aiagents4pharma 1.46.0__tar.gz → 1.46.2__tar.gz

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.2}/.github/dependabot.yml

@@ -43,23 +43,6 @@ updates:
       - "github-actions"
     open-pull-requests-limit: 5
 
-  # Docker
-  - package-ecosystem: "docker"
-    directory: "/"
-    schedule:
-      interval: "monthly"
-      time: "09:00"
-    target-branch: "main"
-    assignees:
-      - "ansh-info"
-    commit-message:
-      prefix: "docker"
-      include: "scope"
-    labels:
-      - "dependencies"
-      - "docker"
-    open-pull-requests-limit: 3
-
   # Disabled for now: repo has no Dockerfiles or Kubernetes manifests
   # in the root directory, causing Dependabot's Docker updater to fail
   # with "No Dockerfiles nor Kubernetes YAML found". Re-enable when
@@ -72,7 +55,7 @@ updates:
   #     time: "09:00"
   #   target-branch: "main"
   #   assignees:
-  #     - "gurdeep330"
+  #     - "ansh-info"
   #   commit-message:
   #     prefix: "docker"
   #     include: "scope"

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.2}/.github/workflows/docker_compose_release.yml

@@ -332,22 +332,49 @@ jobs:
           tar -czf "../aiagents4pharma-compose-${{ needs.detect-changes.outputs.version }}.tar.gz" .
           zip -r "../aiagents4pharma-compose-${{ needs.detect-changes.outputs.version }}.zip" .
 
+      - name: Get release notes from app release
+        id: get_release_notes
+        run: |
+          VERSION="${{ needs.detect-changes.outputs.version }}"
+
+          # Try to get the release title and body from the corresponding app release
+          RELEASE_TITLE=$(gh release view "$VERSION" --json name --jq .name 2>/dev/null || echo "")
+          RELEASE_BODY=$(gh release view "$VERSION" --json body --jq .body 2>/dev/null || echo "")
+
+          # If no release found or empty, create basic release info from git
+          if [ -z "$RELEASE_BODY" ]; then
+            # Get commit info for this version
+            RELEASE_NOTES="$VERSION"$'\n\n'"$(git log --oneline --pretty=format:"%s (%h)" -1 2>/dev/null || echo "Latest updates")"
+          else
+            # Use the release title and body, avoiding duplication
+            if [ -n "$RELEASE_TITLE" ] && [ "$RELEASE_TITLE" != "$VERSION" ]; then
+              RELEASE_NOTES="$RELEASE_TITLE"$'\n\n'"$RELEASE_BODY"
+            else
+              RELEASE_NOTES="$RELEASE_BODY"
+            fi
+          fi
+
+          # Store the release notes (escape newlines for GitHub Actions)
+          echo "RELEASE_NOTES<<EOF" >> $GITHUB_ENV
+          echo "$RELEASE_NOTES" >> $GITHUB_ENV
+          echo "EOF" >> $GITHUB_ENV
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Create Release
         uses: softprops/action-gh-release@v1
         with:
           tag_name: ${{ needs.detect-changes.outputs.version }}
           name: "AIAgents4Pharma ${{ needs.detect-changes.outputs.version }}"
           body: |
+            ${{ env.RELEASE_NOTES }}
+
+            ---
+
             ## 🚀 Ready-to-Deploy Docker Configurations
 
             **One-click deployment** for all AIAgents4Pharma applications with the latest updates from ${{ needs.detect-changes.outputs.version }}.
 
-            ### 📦 What's New in This Release
-            - **Updated Docker images** with latest application code
-            - **Production-ready** compose configurations for CPU & GPU
-            - **Complete setup** with Milvus, Minio, and all dependencies
-            - **Environment templates** for easy configuration
-
             ### ⚡ Quick Deploy
             ```bash
             # Download and extract

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.2}/PKG-INFO

@@ -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 → aiagents4pharma-1.46.2}/README.md

@@ -185,6 +185,7 @@ 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 → aiagents4pharma-1.46.2}/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-1.46.0 → aiagents4pharma-1.46.2}/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-1.46.0 → aiagents4pharma-1.46.2}/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-1.46.0 → aiagents4pharma-1.46.2}/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 → aiagents4pharma-1.46.2}/docs/index.md

@@ -183,6 +183,7 @@ For contributors and developers, we have comprehensive documentation:
 - **[SonarCloud Integration](developer/SONARCLOUD_SETUP.md)** - Code quality analysis and CI/CD integration
 - **[GitHub Workflows](developer/WORKFLOWS.md)** - Understanding our CI/CD pipeline
 - **[Streamlit Security](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 → aiagents4pharma-1.46.2}/package-lock.json

@@ -10,7 +10,7 @@
 				"@semantic-release/github": "^11.0.1",
 				"semantic-release": "^24.0.0"
 			},
-			"version": "1.46.0"
+			"version": "1.46.2"
 		},
 		"node_modules/@babel/code-frame": {
 			"version": "7.26.2",
@@ -11110,5 +11110,5 @@
 			"dev": true
 		}
 	},
-	"version": "1.46.0"
+	"version": "1.46.2"
 }

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.2}/package.json

@@ -26,5 +26,5 @@
 			]
 		]
 	},
-	"version": "1.46.0"
+	"version": "1.46.2"
 }

{aiagents4pharma-1.46.0 → aiagents4pharma-1.46.2}/pyproject.toml

@@ -13,83 +13,83 @@ classifiers = [
   "Operating System :: OS Independent",
 ]
 dependencies = [
-  "anndata==0.11.3",
+  "anndata==0.12.2",
   "cell2sentence==1.1.0",
   "copasi_basico==0.84",
-  "coverage==7.6.4",
-  "einops==0.8.0",
+  "coverage==7.10.6",
+  "einops==0.8.1",
   "gdown==5.2.0",
   "gravis==0.1.0",
-  "gseapy==1.1.8",
-  "h5py==3.13.0",
+  "gseapy==1.1.9",
+  "h5py==3.14.0",
   "huggingface_hub==0.34.4",
   "hydra-core==1.3.2",
-  "igraph==0.11.8",
-  "ipykernel==6.29.5",
+  "igraph==0.11.9",
+  "ipykernel==6.30.1",
   "ipython==8.32.0",
-  "joblib==1.4.2",
+  "joblib==1.5.2",
   "langchain==0.3.7",
   "langchain-community==0.3.5",
   "langchain-core==0.3.40",
-  "langchain-experimental==0.3.3",
-  "langchain-milvus==0.2.0",
+  "langchain-experimental==0.3.4",
+  "langchain-milvus==0.2.1",
   "langchain-nvidia-ai-endpoints==0.3.9",
   "langchain-openai==0.3.0",
   "langchain_ollama==0.2.3",
   "langgraph==0.3.34",
   "langgraph_supervisor==0.0.9",
-  "matplotlib==3.9.2",
+  "matplotlib==3.10.6",
   "mkdocs==1.6.1",
-  "mkdocs-include-markdown-plugin==7.1.2",
+  "mkdocs-include-markdown-plugin==7.1.7",
   "mkdocs-jupyter==0.25.1",
-  "mkdocs-material==9.5.47",
-  "mkdocstrings==0.27.0",
-  "mkdocstrings-python==1.12.2",
+  "mkdocs-material==9.6.18",
+  "mkdocstrings==0.30.0",
+  "mkdocstrings-python==1.18.2",
   "nbformat==5.10.4",
   "numpy==1.26.4",
   "ollama==0.4.7",
   "openai==1.59.6",
   "openpyxl==3.1.5",
-  "pandas==2.2.3",
+  "pandas==2.3.2",
   "pcst_fast==1.0.10",
   "plotly==5.24.1",
   "plotly-express==0.4.1",
   "pubchempy==1.0.4",
-  "pydantic==2.10.5",
+  "pydantic==2.11.7",
   "pygeneconverter==0.3",
-  "pylint==3.3.1",
-  "pymilvus==2.5.11",
+  "pylint==3.3.8",
+  "pymilvus==2.6.1",
   "pypdf==6.0.0",
-  "pytest==8.3.3",
+  "pytest==8.4.1",
   "pytest-asyncio==0.25.2",
-  "pyzotero==1.6.9",
-  "requests==2.32.4",
-  "scanpy==1.11.0",
-  "scipy==1.15.2",
+  "pyzotero==1.6.11",
+  "requests==2.32.5",
+  "scanpy==1.11.4",
+  "scipy==1.16.1",
   "seaborn==0.13.2",
   "setuptools==80.9.0",
   "sentence_transformers==3.3.1",
-  "streamlit==1.41.1",
+  "streamlit==1.49.1",
   "streamlit-feedback==0.1.4",
   "tabulate==0.9.0",
   "torch==2.8.0",
   "torch_geometric==2.6.1",
   "tqdm==4.67.1",
   "transformers==4.55.2",
-  "umap-learn==0.5.7",
+  "umap-learn==0.5.9.post2",
   "xlsxwriter==3.2.5",
   "python-magic==0.4.27",
   "pyarrow==21.0.0",
   "datasets==4.0.0",
-  "beautifulsoup4==4.13.4",
+  "beautifulsoup4==4.13.5",
   "cloudscraper==1.2.71",
   "azure-identity==1.24.0",
 ]
-version = "1.46.0"
+version = "1.46.2"
 
 [project.optional-dependencies]
 dev = [
-  "ruff==0.12.8",
+  "ruff==0.12.11",
   "mypy==1.17.1",
   "bandit==1.8.6",
   "pip-audit==2.9.0",
@@ -133,7 +133,7 @@ extension-pkg-allow-list = ["pcst_fast"]
 disable = ["R0801", "R0902", "W0221", "W0122"]
 
 [tool.ruff]
-target-version = "1.46.0"
+target-version = "1.46.2"
 line-length = 100
 
 [tool.ruff.lint]
@@ -155,7 +155,7 @@ ignore = [
 "__init__.py" = ["F401"]
 
 [tool.mypy]
-python_version = "1.46.0"
+python_version = "1.46.2"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true