Skip to content

Feat/adddocssite#91

Merged
Josephrp merged 35 commits intodevfrom
feat/adddocssite
Oct 7, 2025
Merged

Feat/adddocssite#91
Josephrp merged 35 commits intodevfrom
feat/adddocssite

Conversation

@Josephrp
Copy link
Copy Markdown
Collaborator

@Josephrp Josephrp commented Oct 7, 2025

Pull Request

Description

Type of Change

  • 🐛 Bug fix (non-breaking change which fixes an issue)
  • ✨ New feature (non-breaking change which adds functionality)
  • 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • 📚 Documentation update
  • ⚡ Performance improvement
  • 🧹 Code refactoring
  • 🧪 Test addition or update
  • 🔧 Configuration change
  • 🧬 Bioinformatics enhancement
  • 🔄 Workflow improvement

Component

  • Core Workflow Engine
  • PRIME Flow (Protein Engineering)
  • Bioinformatics Flow (Data Fusion)
  • DeepSearch Flow (Web Research)
  • Challenge Flow (Experimental)
  • Tool Registry
  • Agent System
  • Configuration (Hydra)
  • Pydantic Graph
  • Documentation
  • Tests
  • Other:

Related Issues

  • Fixes #
  • Closes #
  • Related to #

Changes Made

Testing

  • I have tested these changes locally
  • I have added/updated tests for my changes
  • All existing tests pass
  • I have tested with different configurations
  • I have tested with different flows (PRIME, Bioinformatics, DeepSearch, etc.)

Test Configuration

# Example test command
uv run deepresearch question="..." app_mode=single_react

Configuration Changes

  • No configuration changes
  • Added new configuration options
  • Modified existing configuration
  • Removed configuration options

Configuration Details

# Example configuration changes
flows:
  new_flow:
    enabled: true
    params:
      new_param: "value"

Documentation

  • No documentation changes needed
  • Updated README
  • Updated API documentation
  • Updated configuration documentation
  • Added code comments
  • Updated examples

Performance Impact

  • No performance impact
  • Performance improvement
  • Performance regression (explain below)

Performance Details

  • Execution time:
  • Memory usage:
  • Other metrics:

Breaking Changes

  • No breaking changes
  • Breaking change (describe below)

Migration Guide

Checklist

  • My code follows the project's style guidelines
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • My changes generate no new warnings
  • I have added tests that prove my fix is effective or that my feature works
  • New and existing unit tests pass locally with my changes
  • Any dependent changes have been merged and published

Additional Notes

Screenshots/Output

Before

After

Reviewer Notes

Josephrp and others added 30 commits October 5, 2025 06:03
Signed-off-by: Tonic <joseph.pollack@emle.eu>
Signed-off-by: Tonic <joseph.pollack@emle.eu>
…in permissions

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Signed-off-by: Tonic <joseph@legml.ai>
Signed-off-by: Tonic <joseph.pollack@emle.eu>
- Add site/ to .gitignore to exclude built documentation
- Exclude mkdocs.yml from YAML check due to Python object references
- Disable black formatter to avoid conflicts with ruff-format
- Apply automatic formatting fixes to all files
- Remove built site files from git tracking
Signed-off-by: Tonic <joseph.pollack@emle.eu>
…casting with cast(dict[str, Any], config_result) in DeepResearch/src/utils/deepsearch_utils.py

Callable Check: Added explicit callable() check for tools_attr.append in DeepResearch/src/statemachines/deep_agent_graph.py
Hash Method: Added __hash__ method to UsageDetails class in DeepResearch/src/datatypes/agent_framework_usage.py to resolve PLW1641 error
Import Organization: Fixed __all__ sorting issues using ruff --fix --unsafe-fixes
Dictionary Iteration: Fixed PLC0206 errors by using .items() for dictionary iteration
Configuration: Added PLC0415 (imports outside top-level) to the ignore list in pyproject.toml since these are common and acceptable in test files
@Josephrp Josephrp merged commit 91aefba into dev Oct 7, 2025
9 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant