Perf/codecovtrigger #8
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Josephrp
commented
Oct 13, 2025
Josephrp
commented
- try hard
* initial commit - adds bio-informatics tools & mcp * initial commit - adds bio-informatics tools & mcp * improves code quality * refactor bioinformatics tools , utils, prompts * adds docs * adds quite a lot of testing , for windows, docker, linux , testcontainers * adds docker tests and related improvements * Potential fix for code scanning alert no. 21: Workflow does not contain permissions Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Signed-off-by: Tonic <[email protected]> * Potential fix for code scanning alert no. 17: Workflow does not contain permissions Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Signed-off-by: Tonic <[email protected]> * adds optional bioinformatics tests * adds optional bioinformatics tests per branch option to allow fail * adds pytest to replace uv * adds dockers , docker tests , tools tests , ci , make file improvements * merge commit * removes docker from ci * removes docker from ci * feat: add bioinformatics MCP servers and tools infrastructure * fix linter types and checks version , fix tests * improves ci
* trigger codecov report
…/DeepCritical into perf/codecovtrigger
* fix: remove misleading @defer decorator comments Removes all references to non-existent @defer decorator from codebase. The @defer decorator never existed in Pydantic AI. Tools are correctly implemented using standard Pydantic AI patterns. Changes: - Removed 16 @defer comments from tool files - Updated README Known Issues section - All tools continue to work correctly (no functional changes) Fixes #2 * feat: add custom LLM model wrappers for Pydantic AI - Implement VLLMModel wrapper around existing VLLMClient - Add OpenAICompatibleModel for vLLM, llama.cpp, TGI servers - Provide factory methods (from_vllm, from_llamacpp, from_tgi) - Include streaming support and message conversion - Add convenience aliases for VLLMModel and LlamaCppModel * fix: update OpenAICompatibleModel to use OllamaProvider and add tests - Replace non-existent OpenAIProvider with OllamaProvider from pydantic_ai - Remove dataclass decorator to properly inherit from OpenAIChatModel - Fix factory methods to pass model_name as positional argument - Add comprehensive test suite with 8 passing tests - Skip integration tests that require actual vLLM servers * refactor: integrate LLM models with Hydra configuration system - Add from_config() method to support Hydra DictConfig - Update all factory methods (from_vllm, from_llamacpp, from_tgi, from_custom) to accept optional config - Support config override via direct parameters - Extract generation settings from config (temperature, max_tokens, etc.) - Add environment variable fallbacks (LLM_BASE_URL, LLM_API_KEY) - Create config files for llamacpp, tgi, and vllm - Update tests to cover both config-based and direct parameter approaches - All 10 tests passing * feat: add LLM client support with Pydantic validation (#10) - Add LLMModelConfig and GenerationConfig datatypes - Remove redundant vllm_model.py - Update openai_compatible_model.py with validation - Rewrite tests to use actual config files (30 tests) * fix: add LLM datatypes to __all__ export list * solves type and style errors * initial commit - adds bio-informatics tools & mcp * initial commit - adds bio-informatics tools & mcp * improves code quality * refactor bioinformatics tools , utils, prompts * adds docs * adds quite a lot of testing , for windows, docker, linux , testcontainers * adds docker tests and related improvements * Potential fix for code scanning alert no. 21: Workflow does not contain permissions Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Signed-off-by: Tonic <[email protected]> * Potential fix for code scanning alert no. 17: Workflow does not contain permissions Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> Signed-off-by: Tonic <[email protected]> * adds optional bioinformatics tests * adds optional bioinformatics tests per branch option to allow fail * adds pytest to replace uv * adds dockers , docker tests , tools tests , ci , make file improvements * merge commit * removes docker from ci * removes docker from ci * feat: add bioinformatics MCP servers and tools infrastructure * fix linter types and checks version , fix tests * improves ci * trigger codecov report * Update CI to upload test results to Codecov for test analytics * Fix Codecov repository slug to use Josephrp/DeepCritical * adds deepcritical/deepcritical repository slug --------- Signed-off-by: Tonic <[email protected]> Signed-off-by: Tonic <[email protected]> Co-authored-by: MarioAderman <[email protected]> Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>
Signed-off-by: Tonic <[email protected]>
* attempts codecov trigger
…/DeepCritical into perf/codecovtrigger
Signed-off-by: Tonic <[email protected]>
* attempts codecov trigger
…/DeepCritical into perf/codecovtrigger
* attempts codecov trigger
Signed-off-by: Tonic <[email protected]>
* adds codecov cli
…/DeepCritical into perf/codecovtrigger
Signed-off-by: Tonic <[email protected]>
* adds codecov components and upload
Signed-off-by: Tonic <[email protected]>
Signed-off-by: Tonic <[email protected]>
…/DeepCritical into perf/codecovtrigger
* fix permissions
…/DeepCritical into perf/codecovtrigger
- attempts ci fix
Signed-off-by: Tonic <[email protected]>
* attempts ci fix for upload
…/DeepCritical into perf/codecovtrigger
Signed-off-by: Tonic <[email protected]>
- try hard
…/DeepCritical into perf/codecovtrigger
- attempts make upload optional
…/DeepCritical into perf/codecovtrigger
Signed-off-by: Tonic <[email protected]>
- try hardest
…/DeepCritical into perf/codecovtrigger
Signed-off-by: Tonic <[email protected]>
…/DeepCritical into perf/codecovtrigger
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