aiagents4pharma 1.45.0__tar.gz → 1.45.1__tar.gz

aiagents4pharma-1.45.1/.github/CODEOWNERS

@@ -0,0 +1,23 @@
+# All rules intentionally commented out to disable Code Owners
+# while preserving the previous configuration for reference.
+
+# Global code owners - will be automatically requested for review on all PRs
+# * @gurdeep330
+
+# Specific module owners
+# /aiagents4pharma/talk2biomodels/ @gurdeep330
+# /aiagents4pharma/talk2scholars/ @gurdeep330
+# /aiagents4pharma/talk2cells/ @gurdeep330
+# /aiagents4pharma/talk2knowledgegraphs/ @gurdeep330
+# /aiagents4pharma/talk2aiagents4pharma/ @gurdeep330
+
+# CI/CD and configuration
+# /.github/ @gurdeep330
+# /pyproject.toml @gurdeep330
+# /uv.lock @gurdeep330
+# /mkdocs.yml @gurdeep330
+
+# Documentation
+# /docs/ @gurdeep330
+# /README.md @gurdeep330
+# /CONTRIBUTING.md @gurdeep330

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/.github/dependabot.yml

@@ -46,19 +46,23 @@ updates:
     open-pull-requests-limit: 5
 
   # Docker
-  - package-ecosystem: "docker"
-    directory: "/"
-    schedule:
-      interval: "weekly"
-      day: "monday"
-      time: "09:00"
-    target-branch: "main"
-    assignees:
-      - "gurdeep330"
-    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
+  # Dockerfiles are added, or point `directory` at paths that contain them.
+  # - package-ecosystem: "docker"
+  #   directory: "/"
+  #   schedule:
+  #     interval: "weekly"
+  #     day: "monday"
+  #     time: "09:00"
+  #   target-branch: "main"
+  #   assignees:
+  #     - "gurdeep330"
+  #   commit-message:
+  #     prefix: "docker"
+  #     include: "scope"
+  #   labels:
+  #     - "dependencies"
+  #     - "docker"
+  #   open-pull-requests-limit: 3

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/.github/workflows/security_audit.yml

@@ -4,17 +4,17 @@ name: Dependency Security Audit
 on:
   schedule:
     # Run weekly on Sundays at 2 AM UTC
-    - cron: '0 2 * * 0'
+    - cron: "0 2 * * 0"
   push:
     branches: [main]
     paths:
-      - 'pyproject.toml'
-      - 'uv.lock'
+      - "pyproject.toml"
+      - "uv.lock"
   pull_request:
     branches: [main]
     paths:
-      - 'pyproject.toml'
-      - 'uv.lock'
+      - "pyproject.toml"
+      - "uv.lock"
   workflow_dispatch:
 
 jobs:
@@ -63,7 +63,6 @@ jobs:
           name: safety-report
           path: safety-report.json
 
-
   # SARIF upload for GitHub Security tab
   upload-sarif:
     name: Upload Security Results
@@ -147,41 +146,3 @@ jobs:
         with:
           name: security-summary
           path: security-summary.md
-
-  # Integration with SonarCloud (dependency security focus)
-  sonarcloud-security:
-    name: SonarCloud Security Integration
-    needs: [dependency-scan]
-    runs-on: ubuntu-latest
-    if: always() && github.event_name == 'push' && github.ref == 'refs/heads/main'
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Download security reports
-        uses: actions/download-artifact@v4
-        with:
-          pattern: "*-report*"
-          merge-multiple: true
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v4
-
-      - name: Set up Python
-        run: uv python install 3.12
-
-      - name: Install dependencies
-        run: uv sync --frozen --extra dev
-
-      - name: Generate coverage for SonarCloud
-        run: |
-          uv run coverage run --source=aiagents4pharma -m pytest || true
-          uv run coverage xml
-
-      - name: SonarCloud Security Analysis
-        uses: SonarSource/sonarcloud-github-action@master
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.45.0
+Version: 1.45.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
@@ -57,7 +57,6 @@ Requires-Dist: pydantic==2.10.5
 Requires-Dist: pygeneconverter==0.3
 Requires-Dist: pylint==3.3.1
 Requires-Dist: pymilvus==2.5.11
-Requires-Dist: pypdf2==3.0.1
 Requires-Dist: pypdf==6.0.0
 Requires-Dist: pytest-asyncio==0.25.2
 Requires-Dist: pytest==8.3.3
@@ -99,7 +98,7 @@ Description-Content-Type: text/markdown
 <!--  Deployment Workflows -->
 
 [![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
-[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml)
 [![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
 [![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
 

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/README.md

@@ -9,7 +9,7 @@
 <!--  Deployment Workflows -->
 
 [![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
-[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml)
 [![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
 [![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
 

aiagents4pharma-1.45.1/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py

@@ -0,0 +1,123 @@
+"""
+Test cases for utils/pubchem_utils.py
+
+These tests mock PubChem HTTP calls to avoid network dependency and verify
+parsing logic without modifying business logic.
+"""
+
+from types import SimpleNamespace
+
+import pytest
+
+from ..utils import pubchem_utils
+
+
+def _resp(json_data):
+    """Create a minimal response-like object exposing .json()."""
+    return SimpleNamespace(json=lambda: json_data)
+
+
+@pytest.fixture(autouse=True)
+def mock_requests_get(monkeypatch):
+    """Mock requests.get used by pubchem_utils to return deterministic JSON."""
+
+    def _mock_get(url, _timeout=60, **_kwargs):
+        # CAS RN lookup: ethyl carbonate 105-58-8 -> CID 7766
+        if "substance/xref/RN/105-58-8/record/JSON" in url:
+            return _resp(
+                {"PC_Substances": [{"compound": [{"id": {"type": 1, "id": {"cid": 7766}}}]}]}
+            )
+
+        # DrugBank: DB00240 (Alclometasone) -> CID 5311000
+        if (
+            "substance/sourceid//drugbank/DB00240/JSON" in url
+            or "substance/sourceid/drugbank/DB00240/JSON" in url
+        ):
+            return _resp(
+                {"PC_Substances": [{"compound": [{"id": {"type": 1, "id": {"cid": 5311000}}}]}]}
+            )
+
+        # CTD: D002083 (Butylated Hydroxyanisole) -> CID 24667
+        if (
+            "substance/sourceid//comparative toxicogenomics database/D002083/JSON" in url
+            or "substance/sourceid/comparative toxicogenomics database/D002083/JSON" in url
+        ):
+            return _resp(
+                {"PC_Substances": [{"compound": [{"id": {"type": 1, "id": {"cid": 24667}}}]}]}
+            )
+
+        # CID description for 5311000
+        if (
+            "compound/cid//5311000/description/JSON" in url
+            or "compound/cid/5311000/description/JSON" in url
+        ):
+            return _resp(
+                {
+                    "InformationList": {
+                        "Information": [
+                            {
+                                "Description": (
+                                    "Alclometasone is a prednisolone compound having an "
+                                    "alpha-chloro substituent at the 9alpha-position."
+                                ),
+                            }
+                        ]
+                    }
+                }
+            )
+
+        # Default empty response
+        return _resp({})
+
+    monkeypatch.setattr(pubchem_utils.requests, "get", _mock_get)
+    return _mock_get
+
+
+def test_cas_rn2pubchem_cid():
+    """
+    Test the casRN2pubchem_cid function.
+
+    The CAS RN for ethyl carbonate is 105-58-8.
+    The PubChem CID for ethyl carbonate is 7766.
+    """
+    casrn = "105-58-8"
+    pubchem_cid = pubchem_utils.cas_rn2pubchem_cid(casrn)
+    assert pubchem_cid == 7766
+
+
+def test_external_id2pubchem_cid():
+    """
+    Test the external_id2pubchem_cid function.
+
+    The DrugBank ID for Alclometasone is DB00240 -> CID 5311000.
+    The CTD ID for Butylated Hydroxyanisole is D002083 -> CID 24667.
+    """
+    drugbank_id = "DB00240"
+    pubchem_cid = pubchem_utils.external_id2pubchem_cid("drugbank", drugbank_id)
+    assert pubchem_cid == 5311000
+
+    ctd_id = "D002083"
+    pubchem_cid = pubchem_utils.external_id2pubchem_cid(
+        "comparative toxicogenomics database", ctd_id
+    )
+    assert pubchem_cid == 24667
+
+
+def test_pubchem_cid_description():
+    """
+    Test the pubchem_cid_description function.
+
+    The PubChem CID for Alclometasone is 5311000.
+    The description starts with the expected prefix.
+    """
+    pubchem_cid = 5311000
+    description = pubchem_utils.pubchem_cid_description(pubchem_cid)
+    assert description.startswith(
+        "Alclometasone is a prednisolone compound having an alpha-chloro substituent"
+    )
+
+
+def test_mock_fallback_path_coverage():
+    """Exercise the default branch of the mocked requests.get for coverage."""
+    resp = pubchem_utils.requests.get("unknown://unmatched/url", timeout=1)
+    assert resp.json() == {}

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/docs/index.md

@@ -9,7 +9,7 @@
 <!--  Deployment Workflows -->
 
 [![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
-[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml)
 [![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
 [![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
 

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/package-lock.json

@@ -10,7 +10,7 @@
 				"@semantic-release/github": "^11.0.1",
 				"semantic-release": "^24.0.0"
 			},
-			"version": "1.45.0"
+			"version": "1.45.1"
 		},
 		"node_modules/@babel/code-frame": {
 			"version": "7.26.2",
@@ -11110,5 +11110,5 @@
 			"dev": true
 		}
 	},
-	"version": "1.45.0"
+	"version": "1.45.1"
 }

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/package.json

@@ -26,5 +26,5 @@
 			]
 		]
 	},
-	"version": "1.45.0"
+	"version": "1.45.1"
 }

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/pyproject.toml

@@ -60,7 +60,6 @@ dependencies = [
   "pylint==3.3.1",
   "pymilvus==2.5.11",
   "pypdf==6.0.0",
-  "PyPDF2==3.0.1",
   "pytest==8.3.3",
   "pytest-asyncio==0.25.2",
   "pyzotero==1.6.9",
@@ -85,7 +84,7 @@ dependencies = [
   "beautifulsoup4==4.13.4",
   "cloudscraper==1.2.71",
 ]
-version = "1.45.0"
+version = "1.45.1"
 
 [project.optional-dependencies]
 dev = [
@@ -133,7 +132,7 @@ extension-pkg-allow-list = ["pcst_fast"]
 disable = ["R0801", "R0902", "W0221", "W0122"]
 
 [tool.ruff]
-target-version = "1.45.0"
+target-version = "1.45.1"
 line-length = 100
 
 [tool.ruff.lint]
@@ -155,7 +154,7 @@ ignore = [
 "__init__.py" = ["F401"]
 
 [tool.mypy]
-python_version = "1.45.0"
+python_version = "1.45.1"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/sonar-project.properties

@@ -4,7 +4,8 @@ sonar.organization=virtualpatientengine
 
 # Project metadata
 sonar.projectName=AIAgents4Pharma
-sonar.projectDescription=AI Agents for Pharmaceutical Research - Open-source toolkit for interacting with biological data
+sonar.projectVersion=1.0
+sonar.projectDescription=AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 
 # Source code configuration
 sonar.sources=aiagents4pharma

{aiagents4pharma-1.45.0 → aiagents4pharma-1.45.1}/uv.lock

@@ -81,7 +81,6 @@ dependencies = [
     { name = "pylint" },
     { name = "pymilvus" },
     { name = "pypdf" },
-    { name = "pypdf2" },
     { name = "pytest" },
     { name = "pytest-asyncio" },
     { name = "python-magic" },
@@ -171,7 +170,6 @@ requires-dist = [
     { name = "pylint", specifier = "==3.3.1" },
     { name = "pymilvus", specifier = "==2.5.11" },
     { name = "pypdf", specifier = "==6.0.0" },
-    { name = "pypdf2", specifier = "==3.0.1" },
     { name = "pytest", specifier = "==8.3.3" },
     { name = "pytest-asyncio", specifier = "==0.25.2" },
     { name = "python-magic", specifier = "==0.4.27" },
@@ -4085,15 +4083,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/2c/83/2cacc506eb322bb31b747bc06ccb82cc9aa03e19ee9c1245e538e49d52be/pypdf-6.0.0-py3-none-any.whl", hash = "sha256:56ea60100ce9f11fc3eec4f359da15e9aec3821b036c1f06d2b660d35683abb8", size = 310465, upload-time = "2025-08-11T14:22:00.481Z" },
 ]
 
-[[package]]
-name = "pypdf2"
-version = "3.0.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/9f/bb/18dc3062d37db6c491392007dfd1a7f524bb95886eb956569ac38a23a784/PyPDF2-3.0.1.tar.gz", hash = "sha256:a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440", size = 227419, upload-time = "2022-12-31T10:36:13.13Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/8e/5e/c86a5643653825d3c913719e788e41386bee415c2b87b4f955432f2de6b2/pypdf2-3.0.1-py3-none-any.whl", hash = "sha256:d16e4205cfee272fbdc0568b68d82be796540b1537508cef59388f839c191928", size = 232572, upload-time = "2022-12-31T10:36:10.327Z" },
-]
-
 [[package]]
 name = "pysocks"
 version = "1.7.1"

aiagents4pharma-1.45.0/.github/CODEOWNERS

@@ -1,20 +0,0 @@
-# Global code owners - will be automatically requested for review on all PRs
-* @gurdeep330
-
-# Specific module owners
-/aiagents4pharma/talk2biomodels/ @gurdeep330
-/aiagents4pharma/talk2scholars/ @gurdeep330
-/aiagents4pharma/talk2cells/ @gurdeep330
-/aiagents4pharma/talk2knowledgegraphs/ @gurdeep330
-/aiagents4pharma/talk2aiagents4pharma/ @gurdeep330
-
-# CI/CD and configuration
-/.github/ @gurdeep330
-/pyproject.toml @gurdeep330
-/uv.lock @gurdeep330
-/mkdocs.yml @gurdeep330
-
-# Documentation
-/docs/ @gurdeep330
-/README.md @gurdeep330
-/CONTRIBUTING.md @gurdeep330

aiagents4pharma-1.45.0/aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py

@@ -1,53 +0,0 @@
-"""
-Test cases for utils/pubchem_utils.py
-"""
-
-from ..utils import pubchem_utils
-
-
-def test_cas_rn2pubchem_cid():
-    """
-    Test the casRN2pubchem_cid function.
-
-    The CAS RN for ethyl cabonate is 105-58-8.
-    The PubChem CID for ethyl cabonate is 7766.
-    """
-    casrn = "105-58-8"
-    pubchem_cid = pubchem_utils.cas_rn2pubchem_cid(casrn)
-    assert pubchem_cid == 7766
-
-
-def test_external_id2pubchem_cid():
-    """
-    Test the external_id2pubchem_cid function.
-
-    The DrugBank ID for Alclometasone is DB00240.
-    The PubChem CID for Alclometasone is 5311000.
-
-    The CTD ID for Butylated Hydroxyanisole is D002083
-    The PubChem CID for Butylated Hydroxyanisole is 24667.
-    """
-    drugbank_id = "DB00240"
-    pubchem_cid = pubchem_utils.external_id2pubchem_cid("drugbank", drugbank_id)
-    assert pubchem_cid == 5311000
-
-    ctd_id = "D002083"
-    pubchem_cid = pubchem_utils.external_id2pubchem_cid(
-        "comparative toxicogenomics database", ctd_id
-    )
-    assert pubchem_cid == 8456
-
-
-def test_pubchem_cid_description():
-    """
-    Test the pubchem_cid_description function.
-
-    The PubChem CID for Alclometasone is 5311000.
-    The description for Alclometasone starts with
-        "Alclometasone is a prednisolone compound having an alpha-chloro substituent".
-    """
-    pubchem_cid = 5311000
-    description = pubchem_utils.pubchem_cid_description(pubchem_cid)
-    assert description.startswith(
-        "Alclometasone is a prednisolone compound having an alpha-chloro substituent"
-    )