ddi-fw 0.0.187__tar.gz → 0.0.188__tar.gz

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Files changed (109) hide show
  1. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/PKG-INFO +1 -1
  2. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/pyproject.toml +1 -1
  3. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/core.py +2 -2
  4. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/pipeline/pipeline.py +26 -17
  5. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw.egg-info/PKG-INFO +1 -1
  6. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/README.md +0 -0
  7. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/setup.cfg +0 -0
  8. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/__init__.py +0 -0
  9. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/dataset_splitter.py +0 -0
  10. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/db_utils.py +0 -0
  11. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/base.py +0 -0
  12. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/data/event.db +0 -0
  13. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/debug.log +0 -0
  14. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/test_indexes.txt +0 -0
  15. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_0.txt +0 -0
  16. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_1.txt +0 -0
  17. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_2.txt +0 -0
  18. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_3.txt +0 -0
  19. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/train_fold_4.txt +0 -0
  20. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/train_indexes.txt +0 -0
  21. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_0.txt +0 -0
  22. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_1.txt +0 -0
  23. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_2.txt +0 -0
  24. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_3.txt +0 -0
  25. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes/validation_fold_4.txt +0 -0
  26. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/test_indexes.txt +0 -0
  27. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_0.txt +0 -0
  28. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_1.txt +0 -0
  29. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_2.txt +0 -0
  30. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_3.txt +0 -0
  31. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_fold_4.txt +0 -0
  32. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/train_indexes.txt +0 -0
  33. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_0.txt +0 -0
  34. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_1.txt +0 -0
  35. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_2.txt +0 -0
  36. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_3.txt +0 -0
  37. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/indexes_old/validation_fold_4.txt +0 -0
  38. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl/readme.md +0 -0
  39. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/base.py +0 -0
  40. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/data/event.db +0 -0
  41. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/test_indexes.txt +0 -0
  42. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_0.txt +0 -0
  43. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_1.txt +0 -0
  44. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_2.txt +0 -0
  45. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_3.txt +0 -0
  46. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_fold_4.txt +0 -0
  47. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/train_indexes.txt +0 -0
  48. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_0.txt +0 -0
  49. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_1.txt +0 -0
  50. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_2.txt +0 -0
  51. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_3.txt +0 -0
  52. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/ddi_mdl_text/indexes/validation_fold_4.txt +0 -0
  53. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/__init__.py +0 -0
  54. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/base.py +0 -0
  55. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/df_extraction_cleanxiaoyu50.csv +0 -0
  56. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/drug_information_del_noDDIxiaoyu50.csv +0 -0
  57. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/test_indexes.txt +0 -0
  58. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_0.txt +0 -0
  59. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_1.txt +0 -0
  60. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_2.txt +0 -0
  61. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_3.txt +0 -0
  62. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_fold_4.txt +0 -0
  63. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/train_indexes.txt +0 -0
  64. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_0.txt +0 -0
  65. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_1.txt +0 -0
  66. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_2.txt +0 -0
  67. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_3.txt +0 -0
  68. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/indexes/validation_fold_4.txt +0 -0
  69. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/mdf_sa_ddi/mdf-sa-ddi.zip +0 -0
  70. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/datasets/setup_._py +0 -0
  71. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/drugbank/__init__.py +0 -0
  72. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/drugbank/drugbank.xsd +0 -0
  73. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/drugbank/drugbank_parser.py +0 -0
  74. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/drugbank/drugbank_processor.py +0 -0
  75. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/drugbank/drugbank_processor_org.py +0 -0
  76. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/drugbank/event_extractor.py +0 -0
  77. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/langchain/__init__.py +0 -0
  78. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/langchain/embeddings.py +0 -0
  79. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/langchain/sentence_splitter.py +0 -0
  80. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/langchain/storage.py +0 -0
  81. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ml/__init__.py +0 -0
  82. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ml/evaluation_helper.py +0 -0
  83. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ml/ml_helper.py +0 -0
  84. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ml/model_wrapper.py +0 -0
  85. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ml/pytorch_wrapper.py +0 -0
  86. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ml/tensorflow_wrapper.py +0 -0
  87. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ner/__init__.py +0 -0
  88. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ner/mmlrestclient.py +0 -0
  89. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/ner/ner.py +0 -0
  90. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/pipeline/__init__.py +0 -0
  91. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/pipeline/multi_modal_combination_strategy.py +0 -0
  92. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/pipeline/multi_pipeline.py +0 -0
  93. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/pipeline/ner_pipeline.py +0 -0
  94. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/__init__.py +0 -0
  95. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/categorical_data_encoding_checker.py +0 -0
  96. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/enums.py +0 -0
  97. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/json_helper.py +0 -0
  98. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/kaggle.py +0 -0
  99. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/package_helper.py +0 -0
  100. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/py7zr_helper.py +0 -0
  101. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/utils.py +0 -0
  102. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/utils/zip_helper.py +0 -0
  103. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/vectorization/__init__.py +0 -0
  104. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/vectorization/feature_vector_generation.py +0 -0
  105. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw/vectorization/idf_helper.py +0 -0
  106. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw.egg-info/SOURCES.txt +0 -0
  107. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw.egg-info/dependency_links.txt +0 -0
  108. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw.egg-info/requires.txt +0 -0
  109. {ddi_fw-0.0.187 → ddi_fw-0.0.188}/src/ddi_fw.egg-info/top_level.txt +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ddi_fw
3
- Version: 0.0.187
3
+ Version: 0.0.188
4
4
  Summary: Do not use :)
5
5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
6
  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
6
6
 
7
7
  [project]
8
8
  name = "ddi_fw"
9
- version = "0.0.187"
9
+ version = "0.0.188"
10
10
  description = "Do not use :)"
11
11
  readme = "README.md"
12
12
  authors = [
@@ -222,8 +222,8 @@ class BaseDataset(BaseModel):
222
222
 
223
223
  X_train, X_test, y_train, y_test, X_train.index, X_test.index, train_idx_arr, val_idx_arr = self.dataset_splitter.split(
224
224
  X=X, y=y)
225
- self.X_train = np.array(self.X_train)
226
- self.X_test = np.array(self.X_test)
225
+ self.X_train = np.array(X_train)
226
+ self.X_test = np.array(X_test)
227
227
  self.y_train = np.array(y_train.tolist())
228
228
  self.y_test = np.array(y_test.tolist())
229
229
  self.train_indexes = X_train.index
@@ -37,23 +37,24 @@ class Pipeline(BaseModel):
37
37
  model: Optional[Any] = None
38
38
  multi_modal: Optional[Any] = None
39
39
  use_mlflow: bool = False
40
- _items:List=[]
41
- _train_idx_arr:List|None=[]
42
- _val_idx_arr:List|None=[]
43
-
40
+ _items: List = []
41
+ _train_idx_arr: List | None = []
42
+ _val_idx_arr: List | None = []
43
+
44
44
  @property
45
45
  def items(self) -> List:
46
46
  return self._items
47
+
47
48
  @property
48
- def train_idx_arr(self) -> List|None:
49
+ def train_idx_arr(self) -> List | None:
49
50
  return self._train_idx_arr
51
+
50
52
  @property
51
- def val_idx_arr(self) -> List|None:
53
+ def val_idx_arr(self) -> List | None:
52
54
  return self._val_idx_arr
53
55
 
54
56
  class Config:
55
57
  arbitrary_types_allowed = True
56
-
57
58
 
58
59
  def __create_or_update_embeddings__(self, embedding_dict, vector_db_persist_directory, vector_db_collection_name, column=None):
59
60
  """
@@ -146,21 +147,22 @@ class Pipeline(BaseModel):
146
147
  # filename=self.ner_data_file) if self.ner_data_file else None
147
148
 
148
149
  dataset_splitter = self.dataset_splitter_type()
149
-
150
+
150
151
  if issubclass(self.dataset_type, TextDatasetMixin):
151
152
  key, value = next(iter(embedding_dict.items()))
152
153
  embedding_size = value[next(iter(value))][0].shape[0]
153
- pooling_strategy = self.embedding_pooling_strategy_type() if self.embedding_pooling_strategy_type else None
154
+ pooling_strategy = self.embedding_pooling_strategy_type(
155
+ ) if self.embedding_pooling_strategy_type else None
154
156
 
155
157
  dataset = self.dataset_type(
156
158
  embedding_dict=embedding_dict,
157
159
  embedding_size=embedding_size,
158
160
  embeddings_pooling_strategy=pooling_strategy,
159
- dataset_splitter_type = self.dataset_splitter_type,
161
+ dataset_splitter_type=self.dataset_splitter_type,
160
162
  **kwargs)
161
163
  elif self.dataset_type == BaseDataset:
162
- dataset = self.dataset_type(
163
- dataset_splitter_type = self.dataset_splitter_type,
164
+ dataset = self.dataset_type(
165
+ dataset_splitter_type=self.dataset_splitter_type,
164
166
  **kwargs)
165
167
  else:
166
168
  dataset = self.dataset_type(**kwargs)
@@ -168,15 +170,22 @@ class Pipeline(BaseModel):
168
170
  # X_train, X_test, y_train, y_test, train_indexes, test_indexes, train_idx_arr, val_idx_arr = dataset.load()
169
171
  dataset.load()
170
172
  dataframe = dataset.dataframe
171
- b = not( dataset.X_train and dataset.y_train and dataset.X_test and dataset.y_test)
172
- c = dataframe is None or dataframe.empty
173
173
 
174
- if b or c:
174
+ # Check if any of the arrays are None or empty
175
+ is_data_valid = (dataset.X_train is not None and dataset.X_train.size > 0 and
176
+ dataset.y_train is not None and dataset.y_train.size > 0 and
177
+ dataset.X_test is not None and dataset.X_test.size > 0 and
178
+ dataset.y_test is not None and dataset.y_test.size > 0)
179
+
180
+ # Check if the dataframe is None or empty
181
+ is_dataframe_valid = dataframe is not None and not dataframe.empty
182
+
183
+ if not (is_data_valid and is_dataframe_valid):
175
184
  raise ValueError("The dataset is not loaded")
176
-
185
+
177
186
  # column name, train data, train label, test data, test label
178
187
  self._items = dataset.produce_inputs()
179
-
188
+
180
189
  print("Building the experiment with the following settings:")
181
190
  print(
182
191
  f"Name: {self.experiment_name}, Dataset: {dataset}, Model: {self.model}")
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: ddi_fw
3
- Version: 0.0.187
3
+ Version: 0.0.188
4
4
  Summary: Do not use :)
5
5
  Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
6
6
  Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
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