egg-info/top_level.txt +0 -0
  63. {dcnum-0.21.0 → dcnum-0.21.2}/tests/conftest.py +0 -0
  64. {dcnum-0.21.0 → dcnum-0.21.2}/tests/data/fmt-hdf5_cytoshot_extended-moments-features.zip +0 -0
  65. {dcnum-0.21.0 → dcnum-0.21.2}/tests/data/fmt-hdf5_cytoshot_full-features_2023.zip +0 -0
  66. {dcnum-0.21.0 → dcnum-0.21.2}/tests/data/fmt-hdf5_cytoshot_full-features_2024.zip +0 -0
  67. {dcnum-0.21.0 → dcnum-0.21.2}/tests/data/fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip +0 -0
  68. {dcnum-0.21.0 → dcnum-0.21.2}/tests/data/fmt-hdf5_shapein_empty.zip +0 -0
  69. {dcnum-0.21.0 → dcnum-0.21.2}/tests/data/fmt-hdf5_shapein_raw-with-variable-length-logs.zip +0 -0
  70. {dcnum-0.21.0 → dcnum-0.21.2}/tests/helper_methods.py +0 -0
  71. {dcnum-0.21.0 → dcnum-0.21.2}/tests/requirements.txt +0 -0
  72. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_background_base.py +0 -0
  73. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_background_bg_copy.py +0 -0
  74. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_background_bg_roll_median.py +0 -0
  75. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_background_bg_sparsemed.py +0 -0
  76. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_brightness.py +0 -0
  77. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_event_extractor_manager.py +0 -0
  78. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_gate.py +0 -0
  79. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_haralick.py +0 -0
  80. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_moments_based.py +0 -0
  81. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_moments_based_extended.py +0 -0
  82. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_volume.py +0 -0
  83. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_init.py +0 -0
  84. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_logic_job.py +0 -0
  85. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_logic_join.py +0 -0
  86. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_logic_json.py +0 -0
  87. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_logic_pipeline.py +0 -0
  88. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_paths.py +0 -0
  89. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_ppid_base.py +0 -0
  90. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_ppid_bg.py +0 -0
  91. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_ppid_data.py +0 -0
  92. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_ppid_feat.py +0 -0
  93. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_ppid_gate.py +0 -0
  94. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_meta_ppid_segm.py +0 -0
  95. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_read_basin.py +0 -0
  96. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_read_concat_hdf5.py +0 -0
  97. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_read_hdf5.py +0 -0
  98. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_read_hdf5_basins.py +0 -0
  99. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_read_hdf5_index_mapping.py +0 -0
  100. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_segm_base.py +0 -0
  101. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_segm_no_mask_proc.py +0 -0
  102. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_segm_thresh.py +0 -0
  103. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_write_deque_writer_thread.py +0 -0
  104. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_write_queue_collector_thread.py +0 -0
  105. {dcnum-0.21.0 → dcnum-0.21.2}/tests/test_write_writer.py +0 -0
{dcnum-0.21.0 → dcnum-0.21.2}/CHANGELOG RENAMED
@@ -1,3 +1,7 @@
1
+ 0.21.2
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+ - fix: negative argument for time.sleep
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+ 0.21.1
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+ - enh: support boolean images in mask postprocessing
1
5
  0.21.0
2
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  - fix: GPUSegmenter did not perform mask postprocessing
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  - ref: enable mask postprocessing by default for all segmenters
{dcnum-0.21.0/src/dcnum.egg-info → dcnum-0.21.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.1
2
2
  Name: dcnum
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- Version: 0.21.0
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+ Version: 0.21.2
4
4
  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-0.21.0 → dcnum-0.21.2}/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 = '0.21.0'
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- __version_tuple__ = version_tuple = (0, 21, 0)
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+ __version__ = version = '0.21.2'
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+ __version_tuple__ = version_tuple = (0, 21, 2)
{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/event_extractor_manager_thread.py RENAMED
@@ -98,8 +98,8 @@ class EventExtractorManagerThread(threading.Thread):
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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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+ stall_time = (ldq2 - 200) / (ldq - ldq2)
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+ time.sleep(stall_time if stall_time > 0 else 0)
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  self.logger.warning(
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  f"Stalled {stall_time + 1:.1f}s for slow writer "
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  f"({ldq} chunks queued)")
{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/segm/segmenter.py RENAMED
@@ -184,8 +184,8 @@ class Segmenter(abc.ABC):
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  Parameters
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  ----------
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- labels: 2d integer ndarray
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- Labeled input (contains blobs with same number)
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+ labels: 2d integer or boolean ndarray
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+ Labeled input (contains blobs consisting of unique numbers)
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  clear_border: bool
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  clear the image boarder using
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  :func:`skimage.segmentation.clear_border`
@@ -196,6 +196,12 @@ class Segmenter(abc.ABC):
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  if > 0, perform a binary closing with a disk
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  of that radius in pixels
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  """
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+ if labels.dtype == np.bool_:
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+ # Convert mask image to labels
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+ labels, _ = ndi.label(
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+ input=labels,
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+ structure=ndi.generate_binary_structure(2, 2))
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+
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  if clear_border:
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  #
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  # from skimage import segmentation
{dcnum-0.21.0 → dcnum-0.21.2/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: 0.21.0
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+ Version: 0.21.2
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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-0.21.0 → dcnum-0.21.2}/.gitignore RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/.readthedocs.yml RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/LICENSE RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/README.rst RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/docs/conf.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/docs/index.rst RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/pyproject.toml RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/setup.cfg RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/__init__.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/feat/gate.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/logic/ctrl.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/meta/ppid.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/cache.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/const.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/src/dcnum/read/mapped.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/tests/conftest.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/tests/test_feat_gate.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/tests/test_init.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/tests/test_logic_join.py RENAMED
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{dcnum-0.21.0 → dcnum-0.21.2}/tests/test_logic_json.py RENAMED
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