ddi-fw 0.0.155__tar.gz → 0.0.158__tar.gz

ddi_fw-0.0.158/PKG-INFO

@@ -0,0 +1,69 @@
+Metadata-Version: 2.4
+Name: ddi_fw
+Version: 0.0.158
+Summary: Do not use :)
+Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
+Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
+Keywords: Machine Learning
+Classifier: Development Status :: 1 - Planning
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: Pytest
+Classifier: Framework :: tox
+Classifier: Framework :: Sphinx
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: tqdm>=4.66.6
+Requires-Dist: pandas>=2.2.0
+Provides-Extra: llm
+Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "llm"
+Requires-Dist: transformers>=4.42.4; extra == "llm"
+Requires-Dist: stanza==1.9.2; extra == "llm"
+Requires-Dist: tokenizers>=0.19.1; extra == "llm"
+Requires-Dist: openai>=1.52.2; extra == "llm"
+Requires-Dist: langchain>=0.3.4; extra == "llm"
+Requires-Dist: langchain_community==0.3.3; extra == "llm"
+Provides-Extra: ml
+Requires-Dist: scikit-learn==1.5.2; extra == "ml"
+Requires-Dist: tensorflow<2.18.0,>=2.17.0; extra == "ml"
+Requires-Dist: tf-keras==2.17.0; extra == "ml"
+Requires-Dist: mlflow==2.16.1; extra == "ml"
+Requires-Dist: accelerate>=0.33.0; extra == "ml"
+Requires-Dist: numpy>=1.26.4; extra == "ml"
+Requires-Dist: scipy==1.13.1; extra == "ml"
+Requires-Dist: pandas>=2.2.0; extra == "ml"
+Requires-Dist: plotly==5.24.1; extra == "ml"
+Requires-Dist: matplotlib==3.8.0; extra == "ml"
+Requires-Dist: rdkit==2023.3.3; extra == "ml"
+Requires-Dist: datasets==3.0.2; extra == "ml"
+Requires-Dist: tqdm>=4.66.6; extra == "ml"
+Provides-Extra: datasets
+Requires-Dist: datasets==3.0.2; extra == "datasets"
+Requires-Dist: unstructured==0.16.3; extra == "datasets"
+Requires-Dist: py7zr==0.22.0; extra == "datasets"
+Requires-Dist: xmlschema==3.4.2; extra == "datasets"
+Provides-Extra: drugbank
+Requires-Dist: rdkit==2023.3.3; extra == "drugbank"
+Requires-Dist: openai>=1.52.2; extra == "drugbank"
+Provides-Extra: pipeline-and-ner
+Requires-Dist: nltk>=3.8.1; extra == "pipeline-and-ner"
+Requires-Dist: stanza==1.9.2; extra == "pipeline-and-ner"
+Requires-Dist: transformers>=4.42.4; extra == "pipeline-and-ner"
+Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "pipeline-and-ner"
+Requires-Dist: mlflow==2.16.1; extra == "pipeline-and-ner"
+Provides-Extra: utils
+Requires-Dist: pydantic==2.10.6; extra == "utils"
+Requires-Dist: python-stopwatch==1.1.11; extra == "utils"
+Requires-Dist: importlib-resources==6.4.5; extra == "utils"
+Requires-Dist: lxml==5.3.0; extra == "utils"
+Requires-Dist: pyarrow==17.0.0; extra == "utils"
+Requires-Dist: pycryptodomex==3.22.0; extra == "utils"

{ddi_fw-0.0.155 → ddi_fw-0.0.158}/pyproject.toml

@@ -3,9 +3,10 @@
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
+
 [project]
 name = "ddi_fw"
-version = "0.0.155"
+version = "0.0.158"
 description = "Do not use :)"
 readme = "README.md"
 authors = [
@@ -27,56 +28,87 @@ classifiers = [
     "Framework :: tox",
     "Framework :: Sphinx",
     "Programming Language :: Python",
-	"Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3 :: Only",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Information Analysis",
-	"Topic :: Scientific/Engineering :: Medical Science Apps."
-]
-keywords = [
-    "Machine Learning",
+    "Topic :: Scientific/Engineering :: Medical Science Apps."
 ]
+keywords = ["Machine Learning"]
 
 # License Information. This can be any valid SPDX identifiers that can be resolved
 # with URLs like https://spdx.org/licenses/MIT
 # See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
 license = { file = "LICENSE" }
 
+
 requires-python = ">=3.10"
+
+# [project.dependencies]
+# These dependencies are common and always required
 dependencies = [
-"pydantic==2.10.6"
-,"importlib-resources==6.4.5"
-,"python-stopwatch==1.1.11"
-,"lxml==5.3.0"
-,"matplotlib==3.8.0"
-,"mlflow==2.16.1"
-,"nltk>=3.8.1"
-,"numpy>=1.26.4"
+"tqdm>=4.66.6"
 ,"pandas>=2.2.0"
-,"plotly==5.24.1"
-,"rdkit==2023.3.3"
-,"scikit-learn==1.5.2"
-,"scipy==1.13.1"
-,"accelerate>=0.33.0"
-,"sentence-transformers>=3.0.1,<=3.3.1"
-,"transformers>=4.42.4"
-,"stanza==1.9.2"
-,"tokenizers>=0.19.1"
-,"tqdm>=4.66.6"
-,"xmlschema==3.4.2"
-,"zipp>=3.20.2"
-,"py7zr==0.22.0"
-,"openai>=1.52.2"
-,"langchain>=0.3.4"
-,"chromadb>=0.5.15"
-,"langchain_community==0.3.3"
-,"datasets==3.0.2"
-,"unstructured==0.16.3",
-"tensorflow>=2.17.0,<2.18.0"
-,"tf-keras==2.17.0"
 ]
- 
+
+[project.optional-dependencies]
+llm = [
+    "sentence-transformers>=3.0.1,<=3.3.1",
+    "transformers>=4.42.4",
+    "stanza==1.9.2",
+    "tokenizers>=0.19.1",
+    "openai>=1.52.2",
+    "langchain>=0.3.4",
+    "langchain_community==0.3.3"
+]
+
+ml = [
+    "scikit-learn==1.5.2",
+    "tensorflow>=2.17.0,<2.18.0",
+    "tf-keras==2.17.0",
+    "mlflow==2.16.1",
+    "accelerate>=0.33.0",
+    "numpy>=1.26.4",
+    "scipy==1.13.1",
+    "pandas>=2.2.0",
+    "plotly==5.24.1",
+    "matplotlib==3.8.0",
+    "rdkit==2023.3.3",
+    "datasets==3.0.2",
+    "tqdm>=4.66.6"
+]
+
+datasets = [
+    "datasets==3.0.2",
+    "unstructured==0.16.3",
+    "py7zr==0.22.0",
+    "xmlschema==3.4.2"
+]
+
+drugbank = [
+    "rdkit==2023.3.3",
+    "openai>=1.52.2"
+]
+
+pipeline_and_ner = [
+    "nltk>=3.8.1",
+    "stanza==1.9.2",
+    "transformers>=4.42.4",
+    "sentence-transformers>=3.0.1,<=3.3.1",
+    "mlflow==2.16.1"
+]
+
+utils = [
+    "pydantic==2.10.6",
+    "python-stopwatch==1.1.11",
+    "importlib-resources==6.4.5",
+    "lxml==5.3.0",
+    "pyarrow==17.0.0",
+    "pycryptodomex==3.22.0"
+]
+
+
 
 [tool.setuptools]
 package-dir = { "" = "src" }
@@ -99,4 +131,4 @@ addopts = "-ra -q"
 
 testpaths = [
     "tests"
-]
+]

{ddi_fw-0.0.155 → ddi_fw-0.0.158}/src/ddi_fw/datasets/ddi_mdl/base.py

@@ -60,7 +60,6 @@ class DDIMDLDataset(TextDatasetMixin):
         return values
 
     def __init__(self, **kwargs):
-        logger.info(f'{self.dataset_name} is being initialized')
 
         super().__init__(**kwargs)
         self.class_column = 'event_category'

{ddi_fw-0.0.155 → ddi_fw-0.0.158}/src/ddi_fw/datasets/feature_vector_generation.py

@@ -35,7 +35,7 @@ class SimilarityMatrixGenerator:
         return jaccard_sim_matrix
 
     # https://github.com/YifanDengWHU/DDIMDL/blob/master/DDIMDL.py , def Jaccard(matrix):
-    def create_jaccard_similarity_matrices(self, matrix):
+    def create_jaccard_similarity_matrices(self, matrix)->np.ndarray:
         matrix = np.mat(matrix)
         numerator = matrix * matrix.T
         denominator = np.ones(np.shape(matrix)) * matrix.T + \

ddi_fw-0.0.158/src/ddi_fw.egg-info/PKG-INFO

@@ -0,0 +1,69 @@
+Metadata-Version: 2.4
+Name: ddi_fw
+Version: 0.0.158
+Summary: Do not use :)
+Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
+Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
+Keywords: Machine Learning
+Classifier: Development Status :: 1 - Planning
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: Pytest
+Classifier: Framework :: tox
+Classifier: Framework :: Sphinx
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: tqdm>=4.66.6
+Requires-Dist: pandas>=2.2.0
+Provides-Extra: llm
+Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "llm"
+Requires-Dist: transformers>=4.42.4; extra == "llm"
+Requires-Dist: stanza==1.9.2; extra == "llm"
+Requires-Dist: tokenizers>=0.19.1; extra == "llm"
+Requires-Dist: openai>=1.52.2; extra == "llm"
+Requires-Dist: langchain>=0.3.4; extra == "llm"
+Requires-Dist: langchain_community==0.3.3; extra == "llm"
+Provides-Extra: ml
+Requires-Dist: scikit-learn==1.5.2; extra == "ml"
+Requires-Dist: tensorflow<2.18.0,>=2.17.0; extra == "ml"
+Requires-Dist: tf-keras==2.17.0; extra == "ml"
+Requires-Dist: mlflow==2.16.1; extra == "ml"
+Requires-Dist: accelerate>=0.33.0; extra == "ml"
+Requires-Dist: numpy>=1.26.4; extra == "ml"
+Requires-Dist: scipy==1.13.1; extra == "ml"
+Requires-Dist: pandas>=2.2.0; extra == "ml"
+Requires-Dist: plotly==5.24.1; extra == "ml"
+Requires-Dist: matplotlib==3.8.0; extra == "ml"
+Requires-Dist: rdkit==2023.3.3; extra == "ml"
+Requires-Dist: datasets==3.0.2; extra == "ml"
+Requires-Dist: tqdm>=4.66.6; extra == "ml"
+Provides-Extra: datasets
+Requires-Dist: datasets==3.0.2; extra == "datasets"
+Requires-Dist: unstructured==0.16.3; extra == "datasets"
+Requires-Dist: py7zr==0.22.0; extra == "datasets"
+Requires-Dist: xmlschema==3.4.2; extra == "datasets"
+Provides-Extra: drugbank
+Requires-Dist: rdkit==2023.3.3; extra == "drugbank"
+Requires-Dist: openai>=1.52.2; extra == "drugbank"
+Provides-Extra: pipeline-and-ner
+Requires-Dist: nltk>=3.8.1; extra == "pipeline-and-ner"
+Requires-Dist: stanza==1.9.2; extra == "pipeline-and-ner"
+Requires-Dist: transformers>=4.42.4; extra == "pipeline-and-ner"
+Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1; extra == "pipeline-and-ner"
+Requires-Dist: mlflow==2.16.1; extra == "pipeline-and-ner"
+Provides-Extra: utils
+Requires-Dist: pydantic==2.10.6; extra == "utils"
+Requires-Dist: python-stopwatch==1.1.11; extra == "utils"
+Requires-Dist: importlib-resources==6.4.5; extra == "utils"
+Requires-Dist: lxml==5.3.0; extra == "utils"
+Requires-Dist: pyarrow==17.0.0; extra == "utils"
+Requires-Dist: pycryptodomex==3.22.0; extra == "utils"

{ddi_fw-0.0.155 → ddi_fw-0.0.158}/src/ddi_fw.egg-info/requires.txt

@@ -1,30 +1,51 @@
-pydantic==2.10.6
-importlib-resources==6.4.5
-python-stopwatch==1.1.11
-lxml==5.3.0
-matplotlib==3.8.0
-mlflow==2.16.1
-nltk>=3.8.1
-numpy>=1.26.4
+tqdm>=4.66.6
 pandas>=2.2.0
-plotly==5.24.1
+
+[datasets]
+datasets==3.0.2
+unstructured==0.16.3
+py7zr==0.22.0
+xmlschema==3.4.2
+
+[drugbank]
 rdkit==2023.3.3
-scikit-learn==1.5.2
-scipy==1.13.1
-accelerate>=0.33.0
+openai>=1.52.2
+
+[llm]
 sentence-transformers<=3.3.1,>=3.0.1
 transformers>=4.42.4
 stanza==1.9.2
 tokenizers>=0.19.1
-tqdm>=4.66.6
-xmlschema==3.4.2
-zipp>=3.20.2
-py7zr==0.22.0
 openai>=1.52.2
 langchain>=0.3.4
-chromadb>=0.5.15
 langchain_community==0.3.3
-datasets==3.0.2
-unstructured==0.16.3
+
+[ml]
+scikit-learn==1.5.2
 tensorflow<2.18.0,>=2.17.0
 tf-keras==2.17.0
+mlflow==2.16.1
+accelerate>=0.33.0
+numpy>=1.26.4
+scipy==1.13.1
+pandas>=2.2.0
+plotly==5.24.1
+matplotlib==3.8.0
+rdkit==2023.3.3
+datasets==3.0.2
+tqdm>=4.66.6
+
+[pipeline_and_ner]
+nltk>=3.8.1
+stanza==1.9.2
+transformers>=4.42.4
+sentence-transformers<=3.3.1,>=3.0.1
+mlflow==2.16.1
+
+[utils]
+pydantic==2.10.6
+python-stopwatch==1.1.11
+importlib-resources==6.4.5
+lxml==5.3.0
+pyarrow==17.0.0
+pycryptodomex==3.22.0

ddi_fw-0.0.155/PKG-INFO

@@ -1,54 +0,0 @@
-Metadata-Version: 2.4
-Name: ddi_fw
-Version: 0.0.155
-Summary: Do not use :)
-Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
-Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
-Keywords: Machine Learning
-Classifier: Development Status :: 1 - Planning
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Framework :: Pytest
-Classifier: Framework :: tox
-Classifier: Framework :: Sphinx
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-Requires-Dist: pydantic==2.10.6
-Requires-Dist: importlib-resources==6.4.5
-Requires-Dist: python-stopwatch==1.1.11
-Requires-Dist: lxml==5.3.0
-Requires-Dist: matplotlib==3.8.0
-Requires-Dist: mlflow==2.16.1
-Requires-Dist: nltk>=3.8.1
-Requires-Dist: numpy>=1.26.4
-Requires-Dist: pandas>=2.2.0
-Requires-Dist: plotly==5.24.1
-Requires-Dist: rdkit==2023.3.3
-Requires-Dist: scikit-learn==1.5.2
-Requires-Dist: scipy==1.13.1
-Requires-Dist: accelerate>=0.33.0
-Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1
-Requires-Dist: transformers>=4.42.4
-Requires-Dist: stanza==1.9.2
-Requires-Dist: tokenizers>=0.19.1
-Requires-Dist: tqdm>=4.66.6
-Requires-Dist: xmlschema==3.4.2
-Requires-Dist: zipp>=3.20.2
-Requires-Dist: py7zr==0.22.0
-Requires-Dist: openai>=1.52.2
-Requires-Dist: langchain>=0.3.4
-Requires-Dist: chromadb>=0.5.15
-Requires-Dist: langchain_community==0.3.3
-Requires-Dist: datasets==3.0.2
-Requires-Dist: unstructured==0.16.3
-Requires-Dist: tensorflow<2.18.0,>=2.17.0
-Requires-Dist: tf-keras==2.17.0

ddi_fw-0.0.155/src/ddi_fw.egg-info/PKG-INFO

@@ -1,54 +0,0 @@
-Metadata-Version: 2.4
-Name: ddi_fw
-Version: 0.0.155
-Summary: Do not use :)
-Author-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
-Maintainer-email: Kıvanç Bayraktar <bayraktarkivanc@gmail.com>
-Keywords: Machine Learning
-Classifier: Development Status :: 1 - Planning
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Framework :: Pytest
-Classifier: Framework :: tox
-Classifier: Framework :: Sphinx
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Information Analysis
-Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-Requires-Dist: pydantic==2.10.6
-Requires-Dist: importlib-resources==6.4.5
-Requires-Dist: python-stopwatch==1.1.11
-Requires-Dist: lxml==5.3.0
-Requires-Dist: matplotlib==3.8.0
-Requires-Dist: mlflow==2.16.1
-Requires-Dist: nltk>=3.8.1
-Requires-Dist: numpy>=1.26.4
-Requires-Dist: pandas>=2.2.0
-Requires-Dist: plotly==5.24.1
-Requires-Dist: rdkit==2023.3.3
-Requires-Dist: scikit-learn==1.5.2
-Requires-Dist: scipy==1.13.1
-Requires-Dist: accelerate>=0.33.0
-Requires-Dist: sentence-transformers<=3.3.1,>=3.0.1
-Requires-Dist: transformers>=4.42.4
-Requires-Dist: stanza==1.9.2
-Requires-Dist: tokenizers>=0.19.1
-Requires-Dist: tqdm>=4.66.6
-Requires-Dist: xmlschema==3.4.2
-Requires-Dist: zipp>=3.20.2
-Requires-Dist: py7zr==0.22.0
-Requires-Dist: openai>=1.52.2
-Requires-Dist: langchain>=0.3.4
-Requires-Dist: chromadb>=0.5.15
-Requires-Dist: langchain_community==0.3.3
-Requires-Dist: datasets==3.0.2
-Requires-Dist: unstructured==0.16.3
-Requires-Dist: tensorflow<2.18.0,>=2.17.0
-Requires-Dist: tf-keras==2.17.0