ddi-fw 0.0.79__tar.gz → 0.0.81__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 (105) hide show
  1. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/PKG-INFO +1 -1
  2. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/pyproject.toml +1 -1
  3. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ml/ml_helper.py +1 -5
  4. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/pipeline/multi_pipeline.py +7 -1
  5. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/pipeline/pipeline.py +1 -1
  6. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw.egg-info/PKG-INFO +1 -1
  7. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/README.md +0 -0
  8. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/setup.cfg +0 -0
  9. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/__init__.py +0 -0
  10. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/core.py +0 -0
  11. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/db_utils.py +0 -0
  12. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/base.py +0 -0
  13. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  14. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  15. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  16. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  17. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  18. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  19. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  20. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  21. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  22. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  23. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  24. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  25. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  26. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  27. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  28. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  29. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  30. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  31. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  32. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  33. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  34. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  35. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  36. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  37. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  38. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  39. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/embedding_generator.py +0 -0
  40. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/feature_vector_generation.py +0 -0
  41. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/idf_helper.py +0 -0
  42. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  43. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  44. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  45. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  46. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  47. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  48. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  49. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  50. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  51. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  52. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  53. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  54. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  55. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  56. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  57. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  58. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  59. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/datasets/setup_._py +0 -0
  60. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/drugbank/__init__.py +0 -0
  61. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  62. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  63. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  64. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  65. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  66. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/__init__.py +0 -0
  67. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/custom_torch_model.py +0 -0
  68. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/evaluation_helper.py +0 -0
  69. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/pipeline.py +0 -0
  70. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/pipeline_ner.py +0 -0
  71. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/tensorflow_helper.py +0 -0
  72. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/experiments/test.py +0 -0
  73. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/langchain/__init__.py +0 -0
  74. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/langchain/embeddings.py +0 -0
  75. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/langchain/sentence_splitter.py +0 -0
  76. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/langchain/storage.py +0 -0
  77. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ml/__init__.py +0 -0
  78. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ml/model_wrapper.py +0 -0
  79. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ml/pytorch_wrapper.py +0 -0
  80. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ml/tensorflow_wrapper.py +0 -0
  81. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ner/__init__.py +0 -0
  82. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  83. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/ner/ner.py +0 -0
  84. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/pipeline/__init__.py +0 -0
  85. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/pipeline/multi_modal_combination_strategy.py +0 -0
  86. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/basic_test.py +0 -0
  87. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/combination_test.py +0 -0
  88. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/compress_json_test.py +0 -0
  89. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/date_test.py +0 -0
  90. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/idf_score.py +0 -0
  91. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/jaccard_similarity.py +0 -0
  92. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/mlfow_test.py +0 -0
  93. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/sklearn-tfidf.py +0 -0
  94. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/test.py +0 -0
  95. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/torch_cuda_test.py +0 -0
  96. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/test/type_guarding_test.py +0 -0
  97. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/utils/__init__.py +0 -0
  98. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/utils/enums.py +0 -0
  99. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  100. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/utils/utils.py +0 -0
  101. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw/utils/zip_helper.py +0 -0
  102. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw.egg-info/SOURCES.txt +0 -0
  103. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  104. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw.egg-info/requires.txt +0 -0
  105. {ddi_fw-0.0.79 → ddi_fw-0.0.81}/src/ddi_fw.egg-info/top_level.txt +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: ddi_fw
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- Version: 0.0.79
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+ Version: 0.0.81
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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>
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "ddi_fw"
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- version = "0.0.79"
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+ version = "0.0.81"
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  description = "Do not use :)"
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  readme = "README.md"
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  authors = [
@@ -2,7 +2,7 @@ from typing import Dict, List, Tuple
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  from matplotlib import pyplot as plt
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  from ddi_fw.ml.model_wrapper import Result
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  from ddi_fw.ml.pytorch_wrapper import PTModelWrapper
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- from ddi_fw.experiments.ml_tf import TFModelWrapper
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+ from ddi_fw.ml.tensorflow_wrapper import TFModelWrapper
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  import tensorflow as tf
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  from tensorflow import keras
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  from keras.models import Model, Sequential
@@ -28,10 +28,6 @@ tf.random.set_seed(1)
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  np.random.seed(2)
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  np.set_printoptions(precision=4)
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-
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-
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-
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-
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  class MultiModalRunner:
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  # todo model related parameters to config
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  def __init__(self, library ,model_func, batch_size=128, epochs=100):
@@ -1,3 +1,4 @@
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+ from collections import defaultdict
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  import json
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  from pipeline import Pipeline
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  import importlib
@@ -43,6 +44,7 @@ class MultiPipeline():
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  def __init__(self, experiments_config_file):
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  self.experiments_config = load_config(experiments_config_file)
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  self.items = []
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+ self.pipeline_resuts = dict()
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47
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  def __create_pipeline(self, config):
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  library = config["library"]
@@ -108,4 +110,8 @@ class MultiPipeline():
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  batch_size = item['batch_size']
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  epochs = item['epochs']
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  pipeline.build()
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- pipeline.run(model_type, epochs=epochs, batch_size=batch_size)
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+ result = pipeline.run(model_type, epochs=epochs, batch_size=batch_size)
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+ self.pipeline_resuts[item['name']] = result
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+
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+ def results(self):
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+ return self.pipeline_resuts
@@ -7,7 +7,7 @@ from ddi_fw.langchain.embeddings import PoolingStrategy
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  from ddi_fw.datasets import BaseDataset, DDIMDLDataset
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  from ddi_fw.langchain.embeddings import SumPoolingStrategy
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  import mlflow
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- from ml import MultiModalRunner
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+ from ddi_fw.ml import MultiModalRunner
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  class Pipeline:
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: ddi_fw
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- Version: 0.0.79
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+ Version: 0.0.81
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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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