PyPI - aiagents4pharma - Versions diffs - 1.46.2__tar.gz → 1.46.3__tar.gz - Mend

aiagents4pharma 1.46.2tar.gz → 1.46.3tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (561) hide show

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/docker_build.yml RENAMED Viewed

@@ -26,7 +26,7 @@ jobs:
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
@@ -48,7 +48,7 @@ jobs:
       version: ${{ steps.get_version.outputs.version }}
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
@@ -73,7 +73,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Login to Docker Hub
         uses: docker/login-action@v3
@@ -98,7 +98,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Login to Docker Hub
         uses: docker/login-action@v3
@@ -123,7 +123,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Login to Docker Hub
         uses: docker/login-action@v3
@@ -148,7 +148,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Login to Docker Hub
         uses: docker/login-action@v3

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/docker_compose_release.yml RENAMED Viewed

@@ -38,7 +38,7 @@ jobs:
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
@@ -100,7 +100,7 @@ jobs:
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Setup release directory
         run: |
@@ -362,7 +362,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Create Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ needs.detect-changes.outputs.version }}
           name: "AIAgents4Pharma ${{ needs.detect-changes.outputs.version }}"

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/mkdocs_deploy.yml RENAMED Viewed

@@ -15,7 +15,7 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Configure Git Credentials
         run: |
@@ -23,7 +23,7 @@ jobs:
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/package_build.yml RENAMED Viewed

@@ -19,12 +19,12 @@ jobs:
       version: ${{ steps.version.outputs.version }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -75,13 +75,13 @@ jobs:
     steps:
       - name: Download build artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: dist-artifacts
           path: dist/
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/pr-automation.yml RENAMED Viewed

@@ -34,7 +34,7 @@ jobs:
       # Auto-label based on files changed
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Label PR based on files changed
         uses: actions/labeler@v5

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/release.yml RENAMED Viewed

@@ -20,12 +20,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -82,7 +82,7 @@ jobs:
           skip-existing: true
       - name: Create GitHub Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2
         with:
           files: dist/*
           tag_name: ${{ env.RELEASE_VERSION }}

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/security_audit.yml RENAMED Viewed

@@ -24,10 +24,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -71,16 +71,16 @@ jobs:
     if: always()
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Download reports
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           pattern: "*-report*"
           merge-multiple: true
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -111,10 +111,10 @@ jobs:
     if: always()
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Download all reports
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           pattern: "*-report*"
           merge-multiple: true

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/sonarcloud.yml RENAMED Viewed

@@ -21,13 +21,13 @@ jobs:
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0 # Shallow clones should be disabled for better analysis
           ref: ${{ github.event.workflow_run.head_branch }}
       - name: Download test artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           run-id: ${{ github.event.workflow_run.id }}
@@ -43,7 +43,7 @@ jobs:
           fi
       - name: SonarCloud Scan
-        uses: SonarSource/sonarqube-scan-action@v5.0.0
+        uses: SonarSource/sonarqube-scan-action@v5.3.1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2aiagents4pharma.yml RENAMED Viewed

@@ -22,12 +22,12 @@ jobs:
     name: Code Quality
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -76,12 +76,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -169,7 +169,7 @@ jobs:
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           file: ./coverage.xml
           flags: talk2aiagents4pharma

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2biomodels.yml RENAMED Viewed

@@ -19,12 +19,12 @@ jobs:
     name: Code Quality
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -73,12 +73,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -106,7 +106,7 @@ jobs:
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           file: ./coverage.xml
           flags: talk2biomodels

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2cells.yml RENAMED Viewed

@@ -19,12 +19,12 @@ jobs:
     name: Code Quality
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -73,12 +73,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -106,7 +106,7 @@ jobs:
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           file: ./coverage.xml
           flags: talk2cells

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2knowledgegraphs.yml RENAMED Viewed

@@ -20,12 +20,12 @@ jobs:
     name: Code Quality
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -74,12 +74,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -167,7 +167,7 @@ jobs:
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           file: ./coverage.xml
           flags: talk2knowledgegraphs

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/.github/workflows/tests_talk2scholars.yml RENAMED Viewed

@@ -21,12 +21,12 @@ jobs:
     name: Code Quality
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python
         run: uv python install 3.12
@@ -75,12 +75,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v4
+        uses: astral-sh/setup-uv@v6
       - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
@@ -108,7 +108,7 @@ jobs:
       - name: Upload coverage to Codecov
         if: matrix.os == 'ubuntu-latest'
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           file: ./coverage.xml
           flags: talk2scholars

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.46.2
+Version: 1.46.3
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
@@ -51,7 +51,7 @@ Requires-Dist: openpyxl==3.1.5
 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: plotly==6.3.0
 Requires-Dist: pubchempy==1.0.4
 Requires-Dist: pyarrow==21.0.0
 Requires-Dist: pydantic==2.11.7

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/package-lock.json RENAMED Viewed

@@ -10,7 +10,7 @@
 				"@semantic-release/github": "^11.0.1",
 				"semantic-release": "^24.0.0"
 			},
-			"version": "1.46.2"
+			"version": "1.46.3"
 		},
 		"node_modules/@babel/code-frame": {
 			"version": "7.26.2",
@@ -11110,5 +11110,5 @@
 			"dev": true
 		}
 	},
-	"version": "1.46.2"
+	"version": "1.46.3"
 }

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/package.json RENAMED Viewed

@@ -26,5 +26,5 @@
 			]
 		]
 	},
-	"version": "1.46.2"
+	"version": "1.46.3"
 }

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/pyproject.toml RENAMED Viewed

@@ -52,7 +52,7 @@ dependencies = [
   "openpyxl==3.1.5",
   "pandas==2.3.2",
   "pcst_fast==1.0.10",
-  "plotly==5.24.1",
+  "plotly==6.3.0",
   "plotly-express==0.4.1",
   "pubchempy==1.0.4",
   "pydantic==2.11.7",
@@ -85,7 +85,7 @@ dependencies = [
   "cloudscraper==1.2.71",
   "azure-identity==1.24.0",
 ]
-version = "1.46.2"
+version = "1.46.3"
 [project.optional-dependencies]
 dev = [
@@ -133,7 +133,7 @@ extension-pkg-allow-list = ["pcst_fast"]
 disable = ["R0801", "R0902", "W0221", "W0122"]
 [tool.ruff]
-target-version = "1.46.2"
+target-version = "1.46.3"
 line-length = 100
 [tool.ruff.lint]
@@ -155,7 +155,7 @@ ignore = [
 "__init__.py" = ["F401"]
 [tool.mypy]
-python_version = "1.46.2"
+python_version = "1.46.3"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true

{aiagents4pharma-1.46.2 → aiagents4pharma-1.46.3}/uv.lock RENAMED Viewed

@@ -162,7 +162,7 @@ requires-dist = [
     { name = "pandas", specifier = "==2.3.2" },
     { name = "pcst-fast", specifier = "==1.0.10" },
     { name = "pip-audit", marker = "extra == 'dev'", specifier = "==2.9.0" },
-    { name = "plotly", specifier = "==5.24.1" },
+    { name = "plotly", specifier = "==6.3.0" },
     { name = "plotly-express", specifier = "==0.4.1" },
     { name = "pre-commit", marker = "extra == 'dev'", specifier = "==4.3.0" },
     { name = "pubchempy", specifier = "==1.0.4" },
@@ -3837,15 +3837,15 @@ wheels = [
 [[package]]
 name = "plotly"
-version = "5.24.1"
+version = "6.3.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
+    { name = "narwhals" },
     { name = "packaging" },
-    { name = "tenacity" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/79/4f/428f6d959818d7425a94c190a6b26fbc58035cbef40bf249be0b62a9aedd/plotly-5.24.1.tar.gz", hash = "sha256:dbc8ac8339d248a4bcc36e08a5659bacfe1b079390b8953533f4eb22169b4bae", size = 9479398, upload-time = "2024-09-12T15:36:31.068Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/a0/64/850de5076f4436410e1ce4f6a69f4313ef6215dfea155f3f6559335cad29/plotly-6.3.0.tar.gz", hash = "sha256:8840a184d18ccae0f9189c2b9a2943923fd5cae7717b723f36eef78f444e5a73", size = 6923926, upload-time = "2025-08-12T20:22:14.127Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/e5/ae/580600f441f6fc05218bd6c9d5794f4aef072a7d9093b291f1c50a9db8bc/plotly-5.24.1-py3-none-any.whl", hash = "sha256:f67073a1e637eb0dc3e46324d9d51e2fe76e9727c892dde64ddf1e1b51f29089", size = 19054220, upload-time = "2024-09-12T15:36:24.08Z" },
+    { url = "https://files.pythonhosted.org/packages/95/a9/12e2dc726ba1ba775a2c6922d5d5b4488ad60bdab0888c337c194c8e6de8/plotly-6.3.0-py3-none-any.whl", hash = "sha256:7ad806edce9d3cdd882eaebaf97c0c9e252043ed1ed3d382c3e3520ec07806d4", size = 9791257, upload-time = "2025-08-12T20:22:09.205Z" },
 ]
 [[package]]