feat : adds rag

.github/ISSUE_TEMPLATE/bioinformatics.yml

@@ -181,3 +181,5 @@ body:
           required: false
         - label: I can provide additional biological data if needed
           required: false
+
+

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -144,3 +144,5 @@ body:
           required: true
         - label: I am willing to help test the fix
           required: false
+
+

.github/ISSUE_TEMPLATE/config.yml

@@ -9,3 +9,5 @@ contact_links:
   - name: Security Vulnerability
     url: https://github.com/DeepCritical/DeepCritical/security/advisories/new
     about: Report a security vulnerability privately.
+
+

.github/ISSUE_TEMPLATE/documentation.yml

@@ -131,3 +131,5 @@ body:
           required: true
         - label: I am willing to help write or improve the documentation
           required: false
+
+

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -142,3 +142,5 @@ body:
           required: false
         - label: I am willing to help test this feature
           required: false
+
+

.github/ISSUE_TEMPLATE/performance.yml

@@ -179,3 +179,5 @@ body:
           required: true
         - label: I am willing to help test performance improvements
           required: false
+
+

.github/ISSUE_TEMPLATE/question.yml

@@ -123,3 +123,5 @@ body:
           required: true
         - label: I am willing to help improve documentation based on the answer
           required: false
+
+

.github/SECURITY.md

@@ -119,3 +119,5 @@ We thank the security research community for helping keep DeepCritical secure. S
 
 **Last Updated**: 2024-01-01
 **Version**: 1.0
+
+

.github/dependabot.yml

@@ -69,3 +69,5 @@ updates:
     labels:
       - "dependencies"
       - "docker"
+
+

.github/pull_request_template.md

@@ -130,3 +130,5 @@ flows:
 
 ## Reviewer Notes
 <!-- Any specific areas you'd like reviewers to focus on -->
+
+

.github/repository-settings.yml

@@ -258,3 +258,5 @@ secrets:
     description: "Serper API key for web search"
   - name: "CODECOV_TOKEN"
     description: "Codecov token for coverage reporting"
+
+

.github/workflows/ci.yml

@@ -1,14 +1,14 @@
-name: CI
+name: CI/CD Pipeline
+
+env:
+  UV_VERSION: "latest"
+  PYTHON_VERSION: "3.11"
 
 on:
   push:
-    branches: [ main, develop ]
+    branches: [ main, dev ]
   pull_request:
-    branches: [ main, develop ]
-
-env:
-  PYTHON_VERSION: "3.10"
-  UV_VERSION: "latest"
+    branches: [ main, dev ]
 
 jobs:
   lint:
@@ -36,12 +36,11 @@ jobs:
         run: uv run ruff format --check .
 
   test:
-    name: Test
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-    
+        python-version: [3.10, 3.11, 3.12]
+
     steps:
       - name: Checkout code
         uses: actions/checkout@v5
@@ -51,18 +50,20 @@ jobs:
         with:
           version: ${{ env.UV_VERSION }}
 
-      - name: Set up Python
+      - name: Set up Python ${{ matrix.python-version }}
         run: uv python install ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: uv sync --dev
 
-      - name: Run tests
-        run: uv run pytest tests/ -v --cov=DeepResearch --cov-report=xml
+      - name: Test with pytest
+        run: |
+          uv run pytest --cov=DeepResearch --cov-report=xml --cov-report=html
 
-      - name: Upload coverage to Codecov
+      - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v5
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           flags: unittests
           name: codecov-umbrella
@@ -126,10 +127,9 @@ jobs:
           path: bandit-report.json
 
   build:
-    name: Build Package
     runs-on: ubuntu-latest
-    needs: [lint, test, integration-test]
-    
+    needs: test
+
     steps:
       - name: Checkout code
         uses: actions/checkout@v5
@@ -152,19 +152,4 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: dist
-          path: dist/
-
-  all-checks:
-    name: All Checks Passed
-    runs-on: ubuntu-latest
-    needs: [lint, test, integration-test, security, build]
-    if: always()
-
-    steps:
-      - name: Check all jobs
-        run: |
-          if [[ "${{ needs.lint.result }}" != "success" || "${{ needs.test.result }}" != "success" || "${{ needs.integration-test.result }}" != "success" || "${{ needs.build.result }}" != "success" ]]; then
-            echo "One or more checks failed"
-            exit 1
-          fi
-          echo "All checks passed!"
+          path: dist/

.github/workflows/dependabot.yml

@@ -33,3 +33,5 @@ jobs:
           target: minor
           merge-method: squash
           merge-commit-message: 'chore(deps): ${{ github.event.pull_request.title }}'
+
+

.github/workflows/release.yml

@@ -177,3 +177,5 @@ jobs:
         run: |
           echo "Conda-forge upload not yet implemented"
           # This would require a conda-forge feedstock
+
+

.gitignore

@@ -2,6 +2,7 @@ example
 .cursor
 outputs
 docs
+tests
 
 # Python
 __pycache__/
@@ -69,6 +70,9 @@ multirun/
 outputs/
 *.log
 
+# GitHub Actions
+.github/workflows/ci.yml
+
 # OS
 .DS_Store
 .DS_Store?

CHANGELOG.md

@@ -93,3 +93,5 @@ See [SECURITY.md](SECURITY.md) for security policy and vulnerability reporting.
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+

CODE_OF_CONDUCT.md

@@ -99,3 +99,5 @@ For answers to common questions about this code of conduct, see the FAQ at [http
 [Mozilla CoC]: https://github.com/mozilla/diversity
 [FAQ]: https://www.contributor-covenant.org/faq
 [translations]: https://www.contributor-covenant.org/translations
+
+

CONTRIBUTING.md

@@ -394,3 +394,5 @@ Contributors will be recognized in:
 - GitHub contributors page
 
 Thank you for contributing to DeepCritical! 🚀
+
+

DeepResearch/src/agents/agent_orchestrator.py

@@ -467,3 +467,6 @@ def _synthesize_results(self, result: Any, user_input: str) -> str:
 
 
 
+
+
+

DeepResearch/src/agents/deep_agent_implementations.py

@@ -502,3 +502,6 @@ def create_agent_orchestrator(agent_types: List[str] = None) -> AgentOrchestrato
 
 
 
+
+
+