dcnum 0.25.1__tar.gz → 0.25.2__tar.gz

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Files changed (126) hide show
  1. {dcnum-0.25.1 → dcnum-0.25.2}/.github/workflows/check.yml +2 -2
  2. {dcnum-0.25.1 → dcnum-0.25.2}/.github/workflows/deploy_pypi.yml +2 -2
  3. {dcnum-0.25.1 → dcnum-0.25.2}/CHANGELOG +3 -0
  4. {dcnum-0.25.1 → dcnum-0.25.2}/PKG-INFO +9 -9
  5. {dcnum-0.25.1 → dcnum-0.25.2}/pyproject.toml +8 -8
  6. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/_version.py +2 -2
  7. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum.egg-info/PKG-INFO +9 -9
  8. dcnum-0.25.2/src/dcnum.egg-info/requires.txt +11 -0
  9. dcnum-0.25.1/src/dcnum.egg-info/requires.txt +0 -11
  10. {dcnum-0.25.1 → dcnum-0.25.2}/.gitignore +0 -0
  11. {dcnum-0.25.1 → dcnum-0.25.2}/.readthedocs.yml +0 -0
  12. {dcnum-0.25.1 → dcnum-0.25.2}/LICENSE +0 -0
  13. {dcnum-0.25.1 → dcnum-0.25.2}/README.rst +0 -0
  14. {dcnum-0.25.1 → dcnum-0.25.2}/benchmark/.gitignore +0 -0
  15. {dcnum-0.25.1 → dcnum-0.25.2}/benchmark/Readme.md +0 -0
  16. {dcnum-0.25.1 → dcnum-0.25.2}/benchmark/benchmark.py +0 -0
  17. {dcnum-0.25.1 → dcnum-0.25.2}/benchmark/bm_write_deque_writer_thread.py +0 -0
  18. {dcnum-0.25.1 → dcnum-0.25.2}/benchmark/bm_write_queue_collector_thread.py +0 -0
  19. {dcnum-0.25.1 → dcnum-0.25.2}/docs/conf.py +0 -0
  20. {dcnum-0.25.1 → dcnum-0.25.2}/docs/extensions/github_changelog.py +0 -0
  21. {dcnum-0.25.1 → dcnum-0.25.2}/docs/index.rst +0 -0
  22. {dcnum-0.25.1 → dcnum-0.25.2}/docs/requirements.txt +0 -0
  23. {dcnum-0.25.1 → dcnum-0.25.2}/setup.cfg +0 -0
  24. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/__init__.py +0 -0
  25. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/__init__.py +0 -0
  26. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/event_extractor_manager_thread.py +0 -0
  27. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_background/__init__.py +0 -0
  28. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_background/base.py +0 -0
  29. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_background/bg_copy.py +0 -0
  30. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_background/bg_roll_median.py +0 -0
  31. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_background/bg_sparse_median.py +0 -0
  32. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_brightness/__init__.py +0 -0
  33. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_brightness/bright_all.py +0 -0
  34. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_brightness/common.py +0 -0
  35. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_contour/__init__.py +0 -0
  36. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_contour/contour.py +0 -0
  37. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_contour/moments.py +0 -0
  38. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_contour/volume.py +0 -0
  39. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_texture/__init__.py +0 -0
  40. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_texture/common.py +0 -0
  41. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/feat_texture/tex_all.py +0 -0
  42. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/gate.py +0 -0
  43. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/feat/queue_event_extractor.py +0 -0
  44. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/logic/__init__.py +0 -0
  45. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/logic/ctrl.py +0 -0
  46. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/logic/job.py +0 -0
  47. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/logic/json_encoder.py +0 -0
  48. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/meta/__init__.py +0 -0
  49. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/meta/paths.py +0 -0
  50. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/meta/ppid.py +0 -0
  51. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/read/__init__.py +0 -0
  52. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/read/cache.py +0 -0
  53. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/read/const.py +0 -0
  54. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/read/detect_flicker.py +0 -0
  55. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/read/hdf5_data.py +0 -0
  56. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/read/mapped.py +0 -0
  57. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/__init__.py +0 -0
  58. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_thresh.py +0 -0
  59. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/__init__.py +0 -0
  60. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/segm_torch_base.py +0 -0
  61. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/segm_torch_mpo.py +0 -0
  62. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/segm_torch_sto.py +0 -0
  63. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/torch_model.py +0 -0
  64. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/torch_postproc.py +0 -0
  65. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segm_torch/torch_preproc.py +0 -0
  66. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segmenter.py +0 -0
  67. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segmenter_manager_thread.py +0 -0
  68. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segmenter_mpo.py +0 -0
  69. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/segm/segmenter_sto.py +0 -0
  70. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/write/__init__.py +0 -0
  71. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/write/deque_writer_thread.py +0 -0
  72. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/write/queue_collector_thread.py +0 -0
  73. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum/write/writer.py +0 -0
  74. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum.egg-info/SOURCES.txt +0 -0
  75. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum.egg-info/dependency_links.txt +0 -0
  76. {dcnum-0.25.1 → dcnum-0.25.2}/src/dcnum.egg-info/top_level.txt +0 -0
  77. {dcnum-0.25.1 → dcnum-0.25.2}/tests/conftest.py +0 -0
  78. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/fmt-hdf5_cytoshot_extended-moments-features.zip +0 -0
  79. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/fmt-hdf5_cytoshot_full-features_2023.zip +0 -0
  80. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/fmt-hdf5_cytoshot_full-features_2024.zip +0 -0
  81. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip +0 -0
  82. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/fmt-hdf5_shapein_empty.zip +0 -0
  83. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/fmt-hdf5_shapein_raw-with-variable-length-logs.zip +0 -0
  84. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/segm-torch-model_unet-dcnum-test_g1_910c2.zip +0 -0
  85. {dcnum-0.25.1 → dcnum-0.25.2}/tests/data/segm-torch-test-data_unet-dcnum-test_g1_910c2.zip +0 -0
  86. {dcnum-0.25.1 → dcnum-0.25.2}/tests/helper_methods.py +0 -0
  87. {dcnum-0.25.1 → dcnum-0.25.2}/tests/requirements.txt +0 -0
  88. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_background_base.py +0 -0
  89. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_background_bg_copy.py +0 -0
  90. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_background_bg_roll_median.py +0 -0
  91. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_background_bg_sparsemed.py +0 -0
  92. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_brightness.py +0 -0
  93. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_event_extractor_manager.py +0 -0
  94. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_gate.py +0 -0
  95. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_haralick.py +0 -0
  96. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_moments_based.py +0 -0
  97. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_moments_based_extended.py +0 -0
  98. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_feat_volume.py +0 -0
  99. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_init.py +0 -0
  100. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_logic_job.py +0 -0
  101. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_logic_join.py +0 -0
  102. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_logic_json.py +0 -0
  103. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_logic_pipeline.py +0 -0
  104. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_paths.py +0 -0
  105. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_ppid_base.py +0 -0
  106. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_ppid_bg.py +0 -0
  107. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_ppid_data.py +0 -0
  108. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_ppid_feat.py +0 -0
  109. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_ppid_gate.py +0 -0
  110. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_meta_ppid_segm.py +0 -0
  111. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_read_basin.py +0 -0
  112. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_read_concat_hdf5.py +0 -0
  113. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_read_detect_flicker.py +0 -0
  114. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_read_hdf5.py +0 -0
  115. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_read_hdf5_basins.py +0 -0
  116. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_read_hdf5_index_mapping.py +0 -0
  117. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_base.py +0 -0
  118. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_mpo.py +0 -0
  119. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_no_mask_proc.py +0 -0
  120. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_sto.py +0 -0
  121. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_thresh.py +0 -0
  122. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_torch.py +0 -0
  123. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_segm_torch_preproc.py +0 -0
  124. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_write_deque_writer_thread.py +0 -0
  125. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_write_queue_collector_thread.py +0 -0
  126. {dcnum-0.25.1 → dcnum-0.25.2}/tests/test_write_writer.py +0 -0
{dcnum-0.25.1 → dcnum-0.25.2}/.github/workflows/check.yml RENAMED
@@ -10,12 +10,12 @@ jobs:
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  runs-on: ${{ matrix.os }}
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  strategy:
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  matrix:
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- python-version: ['3.10']
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+ python-version: ['3.10', '3.x']
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  os: [macos-latest, ubuntu-latest, windows-latest]
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  timeout-minutes: 30
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  steps:
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- - uses: actions/checkout@v3
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+ - uses: actions/checkout@main
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  with:
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  fetch-depth: 0
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  - name: Set up Python ${{ matrix.python-version }}
{dcnum-0.25.1 → dcnum-0.25.2}/.github/workflows/deploy_pypi.yml RENAMED
@@ -10,7 +10,7 @@ jobs:
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  name: Build source distribution
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  runs-on: ubuntu-latest
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  steps:
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- - uses: actions/checkout@v3
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+ - uses: actions/checkout@main
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  with:
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  fetch-depth: 0
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@@ -29,7 +29,7 @@ jobs:
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  name: Build wheel
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  runs-on: ubuntu-latest
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  steps:
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- - uses: actions/checkout@v3
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+ - uses: actions/checkout@main
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  with:
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  fetch-depth: 0
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{dcnum-0.25.1 → dcnum-0.25.2}/CHANGELOG RENAMED
@@ -1,3 +1,6 @@
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+ 0.25.2
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+ - setup: officially support numpy 2
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+ - setup: pin dependencies
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  0.25.1
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  - fix: catch ValueError when computing relative path on different anchors
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  - ref: replace np.string_ with np.bytes_
{dcnum-0.25.1 → dcnum-0.25.2}/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: 0.25.1
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+ Version: 0.25.2
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
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  Maintainer-email: Paul Müller <dev@craban.de>
@@ -17,14 +17,14 @@ Classifier: Intended Audience :: Science/Research
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  Requires-Python: <4,>=3.10
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  Description-Content-Type: text/x-rst
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  License-File: LICENSE
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- Requires-Dist: h5py>=3.0.0
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- Requires-Dist: hdf5plugin>=3.3.1
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- Requires-Dist: mahotas
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- Requires-Dist: numba
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- Requires-Dist: numpy>=1.21
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- Requires-Dist: opencv-python-headless
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- Requires-Dist: scikit-image
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- Requires-Dist: scipy>=1.8.0
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+ Requires-Dist: h5py<4,>=3.0.0
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+ Requires-Dist: hdf5plugin<6,>=3.3.1
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+ Requires-Dist: mahotas<2,>=1
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+ Requires-Dist: numba<1,>=0.60
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+ Requires-Dist: numpy<3,>=1.21
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+ Requires-Dist: opencv-python-headless<5,>=4
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+ Requires-Dist: scikit-image<1,>=0.24
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+ Requires-Dist: scipy<2,>=1.8.0
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  Provides-Extra: torch
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  Requires-Dist: torch>=2.2; extra == "torch"
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{dcnum-0.25.1 → dcnum-0.25.2}/pyproject.toml RENAMED
@@ -25,14 +25,14 @@ classifiers = [
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  ]
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  license = {text = "MIT"}
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  dependencies = [
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- "h5py>=3.0.0", # BSD
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- "hdf5plugin>=3.3.1", # MIT and others (per plugin)
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- "mahotas", # MIT
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- "numba", # BSD
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- "numpy>=1.21", # BSD
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- "opencv-python-headless", # Apache 2.0
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- "scikit-image", # BSD
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- "scipy>=1.8.0", # BSD
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+ "h5py>=3.0.0, <4", # BSD
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+ "hdf5plugin>=3.3.1, <6", # MIT and others (per plugin)
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+ "mahotas>=1, <2", # MIT
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+ "numba>=0.60, <1", # BSD
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+ "numpy>=1.21, <3", # BSD
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+ "opencv-python-headless>=4, <5", # Apache 2.0
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+ "scikit-image>=0.24, <1", # BSD
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+ "scipy>=1.8.0, <2", # BSD
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  ]
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  dynamic = ["version"]
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{dcnum-0.25.1 → dcnum-0.25.2}/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 = '0.25.1'
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- __version_tuple__ = version_tuple = (0, 25, 1)
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+ __version__ = version = '0.25.2'
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+ __version_tuple__ = version_tuple = (0, 25, 2)
{dcnum-0.25.1 → dcnum-0.25.2}/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: 0.25.1
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+ Version: 0.25.2
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller, Raghava Alajangi
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  Maintainer-email: Paul Müller <dev@craban.de>
@@ -17,14 +17,14 @@ Classifier: Intended Audience :: Science/Research
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  Requires-Python: <4,>=3.10
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  Description-Content-Type: text/x-rst
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  License-File: LICENSE
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- Requires-Dist: h5py>=3.0.0
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- Requires-Dist: hdf5plugin>=3.3.1
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- Requires-Dist: mahotas
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- Requires-Dist: numba
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- Requires-Dist: numpy>=1.21
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- Requires-Dist: opencv-python-headless
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- Requires-Dist: scikit-image
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- Requires-Dist: scipy>=1.8.0
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+ Requires-Dist: h5py<4,>=3.0.0
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+ Requires-Dist: hdf5plugin<6,>=3.3.1
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+ Requires-Dist: mahotas<2,>=1
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+ Requires-Dist: numba<1,>=0.60
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+ Requires-Dist: numpy<3,>=1.21
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+ Requires-Dist: opencv-python-headless<5,>=4
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+ Requires-Dist: scikit-image<1,>=0.24
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+ Requires-Dist: scipy<2,>=1.8.0
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  Provides-Extra: torch
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  Requires-Dist: torch>=2.2; extra == "torch"
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dcnum-0.25.2/src/dcnum.egg-info/requires.txt ADDED
@@ -0,0 +1,11 @@
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+ h5py<4,>=3.0.0
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+ hdf5plugin<6,>=3.3.1
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+ mahotas<2,>=1
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+ numba<1,>=0.60
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+ numpy<3,>=1.21
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+ opencv-python-headless<5,>=4
7
+ scikit-image<1,>=0.24
8
+ scipy<2,>=1.8.0
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+
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+ [torch]
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+ torch>=2.2
dcnum-0.25.1/src/dcnum.egg-info/requires.txt DELETED
@@ -1,11 +0,0 @@
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- h5py>=3.0.0
2
- hdf5plugin>=3.3.1
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- mahotas
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- numba
5
- numpy>=1.21
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- opencv-python-headless
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- scikit-image
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- scipy>=1.8.0
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-
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- [torch]
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- torch>=2.2
{dcnum-0.25.1 → dcnum-0.25.2}/.gitignore RENAMED
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{dcnum-0.25.1 → dcnum-0.25.2}/.readthedocs.yml RENAMED
File without changes
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