ddi-fw 0.0.154__tar.gz → 0.0.157__tar.gz

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Files changed (110) hide show
  1. ddi_fw-0.0.157/PKG-INFO +76 -0
  2. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/pyproject.toml +76 -37
  3. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/base.py +5 -0
  4. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/feature_vector_generation.py +1 -1
  5. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/pipeline/multi_pipeline.py +2 -0
  6. ddi_fw-0.0.157/src/ddi_fw.egg-info/PKG-INFO +76 -0
  7. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw.egg-info/requires.txt +47 -19
  8. ddi_fw-0.0.154/PKG-INFO +0 -54
  9. ddi_fw-0.0.154/src/ddi_fw.egg-info/PKG-INFO +0 -54
  10. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/README.md +0 -0
  11. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/setup.cfg +0 -0
  12. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/__init__.py +0 -0
  13. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/core.py +0 -0
  14. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/dataset_splitter.py +0 -0
  15. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/db_utils.py +0 -0
  16. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  17. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/debug.log +0 -0
  18. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  19. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  20. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  21. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  22. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  23. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  24. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  25. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  26. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  27. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  28. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  29. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  30. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  31. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  32. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  33. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  34. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  35. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  36. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  37. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  38. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  39. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  40. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  41. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  42. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  43. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/base.py +0 -0
  44. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/data/event.db +0 -0
  45. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/test_indexes.txt +0 -0
  46. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_0.txt +0 -0
  47. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_1.txt +0 -0
  48. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_2.txt +0 -0
  49. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_3.txt +0 -0
  50. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_4.txt +0 -0
  51. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_indexes.txt +0 -0
  52. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_0.txt +0 -0
  53. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_1.txt +0 -0
  54. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_2.txt +0 -0
  55. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_3.txt +0 -0
  56. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_4.txt +0 -0
  57. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/embedding_generator.py +0 -0
  58. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/idf_helper.py +0 -0
  59. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  60. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  61. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  62. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  63. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  64. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  65. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  66. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  67. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  68. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  69. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  70. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  71. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  72. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  73. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  74. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  75. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  76. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/datasets/setup_._py +0 -0
  77. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/drugbank/__init__.py +0 -0
  78. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  79. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  80. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  81. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  82. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  83. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/langchain/__init__.py +0 -0
  84. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/langchain/embeddings.py +0 -0
  85. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/langchain/sentence_splitter.py +0 -0
  86. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/langchain/storage.py +0 -0
  87. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ml/__init__.py +0 -0
  88. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ml/evaluation_helper.py +0 -0
  89. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ml/ml_helper.py +0 -0
  90. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ml/model_wrapper.py +0 -0
  91. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ml/pytorch_wrapper.py +0 -0
  92. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ml/tensorflow_wrapper.py +0 -0
  93. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ner/__init__.py +0 -0
  94. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  95. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/ner/ner.py +0 -0
  96. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/pipeline/__init__.py +0 -0
  97. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/pipeline/multi_modal_combination_strategy.py +0 -0
  98. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/pipeline/ner_pipeline.py +0 -0
  99. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/pipeline/pipeline.py +0 -0
  100. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/__init__.py +0 -0
  101. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/enums.py +0 -0
  102. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/json_helper.py +0 -0
  103. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/kaggle.py +0 -0
  104. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/package_helper.py +0 -0
  105. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  106. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/utils.py +0 -0
  107. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw/utils/zip_helper.py +0 -0
  108. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw.egg-info/SOURCES.txt +0 -0
  109. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  110. {ddi_fw-0.0.154 → ddi_fw-0.0.157}/src/ddi_fw.egg-info/top_level.txt +0 -0
@@ -0,0 +1,76 @@
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+ Metadata-Version: 2.4
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+ Name: ddi_fw
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+ Version: 0.0.157
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+ Summary: Do not use :)
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+ Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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+ Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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+ Keywords: Machine Learning
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+ Classifier: Development Status :: 1 - Planning
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+ Classifier: Environment :: Console
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Framework :: Pytest
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+ Classifier: Framework :: tox
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+ Classifier: Framework :: Sphinx
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+ Classifier: Programming Language :: Python
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3 :: Only
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+ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
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+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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+ Classifier: Topic :: Scientific/Engineering :: Information Analysis
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+ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ Requires-Dist: tqdm>=4.66.6
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+ Requires-Dist: pandas>=2.2.0
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+ Provides-Extra: llm
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+ Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "llm"
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+ Requires-Dist: transformers>=4.42.4; extra == "llm"
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+ Requires-Dist: stanza==1.9.2; extra == "llm"
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+ Requires-Dist: tokenizers>=0.19.1; extra == "llm"
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+ Requires-Dist: openai>=1.52.2; extra == "llm"
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+ Requires-Dist: langchain>=0.3.4; extra == "llm"
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+ Requires-Dist: langchain_community==0.3.3; extra == "llm"
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+ Provides-Extra: ml
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+ Requires-Dist: scikit-learn==1.5.2; extra == "ml"
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+ Requires-Dist: tensorflow<2.18.0,>=2.17.0; extra == "ml"
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+ Requires-Dist: tf-keras==2.17.0; extra == "ml"
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+ Requires-Dist: mlflow==2.16.1; extra == "ml"
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+ Requires-Dist: accelerate>=0.33.0; extra == "ml"
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+ Requires-Dist: numpy>=1.26.4; extra == "ml"
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+ Requires-Dist: scipy==1.13.1; extra == "ml"
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+ Requires-Dist: pandas>=2.2.0; extra == "ml"
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+ Requires-Dist: plotly==5.24.1; extra == "ml"
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+ Requires-Dist: matplotlib==3.8.0; extra == "ml"
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+ Requires-Dist: rdkit==2023.3.3; extra == "ml"
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+ Requires-Dist: datasets==3.0.2; extra == "ml"
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+ Requires-Dist: tqdm>=4.66.6; extra == "ml"
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+ Provides-Extra: datasets
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+ Requires-Dist: datasets==3.0.2; extra == "datasets"
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+ Requires-Dist: unstructured==0.16.3; extra == "datasets"
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+ Requires-Dist: py7zr==0.22.0; extra == "datasets"
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+ Requires-Dist: xmlschema==3.4.2; extra == "datasets"
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+ Provides-Extra: drugbank
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+ Requires-Dist: rdkit==2023.3.3; extra == "drugbank"
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+ Requires-Dist: openai>=1.52.2; extra == "drugbank"
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+ Provides-Extra: pipeline-and-ner
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+ Requires-Dist: nltk>=3.8.1; extra == "pipeline-and-ner"
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+ Requires-Dist: stanza==1.9.2; extra == "pipeline-and-ner"
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+ Requires-Dist: transformers>=4.42.4; extra == "pipeline-and-ner"
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+ Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "pipeline-and-ner"
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+ Requires-Dist: mlflow==2.16.1; extra == "pipeline-and-ner"
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+ Provides-Extra: utils
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+ Requires-Dist: pydantic==2.10.6; extra == "utils"
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+ Requires-Dist: python-stopwatch==1.1.11; extra == "utils"
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+ Requires-Dist: importlib-resources==6.4.5; extra == "utils"
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+ Requires-Dist: lxml==5.3.0; extra == "utils"
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+ Requires-Dist: pyarrow==17.0.0; extra == "utils"
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+ Requires-Dist: pycryptodomex==3.22.0; extra == "utils"
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+ Requires-Dist: pydantic-settings-2.8.1; extra == "utils"
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+ Requires-Dist: python-dotenv-1.1.0; extra == "utils"
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+ Requires-Dist: python-iso639-2025.2.18; extra == "utils"
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+ Requires-Dist: python-magic-0.4.27; extra == "utils"
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+ Requires-Dist: pyzstd==0.16.2; extra == "utils"
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+ Requires-Dist: databricks-sdk-0.47.0; extra == "utils"
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+ Requires-Dist: python-tml-1.0.2; extra == "utils"
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  requires = ["setuptools", "wheel"]
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  build-backend = "setuptools.build_meta"
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+
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  [project]
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  name = "ddi_fw"
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- version = "0.0.154"
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+ version = "0.0.157"
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  description = "Do not use :)"
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  readme = "README.md"
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  authors = [
@@ -27,56 +28,94 @@ classifiers = [
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  "Framework :: tox",
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  "Framework :: Sphinx",
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  "Programming Language :: Python",
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- "Programming Language :: Python :: 3.8",
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+ "Programming Language :: Python :: 3.10",
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  "Programming Language :: Python :: 3 :: Only",
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  "Topic :: Scientific/Engineering :: Artificial Intelligence",
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  "Topic :: Scientific/Engineering :: Bio-Informatics",
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  "Topic :: Scientific/Engineering :: Information Analysis",
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- "Topic :: Scientific/Engineering :: Medical Science Apps."
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- ]
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- keywords = [
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- "Machine Learning",
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+ "Topic :: Scientific/Engineering :: Medical Science Apps."
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  ]
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+ keywords = ["Machine Learning"]
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  # License Information. This can be any valid SPDX identifiers that can be resolved
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  # with URLs like https://spdx.org/licenses/MIT
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  # See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
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  license = { file = "LICENSE" }
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+
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  requires-python = ">=3.10"
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+
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+ # [project.dependencies]
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+ # These dependencies are common and always required
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  dependencies = [
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- "pydantic==2.10.6"
49
- ,"importlib-resources==6.4.5"
50
- ,"python-stopwatch==1.1.11"
51
- ,"lxml==5.3.0"
52
- ,"matplotlib==3.8.0"
53
- ,"mlflow==2.16.1"
54
- ,"nltk>=3.8.1"
55
- ,"numpy>=1.26.4"
51
+ "tqdm>=4.66.6"
56
52
  ,"pandas>=2.2.0"
57
- ,"plotly==5.24.1"
58
- ,"rdkit==2023.3.3"
59
- ,"scikit-learn==1.5.2"
60
- ,"scipy==1.13.1"
61
- ,"accelerate>=0.33.0"
62
- ,"sentence-transformers>=3.0.1,<=3.3.1"
63
- ,"transformers>=4.42.4"
64
- ,"stanza==1.9.2"
65
- ,"tokenizers>=0.19.1"
66
- ,"tqdm>=4.66.6"
67
- ,"xmlschema==3.4.2"
68
- ,"zipp>=3.20.2"
69
- ,"py7zr==0.22.0"
70
- ,"openai>=1.52.2"
71
- ,"langchain>=0.3.4"
72
- ,"chromadb>=0.5.15"
73
- ,"langchain_community==0.3.3"
74
- ,"datasets==3.0.2"
75
- ,"unstructured==0.16.3",
76
- "tensorflow>=2.17.0,<2.18.0"
77
- ,"tf-keras==2.17.0"
78
53
  ]
79
-
54
+
55
+ [project.optional-dependencies]
56
+ llm = [
57
+ "sentence-transformers>=3.0.1,<=3.3.1",
58
+ "transformers>=4.42.4",
59
+ "stanza==1.9.2",
60
+ "tokenizers>=0.19.1",
61
+ "openai>=1.52.2",
62
+ "langchain>=0.3.4",
63
+ "langchain_community==0.3.3"
64
+ ]
65
+
66
+ ml = [
67
+ "scikit-learn==1.5.2",
68
+ "tensorflow>=2.17.0,<2.18.0",
69
+ "tf-keras==2.17.0",
70
+ "mlflow==2.16.1",
71
+ "accelerate>=0.33.0",
72
+ "numpy>=1.26.4",
73
+ "scipy==1.13.1",
74
+ "pandas>=2.2.0",
75
+ "plotly==5.24.1",
76
+ "matplotlib==3.8.0",
77
+ "rdkit==2023.3.3",
78
+ "datasets==3.0.2",
79
+ "tqdm>=4.66.6"
80
+ ]
81
+
82
+ datasets = [
83
+ "datasets==3.0.2",
84
+ "unstructured==0.16.3",
85
+ "py7zr==0.22.0",
86
+ "xmlschema==3.4.2"
87
+ ]
88
+
89
+ drugbank = [
90
+ "rdkit==2023.3.3",
91
+ "openai>=1.52.2"
92
+ ]
93
+
94
+ pipeline_and_ner = [
95
+ "nltk>=3.8.1",
96
+ "stanza==1.9.2",
97
+ "transformers>=4.42.4",
98
+ "sentence-transformers>=3.0.1,<=3.3.1",
99
+ "mlflow==2.16.1"
100
+ ]
101
+
102
+ utils = [
103
+ "pydantic==2.10.6",
104
+ "python-stopwatch==1.1.11",
105
+ "importlib-resources==6.4.5",
106
+ "lxml==5.3.0",
107
+ "pyarrow==17.0.0",
108
+ "pycryptodomex==3.22.0",
109
+ "pydantic-settings-2.8.1",
110
+ "python-dotenv-1.1.0",
111
+ "python-iso639-2025.2.18",
112
+ "python-magic-0.4.27",
113
+ "pyzstd==0.16.2",
114
+ "databricks-sdk-0.47.0",
115
+ "python-tml-1.0.2"
116
+ ]
117
+
118
+
80
119
 
81
120
  [tool.setuptools]
82
121
  package-dir = { "" = "src" }
@@ -99,4 +138,4 @@ addopts = "-ra -q"
99
138
 
100
139
  testpaths = [
101
140
  "tests"
102
- ]
141
+ ]
@@ -15,6 +15,9 @@ from abc import ABC, abstractmethod
15
15
  from sklearn.preprocessing import LabelBinarizer
16
16
 
17
17
  from sklearn.model_selection import KFold, StratifiedKFold, train_test_split
18
+ import logging
19
+
20
+ logger = logging.getLogger(__name__)
18
21
 
19
22
  # Constants for embedding, chemical properties, and NER columns
20
23
  LIST_OF_EMBEDDING_COLUMNS = [
@@ -57,6 +60,7 @@ class DDIMDLDataset(TextDatasetMixin):
57
60
  return values
58
61
 
59
62
  def __init__(self, **kwargs):
63
+
60
64
  super().__init__(**kwargs)
61
65
  self.class_column = 'event_category'
62
66
  _db_path = HERE.joinpath('data/event.db')
@@ -67,6 +71,7 @@ class DDIMDLDataset(TextDatasetMixin):
67
71
  # TODO with resource
68
72
  self._conn = create_connection(_db_path.absolute().as_posix())
69
73
  self.load_drugs_and_events()
74
+ logger.info(f'{self.dataset_name} is initialized')
70
75
 
71
76
  def load_drugs_and_events(self):
72
77
  self.drugs_df = self.__select_all_drugs_as_dataframe__()
@@ -35,7 +35,7 @@ class SimilarityMatrixGenerator:
35
35
  return jaccard_sim_matrix
36
36
 
37
37
  # https://github.com/YifanDengWHU/DDIMDL/blob/master/DDIMDL.py , def Jaccard(matrix):
38
- def create_jaccard_similarity_matrices(self, matrix):
38
+ def create_jaccard_similarity_matrices(self, matrix)->np.ndarray:
39
39
  matrix = np.mat(matrix)
40
40
  numerator = matrix * matrix.T
41
41
  denominator = np.ones(np.shape(matrix)) * matrix.T + \
@@ -68,6 +68,7 @@ class MultiPipeline():
68
68
  # Dynamically import the model and dataset classes
69
69
  # model_type = get_import(config.get("model_type"))
70
70
  dataset_type = get_import(config.get("dataset_type"))
71
+ dataset_splitter_type = get_import(config.get("dataset_splitter_type"))
71
72
 
72
73
  combination_type = None
73
74
  kwargs_combination_params=None
@@ -89,6 +90,7 @@ class MultiPipeline():
89
90
  artifact_location=artifact_location,
90
91
  tracking_uri=tracking_uri,
91
92
  dataset_type=dataset_type,
93
+ dataset_splitter_type=dataset_splitter_type,
92
94
  columns=columns,
93
95
  column_embedding_configs=column_embedding_configs,
94
96
  vector_db_persist_directory=vector_db_persist_directory,
@@ -0,0 +1,76 @@
1
+ Metadata-Version: 2.4
2
+ Name: ddi_fw
3
+ Version: 0.0.157
4
+ Summary: Do not use :)
5
+ Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
+ Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
7
+ Keywords: Machine Learning
8
+ Classifier: Development Status :: 1 - Planning
9
+ Classifier: Environment :: Console
10
+ Classifier: Intended Audience :: Science/Research
11
+ Classifier: License :: OSI Approved :: MIT License
12
+ Classifier: Operating System :: OS Independent
13
+ Classifier: Framework :: Pytest
14
+ Classifier: Framework :: tox
15
+ Classifier: Framework :: Sphinx
16
+ Classifier: Programming Language :: Python
17
+ Classifier: Programming Language :: Python :: 3.10
18
+ Classifier: Programming Language :: Python :: 3 :: Only
19
+ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
20
+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
21
+ Classifier: Topic :: Scientific/Engineering :: Information Analysis
22
+ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
23
+ Requires-Python: >=3.10
24
+ Description-Content-Type: text/markdown
25
+ Requires-Dist: tqdm>=4.66.6
26
+ Requires-Dist: pandas>=2.2.0
27
+ Provides-Extra: llm
28
+ Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "llm"
29
+ Requires-Dist: transformers>=4.42.4; extra == "llm"
30
+ Requires-Dist: stanza==1.9.2; extra == "llm"
31
+ Requires-Dist: tokenizers>=0.19.1; extra == "llm"
32
+ Requires-Dist: openai>=1.52.2; extra == "llm"
33
+ Requires-Dist: langchain>=0.3.4; extra == "llm"
34
+ Requires-Dist: langchain_community==0.3.3; extra == "llm"
35
+ Provides-Extra: ml
36
+ Requires-Dist: scikit-learn==1.5.2; extra == "ml"
37
+ Requires-Dist: tensorflow<2.18.0,>=2.17.0; extra == "ml"
38
+ Requires-Dist: tf-keras==2.17.0; extra == "ml"
39
+ Requires-Dist: mlflow==2.16.1; extra == "ml"
40
+ Requires-Dist: accelerate>=0.33.0; extra == "ml"
41
+ Requires-Dist: numpy>=1.26.4; extra == "ml"
42
+ Requires-Dist: scipy==1.13.1; extra == "ml"
43
+ Requires-Dist: pandas>=2.2.0; extra == "ml"
44
+ Requires-Dist: plotly==5.24.1; extra == "ml"
45
+ Requires-Dist: matplotlib==3.8.0; extra == "ml"
46
+ Requires-Dist: rdkit==2023.3.3; extra == "ml"
47
+ Requires-Dist: datasets==3.0.2; extra == "ml"
48
+ Requires-Dist: tqdm>=4.66.6; extra == "ml"
49
+ Provides-Extra: datasets
50
+ Requires-Dist: datasets==3.0.2; extra == "datasets"
51
+ Requires-Dist: unstructured==0.16.3; extra == "datasets"
52
+ Requires-Dist: py7zr==0.22.0; extra == "datasets"
53
+ Requires-Dist: xmlschema==3.4.2; extra == "datasets"
54
+ Provides-Extra: drugbank
55
+ Requires-Dist: rdkit==2023.3.3; extra == "drugbank"
56
+ Requires-Dist: openai>=1.52.2; extra == "drugbank"
57
+ Provides-Extra: pipeline-and-ner
58
+ Requires-Dist: nltk>=3.8.1; extra == "pipeline-and-ner"
59
+ Requires-Dist: stanza==1.9.2; extra == "pipeline-and-ner"
60
+ Requires-Dist: transformers>=4.42.4; extra == "pipeline-and-ner"
61
+ Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "pipeline-and-ner"
62
+ Requires-Dist: mlflow==2.16.1; extra == "pipeline-and-ner"
63
+ Provides-Extra: utils
64
+ Requires-Dist: pydantic==2.10.6; extra == "utils"
65
+ Requires-Dist: python-stopwatch==1.1.11; extra == "utils"
66
+ Requires-Dist: importlib-resources==6.4.5; extra == "utils"
67
+ Requires-Dist: lxml==5.3.0; extra == "utils"
68
+ Requires-Dist: pyarrow==17.0.0; extra == "utils"
69
+ Requires-Dist: pycryptodomex==3.22.0; extra == "utils"
70
+ Requires-Dist: pydantic-settings-2.8.1; extra == "utils"
71
+ Requires-Dist: python-dotenv-1.1.0; extra == "utils"
72
+ Requires-Dist: python-iso639-2025.2.18; extra == "utils"
73
+ Requires-Dist: python-magic-0.4.27; extra == "utils"
74
+ Requires-Dist: pyzstd==0.16.2; extra == "utils"
75
+ Requires-Dist: databricks-sdk-0.47.0; extra == "utils"
76
+ Requires-Dist: python-tml-1.0.2; extra == "utils"
@@ -1,30 +1,58 @@
1
- pydantic==2.10.6
2
- importlib-resources==6.4.5
3
- python-stopwatch==1.1.11
4
- lxml==5.3.0
5
- matplotlib==3.8.0
6
- mlflow==2.16.1
7
- nltk>=3.8.1
8
- numpy>=1.26.4
1
+ tqdm>=4.66.6
9
2
  pandas>=2.2.0
10
- plotly==5.24.1
3
+
4
+ [datasets]
5
+ datasets==3.0.2
6
+ unstructured==0.16.3
7
+ py7zr==0.22.0
8
+ xmlschema==3.4.2
9
+
10
+ [drugbank]
11
11
  rdkit==2023.3.3
12
- scikit-learn==1.5.2
13
- scipy==1.13.1
14
- accelerate>=0.33.0
12
+ openai>=1.52.2
13
+
14
+ [llm]
15
15
  sentence-transformers<=3.3.1,>=3.0.1
16
16
  transformers>=4.42.4
17
17
  stanza==1.9.2
18
18
  tokenizers>=0.19.1
19
- tqdm>=4.66.6
20
- xmlschema==3.4.2
21
- zipp>=3.20.2
22
- py7zr==0.22.0
23
19
  openai>=1.52.2
24
20
  langchain>=0.3.4
25
- chromadb>=0.5.15
26
21
  langchain_community==0.3.3
27
- datasets==3.0.2
28
- unstructured==0.16.3
22
+
23
+ [ml]
24
+ scikit-learn==1.5.2
29
25
  tensorflow<2.18.0,>=2.17.0
30
26
  tf-keras==2.17.0
27
+ mlflow==2.16.1
28
+ accelerate>=0.33.0
29
+ numpy>=1.26.4
30
+ scipy==1.13.1
31
+ pandas>=2.2.0
32
+ plotly==5.24.1
33
+ matplotlib==3.8.0
34
+ rdkit==2023.3.3
35
+ datasets==3.0.2
36
+ tqdm>=4.66.6
37
+
38
+ [pipeline_and_ner]
39
+ nltk>=3.8.1
40
+ stanza==1.9.2
41
+ transformers>=4.42.4
42
+ sentence-transformers<=3.3.1,>=3.0.1
43
+ mlflow==2.16.1
44
+
45
+ [utils]
46
+ pydantic==2.10.6
47
+ python-stopwatch==1.1.11
48
+ importlib-resources==6.4.5
49
+ lxml==5.3.0
50
+ pyarrow==17.0.0
51
+ pycryptodomex==3.22.0
52
+ pydantic-settings-2.8.1
53
+ python-dotenv-1.1.0
54
+ python-iso639-2025.2.18
55
+ python-magic-0.4.27
56
+ pyzstd==0.16.2
57
+ databricks-sdk-0.47.0
58
+ python-tml-1.0.2
ddi_fw-0.0.154/PKG-INFO DELETED
@@ -1,54 +0,0 @@
1
- Metadata-Version: 2.4
2
- Name: ddi_fw
3
- Version: 0.0.154
4
- Summary: Do not use :)
5
- Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
- Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
7
- Keywords: Machine Learning
8
- Classifier: Development Status :: 1 - Planning
9
- Classifier: Environment :: Console
10
- Classifier: Intended Audience :: Science/Research
11
- Classifier: License :: OSI Approved :: MIT License
12
- Classifier: Operating System :: OS Independent
13
- Classifier: Framework :: Pytest
14
- Classifier: Framework :: tox
15
- Classifier: Framework :: Sphinx
16
- Classifier: Programming Language :: Python
17
- Classifier: Programming Language :: Python :: 3.8
18
- Classifier: Programming Language :: Python :: 3 :: Only
19
- Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
20
- Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
21
- Classifier: Topic :: Scientific/Engineering :: Information Analysis
22
- Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
23
- Requires-Python: >=3.10
24
- Description-Content-Type: text/markdown
25
- Requires-Dist: pydantic==2.10.6
26
- Requires-Dist: importlib-resources==6.4.5
27
- Requires-Dist: python-stopwatch==1.1.11
28
- Requires-Dist: lxml==5.3.0
29
- Requires-Dist: matplotlib==3.8.0
30
- Requires-Dist: mlflow==2.16.1
31
- Requires-Dist: nltk>=3.8.1
32
- Requires-Dist: numpy>=1.26.4
33
- Requires-Dist: pandas>=2.2.0
34
- Requires-Dist: plotly==5.24.1
35
- Requires-Dist: rdkit==2023.3.3
36
- Requires-Dist: scikit-learn==1.5.2
37
- Requires-Dist: scipy==1.13.1
38
- Requires-Dist: accelerate>=0.33.0
39
- Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1
40
- Requires-Dist: transformers>=4.42.4
41
- Requires-Dist: stanza==1.9.2
42
- Requires-Dist: tokenizers>=0.19.1
43
- Requires-Dist: tqdm>=4.66.6
44
- Requires-Dist: xmlschema==3.4.2
45
- Requires-Dist: zipp>=3.20.2
46
- Requires-Dist: py7zr==0.22.0
47
- Requires-Dist: openai>=1.52.2
48
- Requires-Dist: langchain>=0.3.4
49
- Requires-Dist: chromadb>=0.5.15
50
- Requires-Dist: langchain_community==0.3.3
51
- Requires-Dist: datasets==3.0.2
52
- Requires-Dist: unstructured==0.16.3
53
- Requires-Dist: tensorflow<2.18.0,>=2.17.0
54
- Requires-Dist: tf-keras==2.17.0
@@ -1,54 +0,0 @@
1
- Metadata-Version: 2.4
2
- Name: ddi_fw
3
- Version: 0.0.154
4
- Summary: Do not use :)
5
- Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
- Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
7
- Keywords: Machine Learning
8
- Classifier: Development Status :: 1 - Planning
9
- Classifier: Environment :: Console
10
- Classifier: Intended Audience :: Science/Research
11
- Classifier: License :: OSI Approved :: MIT License
12
- Classifier: Operating System :: OS Independent
13
- Classifier: Framework :: Pytest
14
- Classifier: Framework :: tox
15
- Classifier: Framework :: Sphinx
16
- Classifier: Programming Language :: Python
17
- Classifier: Programming Language :: Python :: 3.8
18
- Classifier: Programming Language :: Python :: 3 :: Only
19
- Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
20
- Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
21
- Classifier: Topic :: Scientific/Engineering :: Information Analysis
22
- Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
23
- Requires-Python: >=3.10
24
- Description-Content-Type: text/markdown
25
- Requires-Dist: pydantic==2.10.6
26
- Requires-Dist: importlib-resources==6.4.5
27
- Requires-Dist: python-stopwatch==1.1.11
28
- Requires-Dist: lxml==5.3.0
29
- Requires-Dist: matplotlib==3.8.0
30
- Requires-Dist: mlflow==2.16.1
31
- Requires-Dist: nltk>=3.8.1
32
- Requires-Dist: numpy>=1.26.4
33
- Requires-Dist: pandas>=2.2.0
34
- Requires-Dist: plotly==5.24.1
35
- Requires-Dist: rdkit==2023.3.3
36
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37
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38
- Requires-Dist: accelerate>=0.33.0
39
- Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1
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- Requires-Dist: transformers>=4.42.4
41
- Requires-Dist: stanza==1.9.2
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45
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46
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48
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- Requires-Dist: chromadb>=0.5.15
50
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51
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52
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- Requires-Dist: tensorflow<2.18.0,>=2.17.0
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File without changes
File without changes
File without changes