aiagents4pharma 1.46.0__py3-none-any.whl → 1.46.2__py3-none-any.whl

aiagents4pharma/talk2biomodels/api/__init__.py

@@ -2,4 +2,4 @@
 This file is used to import the modules in the package.
 """
 
-from . import kegg, ols, uniprot
+from . import ols, uniprot

aiagents4pharma/talk2biomodels/tests/test_api.py

@@ -2,7 +2,6 @@
 Test cases for Talk2Biomodels.
 """
 
-from ..api.kegg import fetch_from_api, fetch_kegg_names
 from ..api.ols import fetch_from_ols
 from ..api.uniprot import search_uniprot_labels
 
@@ -30,32 +29,3 @@ def test_fetch_from_ols():
     assert isinstance(label_2, str), f"Expected string, got {type(label_2)}"
     assert label_1 == "plasma membrane"
     assert label_2.startswith("Error: 404")
-
-
-def test_fetch_kegg_names():
-    """
-    Test the fetch_kegg_names function.
-    """
-    ids = ["C00001", "C00002"]
-    results = fetch_kegg_names(ids)
-    assert results["C00001"] == "H2O"
-    assert results["C00002"] == "ATP"
-
-    # Try with an empty list
-    results = fetch_kegg_names([])
-    assert not results
-
-
-def test_fetch_from_api():
-    """
-    Test the fetch_from_api function.
-    """
-    base_url = "https://rest.kegg.jp/get/"
-    query = "C00001"
-    entry_data = fetch_from_api(base_url, query)
-    assert entry_data.startswith("ENTRY       C00001")
-
-    # Try with an invalid query
-    query = "C0000Q"
-    entry_data = fetch_from_api(base_url, query)
-    assert not entry_data

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -126,7 +126,7 @@ def test_all_species_annotations(make_graph):
     Here, we test the tool with three models since they have different use cases:
         - model 12 contains a species with no URL provided.
         - model 20 contains a species without description.
-        - model 56 contains a species with database outside of KEGG, UniProt, and OLS.
+        - model 56 contains a species with database outside of UniProt, and OLS.
 
     We are testing a condition where the user asks for annotations
     of all species in a specific model.

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -19,7 +19,6 @@ from langgraph.prebuilt import InjectedState
 from langgraph.types import Command
 from pydantic import BaseModel, Field
 
-from ..api.kegg import fetch_kegg_annotations
 from ..api.ols import search_ols_labels
 from ..api.uniprot import search_uniprot_labels
 
@@ -298,8 +297,6 @@ class GetAnnotationTool(BaseTool):
         for ols_ontology_abbreviation in ols_ontology_abbreviations:
             if ols_ontology_abbreviation + "/" in link:
                 link = link.replace(f"{ols_ontology_abbreviation}/", "")
-        if "kegg.compound" in link:
-            link = link.replace("kegg.compound/", "kegg.compound:")
         return link
 
     def _fetch_descriptions(self, data: list[dict[str, str]]) -> dict[str, str]:
@@ -338,14 +335,8 @@ class GetAnnotationTool(BaseTool):
                 )
                 for identifier in identifiers:
                     results[identifier] = annotations.get(database, {}).get(identifier, "-")
-            elif database == "kegg.compound":
-                data = [
-                    {"Id": identifier, "Database": "kegg.compound"} for identifier in identifiers
-                ]
-                annotations = fetch_kegg_annotations(data)
-                for identifier in identifiers:
-                    results[identifier] = annotations.get(database, {}).get(identifier, "-")
             else:
+                # For any other database types, do not fetch; mark as unknown
                 for identifier in identifiers:
                     results[identifier] = "-"
         return results

{aiagents4pharma-1.46.0.dist-info → aiagents4pharma-1.46.2.dist-info}/METADATA

@@ -1,89 +1,89 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.46.0
+Version: 1.46.2
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
-Requires-Dist: anndata==0.11.3
+Requires-Dist: anndata==0.12.2
 Requires-Dist: azure-identity==1.24.0
-Requires-Dist: beautifulsoup4==4.13.4
+Requires-Dist: beautifulsoup4==4.13.5
 Requires-Dist: cell2sentence==1.1.0
 Requires-Dist: cloudscraper==1.2.71
 Requires-Dist: copasi-basico==0.84
-Requires-Dist: coverage==7.6.4
+Requires-Dist: coverage==7.10.6
 Requires-Dist: datasets==4.0.0
-Requires-Dist: einops==0.8.0
+Requires-Dist: einops==0.8.1
 Requires-Dist: gdown==5.2.0
 Requires-Dist: gravis==0.1.0
-Requires-Dist: gseapy==1.1.8
-Requires-Dist: h5py==3.13.0
+Requires-Dist: gseapy==1.1.9
+Requires-Dist: h5py==3.14.0
 Requires-Dist: huggingface-hub==0.34.4
 Requires-Dist: hydra-core==1.3.2
-Requires-Dist: igraph==0.11.8
-Requires-Dist: ipykernel==6.29.5
+Requires-Dist: igraph==0.11.9
+Requires-Dist: ipykernel==6.30.1
 Requires-Dist: ipython==8.32.0
-Requires-Dist: joblib==1.4.2
+Requires-Dist: joblib==1.5.2
 Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.40
-Requires-Dist: langchain-experimental==0.3.3
-Requires-Dist: langchain-milvus==0.2.0
+Requires-Dist: langchain-experimental==0.3.4
+Requires-Dist: langchain-milvus==0.2.1
 Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
 Requires-Dist: langchain-ollama==0.2.3
 Requires-Dist: langchain-openai==0.3.0
 Requires-Dist: langchain==0.3.7
 Requires-Dist: langgraph-supervisor==0.0.9
 Requires-Dist: langgraph==0.3.34
-Requires-Dist: matplotlib==3.9.2
-Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: matplotlib==3.10.6
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.7
 Requires-Dist: mkdocs-jupyter==0.25.1
-Requires-Dist: mkdocs-material==9.5.47
+Requires-Dist: mkdocs-material==9.6.18
 Requires-Dist: mkdocs==1.6.1
-Requires-Dist: mkdocstrings-python==1.12.2
-Requires-Dist: mkdocstrings==0.27.0
+Requires-Dist: mkdocstrings-python==1.18.2
+Requires-Dist: mkdocstrings==0.30.0
 Requires-Dist: nbformat==5.10.4
 Requires-Dist: numpy==1.26.4
 Requires-Dist: ollama==0.4.7
 Requires-Dist: openai==1.59.6
 Requires-Dist: openpyxl==3.1.5
-Requires-Dist: pandas==2.2.3
+Requires-Dist: pandas==2.3.2
 Requires-Dist: pcst-fast==1.0.10
 Requires-Dist: plotly-express==0.4.1
 Requires-Dist: plotly==5.24.1
 Requires-Dist: pubchempy==1.0.4
 Requires-Dist: pyarrow==21.0.0
-Requires-Dist: pydantic==2.10.5
+Requires-Dist: pydantic==2.11.7
 Requires-Dist: pygeneconverter==0.3
-Requires-Dist: pylint==3.3.1
-Requires-Dist: pymilvus==2.5.11
+Requires-Dist: pylint==3.3.8
+Requires-Dist: pymilvus==2.6.1
 Requires-Dist: pypdf==6.0.0
 Requires-Dist: pytest-asyncio==0.25.2
-Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest==8.4.1
 Requires-Dist: python-magic==0.4.27
-Requires-Dist: pyzotero==1.6.9
-Requires-Dist: requests==2.32.4
-Requires-Dist: scanpy==1.11.0
-Requires-Dist: scipy==1.15.2
+Requires-Dist: pyzotero==1.6.11
+Requires-Dist: requests==2.32.5
+Requires-Dist: scanpy==1.11.4
+Requires-Dist: scipy==1.16.1
 Requires-Dist: seaborn==0.13.2
 Requires-Dist: sentence-transformers==3.3.1
 Requires-Dist: setuptools==80.9.0
 Requires-Dist: streamlit-feedback==0.1.4
-Requires-Dist: streamlit==1.41.1
+Requires-Dist: streamlit==1.49.1
 Requires-Dist: tabulate==0.9.0
 Requires-Dist: torch-geometric==2.6.1
 Requires-Dist: torch==2.8.0
 Requires-Dist: tqdm==4.67.1
 Requires-Dist: transformers==4.55.2
-Requires-Dist: umap-learn==0.5.7
+Requires-Dist: umap-learn==0.5.9.post2
 Requires-Dist: xlsxwriter==3.2.5
 Provides-Extra: dev
 Requires-Dist: bandit==1.8.6; extra == 'dev'
 Requires-Dist: mypy==1.17.1; extra == 'dev'
 Requires-Dist: pip-audit==2.9.0; extra == 'dev'
 Requires-Dist: pre-commit==4.3.0; extra == 'dev'
-Requires-Dist: ruff==0.12.8; extra == 'dev'
+Requires-Dist: ruff==0.12.11; extra == 'dev'
 Requires-Dist: safety==3.2.9; extra == 'dev'
 Requires-Dist: twine==6.1.0; extra == 'dev'
 Description-Content-Type: text/markdown
@@ -275,6 +275,7 @@ For contributors and developers, we have comprehensive documentation:
 - **[SonarCloud Integration](docs/developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
 - **[GitHub Workflows](docs/developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
 - **[Streamlit Security](docs/developer/STREAMLIT_SECURITY.md)** - File upload security implementation
+- **[Azure Deployment](developer/AZURE_DEPLOYMENT.md)** - Understanding our Azure deployment setup
 
 #### How to contribute
 

{aiagents4pharma-1.46.0.dist-info → aiagents4pharma-1.46.2.dist-info}/RECORD

@@ -28,8 +28,7 @@ aiagents4pharma/talk2biomodels/__init__.py,sha256=DxARZJu91m4WHW4PBSZvlMb1MCbjvk
 aiagents4pharma/talk2biomodels/install.md,sha256=9YAEeW_vG5hv7WiMnNEzgKQIgVyHnpk1IIWXg_jhLxE,1520
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=4wPy6hWRJksX6z8qX1cVjFctZLpsja8JMngKHqn49N4,129
 aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=b_9pjnY3VGPRrzy-LCFrbJCkP1PT3M30NiQq6gbavaA,3267
-aiagents4pharma/talk2biomodels/api/__init__.py,sha256=2fKfvp7tj6fr6mhesQo2flaNpW5cINjzx_o_zUpTzZc,98
-aiagents4pharma/talk2biomodels/api/kegg.py,sha256=znaXYtw6HZe5XoX7wyl0hi1anHd2vzKRgVzt0HZ_TU0,2836
+aiagents4pharma/talk2biomodels/api/__init__.py,sha256=KGok9mCa6RT8whDj3jT3kcpFO1yHxk5vVD8IExsI5Bc,92
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=QSvbsD0V07-w0OU-wPQ4EypXi9bn_xl0NyliZQxRvCU,2173
 aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=jXoyd7BhIQA9JNaGMVPzORpQ5k1Ix9iYYduMv6YG7hw,1147
 aiagents4pharma/talk2biomodels/configs/__init__.py,sha256=WgGZbEtZiVR8EVJeH3iIJ6LxBGFafAjfCftptnTm2Ds,75
@@ -55,10 +54,10 @@ aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=kKtVBfSK92h
 aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml,sha256=RkWbstfLrT1mAfOtZf7JsBz6poyWg6-5G7H_IdVXEXg,72630
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
 aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf,sha256=rfBnG9XSGRZodq-NQsouQQ3dvm4JKcrAqEkoAQJmuDc,470738
-aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=0Gyakd5Yaa0CxUH18040xl-TBrNKGi6aDaIyVFF1d9A,1724
+aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=rfH2_K2pC5fm3DcyKJSHOBcN6Mzz3D37oJEpFCE1Jek,970
 aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=lMrFI5URqUEz0Cv3WOoj8vhR_ciwDOgoJlqh1dOdaik,1523
 aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=F_1AbFRcXIDahQKcS-Nq0v45bEozLUOYx_oyyFN0hxw,2429
-aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=T5RvNfiyz9Z49LBo6FkOOaD7f3vSalklF6Oi1Qj3-Kk,8179
+aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=L4fTQaY2rnkfHwfPSC6GdXD2T3NGTIqNoF2dRklBIQA,8173
 aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=PlVDIQZaZw8a94_Muw5GMa2Kop6foEBGhp3x-412cQA,3258
 aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=t8jR45pX7hKBGOjXySQ-XG5wJpTt41jGba74T8zuIdI,4838
 aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py,sha256=8nVSDa8_z85dyvxa8aYGQR0YGZDtpzLF5HhBmifCk6w,895
@@ -71,7 +70,7 @@ aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=poMxOsKhg8USnp
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=j6wTW09BOwFMzHERfJbsajctDsNxJDtWJHUE3FmTu-A,279
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=IbolM6zbYKHd_UCfLMa8bawt9fJH59cCUtkLB_wtxKI,4495
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=dk5HUmPwSTIRp2sbd8Q8__fwSE8m13UseonvcpyDs00,6636
-aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=spP_EVDlkbg7DfpzZw4YyIIYAsiax5EoJxB0f0gjVbM,13312
+aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=oHERHdY4KinQFg9udufEgJP3tE3x0gtoWWy4Kna9H78,12854
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=mVAqO2TRWIlD93ZsMggs2N3629sxHZWnOisW7r_yBU0,5987
 aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=LZQNkAikXhG0AKRnfLUqqpa5hNAyVGSwPQ4_nBu-DSw,4009
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=025-E5qo2uiJVvHIhyeDh1tfmXTeIguSgS0KIY0LiyY,1208
@@ -329,7 +328,7 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=-q-UuzP
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=K1EatPfC-riGyFmkOAS3ReNBaGPY-znne1KqOnFahkI,7339
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=sKkfJu3u4LKSZjfoQRfeqz26IESHRwBtcSDzLMLlJMo,6311
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=DBrF5IiF7VRP58hUK8T9LST3lQWLFixLUfnpMSTccoQ,4614
-aiagents4pharma-1.46.0.dist-info/METADATA,sha256=AVFonSHolN2s2XvewoYumpZQpWkWI2wuiTgVF3AvNpE,16928
-aiagents4pharma-1.46.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-aiagents4pharma-1.46.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.46.0.dist-info/RECORD,,
+aiagents4pharma-1.46.2.dist-info/METADATA,sha256=EnSy3phI9yOyB4Rlkagi5T2jneuEGBITExl3Zt9MHCQ,17036
+aiagents4pharma-1.46.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+aiagents4pharma-1.46.2.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.46.2.dist-info/RECORD,,

aiagents4pharma/talk2biomodels/api/kegg.py

@@ -1,87 +0,0 @@
-"""
-This module contains the API for fetching Kegg database
-"""
-
-import re
-
-import requests
-
-
-def fetch_from_api(base_url: str, query: str) -> str:
-    """Fetch data from the given API endpoint."""
-    try:
-        response = requests.get(base_url + query, timeout=10)
-        response.raise_for_status()
-        return response.text
-    except requests.exceptions.RequestException as e:
-        print(f"Error fetching data for query {query}: {e}")
-        return ""
-
-
-def fetch_kegg_names(ids: list[str], batch_size: int = 10) -> dict[str, str]:
-    """
-    Fetch the names of multiple KEGG entries using the KEGG REST API in batches.
-
-    Args:
-        ids (List[str]): List of KEGG IDs.
-        batch_size (int): Maximum number of IDs to include in a single request.
-
-    Returns:
-        Dict[str, str]: A mapping of KEGG IDs to their names.
-    """
-    if not ids:
-        return {}
-
-    base_url = "https://rest.kegg.jp/get/"
-    entry_name_map = {}
-
-    # Process IDs in batches
-    for i in range(0, len(ids), batch_size):
-        batch = ids[i : i + batch_size]
-        query = "+".join(batch)
-        entry_data = fetch_from_api(base_url, query)
-
-        # if not entry_data:
-        #     continue
-        entries = entry_data.split("///")
-        for entry in entries:
-            if not entry.strip():
-                continue
-            lines = entry.strip().split("\n")
-            entry_line = next((line for line in lines if line.startswith("ENTRY")), None)
-            name_line = next((line for line in lines if line.startswith("NAME")), None)
-
-            # if not entry_line and not name_line:
-            #     continue
-            entry_id = entry_line.split()[1]
-            # Split multiple names in the NAME field and clean them
-            names = [
-                re.sub(r"[^a-zA-Z0-9\s]", "", name).strip()
-                for name in name_line.replace("NAME", "").strip().split(";")
-            ]
-            # Join cleaned names into a single string
-            entry_name_map[entry_id] = " ".join(names).strip()
-
-    return entry_name_map
-
-
-def fetch_kegg_annotations(
-    data: list[dict[str, str]], batch_size: int = 10
-) -> dict[str, dict[str, str]]:
-    """Fetch KEGG entry descriptions grouped by database type."""
-    grouped_data = {}
-    for entry in data:
-        db_type = entry["Database"].lower()
-        grouped_data.setdefault(db_type, []).append(entry["Id"])
-
-    results = {}
-    for db_type, ids in grouped_data.items():
-        results[db_type] = fetch_kegg_names(ids, batch_size=batch_size)
-
-    return results
-
-
-# def get_protein_name_or_label(data: List[Dict[str, str]],
-#                               batch_size: int = 10) -> Dict[str, Dict[str, str]]:
-#     """Fetch descriptions for KEGG-related identifiers."""
-#     return fetch_kegg_annotations(data, batch_size=batch_size)