aiagents4pharma 1.35.0__py3-none-any.whl → 1.36.0__py3-none-any.whl

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py

@@ -2,17 +2,23 @@
 Test cases for utils/embeddings/sentence_transformer.py
 """
 
-import pytest
 import numpy as np
+import pytest
+
 from ..utils.embeddings.sentence_transformer import EmbeddingWithSentenceTransformer
 
+
 @pytest.fixture(name="embedding_model")
 def embedding_model_fixture():
     """
     Fixture for creating an instance of EmbeddingWithSentenceTransformer.
     """
     model_name = "sentence-transformers/all-MiniLM-L6-v1"  # Small model for testing
-    return EmbeddingWithSentenceTransformer(model_name=model_name)
+    embedding_model = EmbeddingWithSentenceTransformer(model_name=model_name)
+    # Move underlying model to CPU for testing
+    embedding_model.model.to("cpu")
+    return embedding_model
+
 
 def test_embed_documents(embedding_model):
     """
@@ -27,6 +33,7 @@ def test_embed_documents(embedding_model):
     assert len(embeddings[0]) == 384
     assert embeddings.dtype == np.float32
 
+
 def test_embed_query(embedding_model):
     """
     Test the embed_query method of EmbeddingWithSentenceTransformer class.

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py

@@ -19,24 +19,28 @@ from ..utils.enrichments.ols_terms import EnrichmentWithOLS
 CL_DESC = "CD4-positive, alpha-beta T cell"
 GO_DESC = "Any process that activates or increases the frequency, rate or extent"
 UBERON_DESC = "The olfactory organ of vertebrates, consisting of nares"
-HP_DESC = "Hypoplasia of the antihelix"
+HP_DESC = "Developmental hypoplasia of the antihelix"
 MONDO_DESC = "A gastrointestinal disorder characterized by chronic inflammation"
 
 # The expected description for the non-existing term is None
 
+
 @pytest.fixture(name="enrich_obj")
 def fixture_uniprot_config():
     """Return a dictionary with the configuration for OLS enrichment."""
     return EnrichmentWithOLS()
 
+
 def test_enrich_documents(enrich_obj):
     """Test the enrich_documents method."""
-    ols_terms = ["CL_0000899",
-                 "GO_0046427",
-                 "UBERON_0000004",
-                 "HP_0009739",
-                 "MONDO_0005011",
-                 "XYZ_0000000"]
+    ols_terms = [
+        "CL_0000899",
+        "GO_0046427",
+        "UBERON_0000004",
+        "HP_0009739",
+        "MONDO_0005011",
+        "XYZ_0000000",
+    ]
     descriptions = enrich_obj.enrich_documents(ols_terms)
     assert descriptions[0].startswith(CL_DESC)
     assert descriptions[1].startswith(GO_DESC)
@@ -45,14 +49,17 @@ def test_enrich_documents(enrich_obj):
     assert descriptions[4].startswith(MONDO_DESC)
     assert descriptions[5] is None
 
+
 def test_enrich_documents_with_rag(enrich_obj):
     """Test the enrich_documents_with_rag method."""
-    ols_terms = ["CL_0000899",
-                 "GO_0046427",
-                 "UBERON_0000004",
-                 "HP_0009739",
-                 "MONDO_0005011",
-                 "XYZ_0000000"]
+    ols_terms = [
+        "CL_0000899",
+        "GO_0046427",
+        "UBERON_0000004",
+        "HP_0009739",
+        "MONDO_0005011",
+        "XYZ_0000000",
+    ]
     descriptions = enrich_obj.enrich_documents_with_rag(ols_terms, None)
     assert descriptions[0].startswith(CL_DESC)
     assert descriptions[1].startswith(GO_DESC)

{aiagents4pharma-1.35.0.dist-info → aiagents4pharma-1.36.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.35.0
+Version: 1.36.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -90,6 +90,17 @@ Our toolkit currently consists of the following agents:
 
 ![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
 
+## News
+
+- T2B and T2KG accepted at the MLGenX workshop during ICLR #2025 in Singapore. [Read More](https://openreview.net/forum?id=av4QhBNeZo)
+
+<div align="center">
+  <strong>Watch the presentation:</strong><br><br>
+  <a href="https://www.youtube.com/watch?v=3cU_OxY4HiE">
+    <img src="https://img.youtube.com/vi/3cU_OxY4HiE/0.jpg" alt="Watch the presentation" width="480">
+  </a>
+</div>
+
 ## Getting Started
 
 ### Installation
@@ -250,15 +261,19 @@ If you are using docker on Windows, please follow these [Windows Setup Notes](#n
 ![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 1. **Clone the repository:**
-   ```sh
-   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
-   cd AIAgents4Pharma
-   ```
+
+```sh
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+cd AIAgents4Pharma
+```
+
 2. **Install dependencies:**
 
-   ```python
-   pip install -r requirements.txt
-   ```
+We use Conda as our environment manager, Follow the official [Quickstart](https://www.anaconda.com/docs/getting-started/miniconda/install#quickstart-install-instructions) install instructions provided by anaconda/miniconda.
+
+```python
+conda create --name AIAgents4Pharma python=3.12 -y && conda activate AIAgents4Pharma && pip install --upgrade pip && pip install -r requirements.txt
+```
 
 3. **Initialize API Keys**
 

{aiagents4pharma-1.35.0.dist-info → aiagents4pharma-1.36.0.dist-info}/RECORD

@@ -108,10 +108,10 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_embeddings.py,s
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_huggingface.py,sha256=hzX84pheZdEsTtikF2KtBFiH44_xPjYXxLA6p4Ax1CY,1623
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_nim_molmim.py,sha256=LwtTZ-M7lHGxvRrGBXbyIT8AkA3T2OpeKqtNq3RK7Ik,2164
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_ollama.py,sha256=jn-TrPwF0aR9kVoerwkbMZa3U6Hc6HjV6Zoau4qSH4g,1834
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py,sha256=Qxo6WeIDRy8aLh1tNKw0kSlzmUj3MtTak63oW2YwB24,1327
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_embeddings_sentencetransformer.py,sha256=Xkuf2UFGCXldj1zcsh6kqfQYLDf5i0B6KP3KcmNLSzQ,1452
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_enrichments.py,sha256=N6HRr4lWHXY7bTHe2uXJe4D_EG9WqZPibZne6qLl9_k,1447
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ollama.py,sha256=JhY7axvVULLywDJ2ctA-gob5YPeaJYWsaMNjHT6L9CU,3021
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py,sha256=woSm723ns9fHieu-QWFiniLlm5h22v1qzO4v6n20K5g,2413
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_ols.py,sha256=5GTSkfKSDS5geR0YfilfnDyUsYli0hv7N8PiDwRvlIE,2370
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_pubchem.py,sha256=0SgYvqdvxseUYTHx2KuSNI2hnmQ3VVVz0F-79_-P41o,1769
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py,sha256=r1D74mavsnSCm4xnWl0n0nM9PZqgm3doD2dulNrKNVQ,1754
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=G13Diw7cA5TGINUNO1CDnN4rM6KbepxRXNjuzY578DI,1611
@@ -225,8 +225,8 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/read_helper.py,sha256=lyrfpx8NH
 aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=IPD1V9yrBYaDnRe7sR6PrpwR82OBJbA2P_Tc6RbxAbM,2748
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=ALwLecy1QVebbsmXJiDj1GhGmyhq2R2tZlAyEl1vfhw,7410
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=oIrfbOySgts50ksHKyjcWjRkPRIS88g3Lc0v9mBkU8w,6375
-aiagents4pharma-1.35.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.35.0.dist-info/METADATA,sha256=hxxS-4rneg7sMK4zjMbPx2_ppuDP-OcKwVdKgu3Uf-M,16043
-aiagents4pharma-1.35.0.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
-aiagents4pharma-1.35.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.35.0.dist-info/RECORD,,
+aiagents4pharma-1.36.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.36.0.dist-info/METADATA,sha256=4S4eCTvL7mAxQUmSDp4SIyn2WAYuOivLpcCdL-j5dGQ,16757
+aiagents4pharma-1.36.0.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
+aiagents4pharma-1.36.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.36.0.dist-info/RECORD,,