spacr 0.9.24__tar.gz → 0.9.25__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 (370) hide show
  1. {spacr-0.9.24/spacr.egg-info → spacr-0.9.25}/PKG-INFO +3 -3
  2. {spacr-0.9.24 → spacr-0.9.25}/README.rst +2 -2
  3. {spacr-0.9.24 → spacr-0.9.25}/setup.py +1 -1
  4. {spacr-0.9.24 → spacr-0.9.25/spacr.egg-info}/PKG-INFO +3 -3
  5. {spacr-0.9.24 → spacr-0.9.25}/LICENSE +0 -0
  6. {spacr-0.9.24 → spacr-0.9.25}/MANIFEST.in +0 -0
  7. {spacr-0.9.24 → spacr-0.9.25}/deploy_docs.sh +0 -0
  8. {spacr-0.9.24 → spacr-0.9.25}/docs/.doctrees/environment.pickle +0 -0
  9. {spacr-0.9.24 → spacr-0.9.25}/docs/_images/logo_spacr.png +0 -0
  10. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/SetupDict.html +0 -0
  11. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/BasePredictor.html +0 -0
  12. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/BaseTrainer.html +0 -0
  13. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/Baseline/Predictor.html +0 -0
  14. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/Baseline/Trainer.html +0 -0
  15. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/Baseline/utils.html +0 -0
  16. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/MEDIAR/EnsemblePredictor.html +0 -0
  17. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/MEDIAR/Predictor.html +0 -0
  18. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/MEDIAR/Trainer.html +0 -0
  19. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/MEDIAR/utils.html +0 -0
  20. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/core/utils.html +0 -0
  21. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/evaluate.html +0 -0
  22. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/generate_mapping.html +0 -0
  23. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/index.html +0 -0
  24. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/main.html +0 -0
  25. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/predict.html +0 -0
  26. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_annotate.html +0 -0
  27. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_classify.html +0 -0
  28. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_make_masks.html +0 -0
  29. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_mask.html +0 -0
  30. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_measure.html +0 -0
  31. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_sequencing.html +0 -0
  32. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/app_umap.html +0 -0
  33. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/chat_bot.html +0 -0
  34. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/core.html +0 -0
  35. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/deep_spacr.html +0 -0
  36. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/gui.html +0 -0
  37. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/gui_core.html +0 -0
  38. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/gui_elements.html +0 -0
  39. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/gui_utils.html +0 -0
  40. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/io.html +0 -0
  41. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/logger.html +0 -0
  42. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/measure.html +0 -0
  43. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/mediar.html +0 -0
  44. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/ml.html +0 -0
  45. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/plot.html +0 -0
  46. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/sequencing.html +0 -0
  47. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/settings.html +0 -0
  48. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/sim.html +0 -0
  49. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/sp_stats.html +0 -0
  50. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/spacr_cellpose.html +0 -0
  51. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/submodules.html +0 -0
  52. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/timelapse.html +0 -0
  53. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/toxo.html +0 -0
  54. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/utils.html +0 -0
  55. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/spacr/version.html +0 -0
  56. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/data_utils/custom/CellAware.html +0 -0
  57. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/data_utils/custom/LoadImage.html +0 -0
  58. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/data_utils/custom/NormalizeImage.html +0 -0
  59. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/data_utils/datasetter.html +0 -0
  60. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/data_utils/transforms.html +0 -0
  61. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/data_utils/utils.html +0 -0
  62. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/measures.html +0 -0
  63. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/models/MEDIARFormer.html +0 -0
  64. {spacr-0.9.24 → spacr-0.9.25}/docs/_modules/train_tools/utils.html +0 -0
  65. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/SetupDict/index.rst.txt +0 -0
  66. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/BasePredictor/index.rst.txt +0 -0
  67. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/BaseTrainer/index.rst.txt +0 -0
  68. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/Baseline/Predictor/index.rst.txt +0 -0
  69. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/Baseline/Trainer/index.rst.txt +0 -0
  70. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/Baseline/index.rst.txt +0 -0
  71. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/Baseline/utils/index.rst.txt +0 -0
  72. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/MEDIAR/EnsemblePredictor/index.rst.txt +0 -0
  73. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/MEDIAR/Predictor/index.rst.txt +0 -0
  74. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/MEDIAR/Trainer/index.rst.txt +0 -0
  75. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/MEDIAR/index.rst.txt +0 -0
  76. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/MEDIAR/utils/index.rst.txt +0 -0
  77. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/index.rst.txt +0 -0
  78. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/core/utils/index.rst.txt +0 -0
  79. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/evaluate/index.rst.txt +0 -0
  80. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/generate_mapping/index.rst.txt +0 -0
  81. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/index.rst.txt +0 -0
  82. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/main/index.rst.txt +0 -0
  83. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/predict/index.rst.txt +0 -0
  84. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_annotate/index.rst.txt +0 -0
  85. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_classify/index.rst.txt +0 -0
  86. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_make_masks/index.rst.txt +0 -0
  87. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_mask/index.rst.txt +0 -0
  88. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_measure/index.rst.txt +0 -0
  89. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_sequencing/index.rst.txt +0 -0
  90. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/app_umap/index.rst.txt +0 -0
  91. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/chat_bot/index.rst.txt +0 -0
  92. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/core/index.rst.txt +0 -0
  93. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/deep_spacr/index.rst.txt +0 -0
  94. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/gui/index.rst.txt +0 -0
  95. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/gui_core/index.rst.txt +0 -0
  96. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/gui_elements/index.rst.txt +0 -0
  97. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/gui_utils/index.rst.txt +0 -0
  98. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/index.rst.txt +0 -0
  99. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/io/index.rst.txt +0 -0
  100. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/logger/index.rst.txt +0 -0
  101. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/measure/index.rst.txt +0 -0
  102. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/mediar/index.rst.txt +0 -0
  103. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/ml/index.rst.txt +0 -0
  104. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/openai/index.rst.txt +0 -0
  105. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/plot/index.rst.txt +0 -0
  106. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/sequencing/index.rst.txt +0 -0
  107. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/settings/index.rst.txt +0 -0
  108. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/sim/index.rst.txt +0 -0
  109. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/sp_stats/index.rst.txt +0 -0
  110. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/spacr_cellpose/index.rst.txt +0 -0
  111. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/submodules/index.rst.txt +0 -0
  112. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/timelapse/index.rst.txt +0 -0
  113. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/toxo/index.rst.txt +0 -0
  114. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/utils/index.rst.txt +0 -0
  115. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/spacr/version/index.rst.txt +0 -0
  116. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/custom/CellAware/index.rst.txt +0 -0
  117. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/custom/LoadImage/index.rst.txt +0 -0
  118. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/custom/NormalizeImage/index.rst.txt +0 -0
  119. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/custom/index.rst.txt +0 -0
  120. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/datasetter/index.rst.txt +0 -0
  121. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/index.rst.txt +0 -0
  122. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/transforms/index.rst.txt +0 -0
  123. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/data_utils/utils/index.rst.txt +0 -0
  124. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/index.rst.txt +0 -0
  125. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/measures/index.rst.txt +0 -0
  126. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/models/MEDIARFormer/index.rst.txt +0 -0
  127. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/models/index.rst.txt +0 -0
  128. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/api/train_tools/utils/index.rst.txt +0 -0
  129. {spacr-0.9.24 → spacr-0.9.25}/docs/_sources/index.rst.txt +0 -0
  130. {spacr-0.9.24 → spacr-0.9.25}/docs/_static/basic.css +0 -0
  131. {spacr-0.9.24 → spacr-0.9.25}/docs/_static/css/badge_only.css +0 -0
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  369. {spacr-0.9.24 → spacr-0.9.25}/spacr.egg-info/requires.txt +0 -0
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{spacr-0.9.24/spacr.egg-info → spacr-0.9.25}/PKG-INFO RENAMED
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  Metadata-Version: 2.1
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  Name: spacr
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- Version: 0.9.24
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+ Version: 0.9.25
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  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
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  Home-page: https://github.com/EinarOlafsson/spacr
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  Author: Einar Birnir Olafsson
@@ -167,7 +167,7 @@ Data Availability
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  - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
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- - **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
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+ - **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2076>`_
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  Example Notebooks
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  -----------------
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  How to Cite
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  -----------
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  If you use spaCR in your research, please cite:
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- Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
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+ Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
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  - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
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- - **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
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+ - **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2076>`_
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  Example Notebooks
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  -----------------
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  How to Cite
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  -----------
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  If you use spaCR in your research, please cite:
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- Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
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+ Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
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{spacr-0.9.24 → spacr-0.9.25}/setup.py RENAMED
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  'huggingface-hub>=0.24.0,<0.25'
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{spacr-0.9.24 → spacr-0.9.25/spacr.egg-info}/PKG-INFO RENAMED
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  Metadata-Version: 2.1
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  Name: spacr
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- Version: 0.9.24
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+ Version: 0.9.25
4
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  Summary: Spatial phenotype analysis of crisp screens (SpaCr)
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  Home-page: https://github.com/EinarOlafsson/spacr
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  Author: Einar Birnir Olafsson
@@ -167,7 +167,7 @@ Data Availability
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  - **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
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- - **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_
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+ - **Image data** is deposited at EBI BioStudies under accession: `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2076>`_
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  Example Notebooks
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  -----------------
@@ -200,5 +200,5 @@ See the `LICENSE <https://github.com/EinarOlafsson/spacr/blob/main/LICENSE>`_ fi
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  How to Cite
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  -----------
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  If you use spaCR in your research, please cite:
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- Einar Olafsson, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
203
+ Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
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