Merge pull request #136 from SCAI-BIO/refactor-remove-deprecated

chore: remove legacy functions and modules

Author: mehmetcanay

datastew/__init__.py

@@ -1,22 +1,50 @@
 from ._version import __version__
-from .embedding import *
+from .embedding import EmbeddingModel, GPT4Adapter, HuggingFaceAdapter, OllamaAdapter, Vectorizer
 
 # Importing submodules to expose their attributes if needed
-from .process import mapping, parsing
-from .repository import Concept, Mapping, Terminology, base, model, sqllite, weaviate
-from .visualisation import *
+from .process import jsonl_adapter, mapping, ols, parsing
+from .repository import (
+    Concept,
+    Mapping,
+    Terminology,
+    base,
+    model,
+    pagination,
+    postgresql,
+    sqllite,
+    weaviate,
+    weaviate_schema,
+)
+from .visualisation import (
+    bar_chart_average_acc_two_distributions,
+    enrichment_plot,
+    get_plot_for_current_database_state,
+    plot_embeddings,
+)
 
 __all__ = [
+    "__version__",
+    "jsonl_adapter",
     "mapping",
+    "ols",
     "parsing",
-    "model",
     "base",
+    "model",
+    "pagination",
+    "postgresql",
     "sqllite",
     "weaviate",
-    "DataDictionarySource",
+    "weaviate_schema",
+    "EmbeddingModel",
+    "GPT4Adapter",
     "HuggingFaceAdapter",
+    "OllamaAdapter",
+    "Vectorizer",
     "Terminology",
     "Concept",
     "Mapping",
-    "get_default_embedding_model"
+    "bar_chart_average_acc_two_distributions",
+    "enrichment_plot",
+    "get_plot_for_current_database_state",
+    "plot_embeddings",
 ]

datastew/_mapping.py

@@ -7,7 +7,6 @@
 from cachetools import LRUCache
 from ollama import Client
 from sentence_transformers import SentenceTransformer
-from typing_extensions import deprecated
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
 
@@ -331,10 +330,3 @@ def get_embedding(self, text: str):
 
     def get_embeddings(self, messages: List[str]):
         return self.model.get_embeddings(messages)
-
-
-@deprecated("This class is deprecated and will be removed in the next major release due to refactoring of artifacts.")
-class TextEmbedding:
-    def __init__(self, text: str, embedding: List[float]):
-        self.text = text
-        self.embedding = embedding