EvoScientist 0.0.1.dev4__py3-none-any.whl → 0.1.0rc2__py3-none-any.whl

{evoscientist-0.0.1.dev4.dist-info → evoscientist-0.1.0rc2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: EvoScientist
-Version: 0.0.1.dev4
+Version: 0.1.0rc2
 Summary: EvoScientist: Towards Self-Evolving AI Scientists for End-to-End Scientific Discovery
 Author: Xi Zhang
 Maintainer: Xi Zhang
@@ -16,14 +16,11 @@ License-File: LICENSE
 Requires-Dist: deepagents>=0.3.6
 Requires-Dist: langchain>=1.2
 Requires-Dist: langchain-anthropic>=1.3
-Requires-Dist: langchain-openai>=0.3
-Requires-Dist: langchain-nvidia-ai-endpoints>=0.3
+Requires-Dist: anthropic>=0.76
 Requires-Dist: tavily-python>=0.7
 Requires-Dist: pyyaml>=6.0
 Requires-Dist: rich>=14.0
 Requires-Dist: prompt-toolkit>=3.0
-Requires-Dist: questionary>=2.0.1
-Requires-Dist: typer>=0.12
 Requires-Dist: python-dotenv>=1.0
 Requires-Dist: langgraph-cli[inmem]>=0.4
 Requires-Dist: httpx>=0.27
@@ -31,8 +28,6 @@ Requires-Dist: markdownify>=0.14
 Provides-Extra: dev
 Requires-Dist: pytest>=8.0; extra == "dev"
 Requires-Dist: pytest-cov>=5.0; extra == "dev"
-Requires-Dist: ruff>=0.5; extra == "dev"
-Requires-Dist: build>=1.0; extra == "dev"
 Dynamic: license-file
 
 <!-- Add logo here -->
@@ -46,12 +41,11 @@ Dynamic: license-file
 
 <a href="https://git.io/typing-svg"><img src="https://readme-typing-svg.demolab.com?font=Fira+Code&pause=1000&width=435&lines=Towards+Self-Evolving+AI+Scientists+for+End-to-End+Scientific+Discovery" alt="Typing SVG" /></a>
 
-[![PyPI](https://img.shields.io/badge/PyPI-EvoScientist%20v0.0.1-3da9fc?style=for-the-badge&logo=python&logoColor=3da9fc)](https://pypi.org/project/EvoScientist/)
-[![Project Page](https://img.shields.io/badge/Project-Page-ff8e3c?style=for-the-badge&logo=googlelens&logoColor=ff8e3c)]()
+[![Project Page](https://img.shields.io/badge/Project-Page-4285F4?style=for-the-badge&logo=googlelens&logoColor=4285F4)]()
 [![arXiv](https://img.shields.io/badge/arXiv-xxxx.xxxx-b31b1b?style=for-the-badge&logo=arxiv&logoColor=b31b1b)]()
+[![Gradio Demo](https://img.shields.io/badge/Gradio-Online_Demo-FFCC00?style=for-the-badge&logo=gradio&logoColor=yellow&labelColor=grey)]()
+[![Evaluation Split](https://img.shields.io/badge/HF-Test_Dataset-AECBFA?style=for-the-badge&logo=huggingface&logoColor=FFCC00&labelColor=grey)]()
 [![License](https://img.shields.io/badge/License-MIT-green?style=for-the-badge)]()
-<!-- [![Gradio Demo](https://img.shields.io/badge/Gradio-Online_Demo-FFCC00?style=for-the-badge&logo=gradio&logoColor=yellow&labelColor=grey)]()
-[![Evaluation Split](https://img.shields.io/badge/HF-Test_Dataset-AECBFA?style=for-the-badge&logo=huggingface&logoColor=FFCC00&labelColor=grey)]() -->
 
 </div>
 
@@ -65,9 +59,7 @@ Dynamic: license-file
 
 
 ## 📖 Contents
-- [🤖 Supported Models](#-supported-models)
 - [⛏️ Installation](#️-installation)
-- [🔑 API Key Configuration](#-api-key-configuration)
 - [⚡ Quick Start](#-quick-start)
   - [CLI Inference](#cli-inference)
   - [Script Inference](#script-inference)
@@ -78,24 +70,6 @@ Dynamic: license-file
 - [📦 Codebase Contributors](#-codebase-contributors)
 - [📜 License](#-license)
 
-## 🤖 Supported Models
-
-| Provider | Short Name | Model ID |
-|----------|-----------|----------|
-| Anthropic | `claude-sonnet-4-5` | `claude-sonnet-4-5-20250929` |
-| Anthropic | `claude-opus-4-5` | `claude-opus-4-5-20251101` |
-| Anthropic | `claude-3-5-sonnet` | `claude-3-5-sonnet-20241022` |
-| Anthropic | `claude-3-5-haiku` | `claude-3-5-haiku-20241022` |
-| OpenAI | `gpt-4o` | `gpt-4o` |
-| OpenAI | `gpt-4o-mini` | `gpt-4o-mini` |
-| OpenAI | `o1` | `o1` |
-| OpenAI | `o1-mini` | `o1-mini` |
-| NVIDIA | `glm4.7` | `z-ai/glm4.7` |
-| NVIDIA | `deepseek-v3.1` | `deepseek-ai/deepseek-v3.1-terminus` |
-| NVIDIA | `nemotron-nano` | `nvidia/nemotron-3-nano-30b-a3b` |
-
-You can also use any full model ID directly — the provider will be inferred automatically.
-
 ## ⛏️ Installation
 
 > [!TIP]  
@@ -131,56 +105,6 @@ uv pip install -e .
 
 </details>
 
-## 🔑 API Key Configuration
-
-EvoScientist requires API keys for LLM inference and web search. You can configure them in three ways:
-
-### Option A: Interactive Setup Wizard (Recommended)
-
-```Shell
-EvoSci onboard
-```
-
-The wizard guides you through selecting a provider, entering API keys, choosing a model, and configuring workspace settings. Keys are validated automatically.
-
-### Option B: Environment Variables (Global)
-
-Set keys directly in your terminal session. Add these to your shell profile (`~/.bashrc`, `~/.zshrc`, etc.) to persist across sessions:
-
-```Shell
-export ANTHROPIC_API_KEY="your_anthropic_api_key_here"
-export TAVILY_API_KEY="your_tavily_api_key_here"
-
-# Optional: OpenAI or NVIDIA provider
-export OPENAI_API_KEY="your_openai_api_key_here"
-export NVIDIA_API_KEY="your_nvidia_api_key_here"
-```
-
-### Option C: `.env` File (Project-level)
-
-Create a `.env` file in the project root. This keeps keys scoped to the project and out of your shell history:
-
-```Shell
-cp .env.example .env
-```
-
-Then edit `.env` and fill in your keys:
-
-```
-ANTHROPIC_API_KEY=your_anthropic_api_key_here
-TAVILY_API_KEY=your_tavily_api_key_here
-```
-
-> [!WARNING]
-> Never commit `.env` files containing real API keys to version control. The `.env` file is already included in `.gitignore`.
-
-| Key | Required | Description |
-|-----|----------|-------------|
-| `ANTHROPIC_API_KEY` | For Anthropic | Anthropic API key for Claude ([console.anthropic.com](https://console.anthropic.com/)) |
-| `OPENAI_API_KEY` | For OpenAI | OpenAI API key for GPT models ([platform.openai.com](https://platform.openai.com/)) |
-| `NVIDIA_API_KEY` | For NVIDIA | NVIDIA API key for NIM models ([build.nvidia.com](https://build.nvidia.com/)) |
-| `TAVILY_API_KEY` | Yes | Tavily API key for web search ([app.tavily.com](https://app.tavily.com/)) |
-
 ## ⚡ Quick Start
 
 ### CLI Inference  
@@ -189,80 +113,11 @@ You can perform inference directly from the command line using our CLI tool:
 ![demo](./assets/EvoScientist_cli.png)
 
 ```Shell
-python -m EvoScientist 
-```
-or
-```Shell
-EvoSci # or EvoScientist
+python -m EvoScientist
 ```
-**Optional arguments:**
-
-```
---mode <mode>      Workspace mode: 'daemon' (persistent) or 'run' (isolated per-session)
---workdir <path>   Override workspace directory for this session
---use-cwd          Use current working directory as workspace
---thread-id <id>   Resume a conversation thread
---no-thinking      Disable thinking display
--p, --prompt <q>   Single-shot mode: execute query and exit
-```
-
-**Configuration commands:**
-
-```Shell
-EvoSci onboard                # Interactive setup wizard
-EvoSci onboard --skip-validation  # Skip API key validation
-EvoSci config                 # List all configuration values
-EvoSci config get <key>       # Get a single value
-EvoSci config set <key> <val> # Set a single value
-EvoSci config reset --yes     # Reset to defaults
-EvoSci config path            # Show config file path
-```
-
-**Interactive Commands:**
-
-| Command | Description |
-|---------|-------------|
-| `/exit` | Quit the session |
-| `/new` | Start a new session (new workspace + thread) |
-| `/thread` | Show current thread ID and workspace path |
-| `/skills` | List installed user skills |
-| `/install-skill <source>` | Install a skill from local path or GitHub |
-| `/uninstall-skill <name>` | Uninstall a user-installed skill |
-
-**Skill Installation Examples:**
+**Optional arguments:**  
 
-```bash
-# Install from local path
-/install-skill ./my-skill
-
-# Install from GitHub URL
-/install-skill https://github.com/owner/repo/tree/main/skill-name
-
-# Install from GitHub shorthand
-/install-skill owner/repo@skill-name
-```
-
-### Runtime Directories
-
-By default, the **workspace** is created under the current directory:
-
-```
-./workspace/
-  memory/   # shared MEMORY.md (persistent across sessions)
-  skills/   # user-installed skills
-  runs/     # per-session workspaces
-```
-
-You can force workspace to be the current directory via `--use-cwd`.
-
-Override individual paths via environment variables:
-
-| Variable | Default | Description |
-|----------|---------|-------------|
-| `EVOSCIENTIST_WORKSPACE_DIR` | `./workspace` | Root workspace directory |
-| `EVOSCIENTIST_RUNS_DIR` | `./workspace/runs` | Per-session run directories |
-| `EVOSCIENTIST_MEMORY_DIR` | `./workspace/memory` | Shared memory storage |
-| `EVOSCIENTIST_SKILLS_DIR` | `./workspace/skills` | User-installed skills |
+> TODO
 
 ### Script Inference
 ```python

{evoscientist-0.0.1.dev4.dist-info → evoscientist-0.1.0rc2.dist-info}/RECORD

@@ -1,20 +1,13 @@
-EvoScientist/EvoScientist.py,sha256=qhiCOOZvH6cmjLiKRMvfr74xJM7x-dZrrRoX9xrfLtQ,6053
-EvoScientist/__init__.py,sha256=BN8yi3iCIaq2gNfKORrI9OvMq49a2LrYWgEqW86vYLw,1120
+EvoScientist/EvoScientist.py,sha256=j0J-bIIxAvG1acsDCcEYmb4FIYoyibdRSQSkzoQUcg4,4627
+EvoScientist/__init__.py,sha256=yj4YJUPldtq4xx8geadIoZ1n-BmgsM2Z_S2W8ld9S1k,702
 EvoScientist/__main__.py,sha256=P5USQ_BiiY0TBhtajGMuX5AMXlQ5joz1kvljHeacqmA,91
-EvoScientist/backends.py,sha256=3fIYRdOecL-KZx2hSNolsLO-2_rMzey-NpVMDMN701U,13355
-EvoScientist/cli.py,sha256=5y_yTBhLnXxI5JVFawcYbsbDEWMED_t2-X4LVbT24kY,25978
-EvoScientist/config.py,sha256=rXD_qlrTxP3HLH7H6DxvqKP4WwymyrzRyS8665igd6k,8649
-EvoScientist/memory.py,sha256=ZgITkiLezjAeo9z12UWRZurE1hZU7ehF-SAKrchPIEs,26475
-EvoScientist/middleware.py,sha256=hBHov8wFhe-AS-C84BFRDgikl5q8Xb9AMU4FfNxs9Jg,2620
-EvoScientist/onboard.py,sha256=x6THI4ryTMTBQBb90JRFhcZmPsc970yh77_VCuNqwm8,22200
-EvoScientist/paths.py,sha256=r3u632RJXfl8KPVhWBwVKPx9zFbvj1CZCIf7NeFBja4,1346
+EvoScientist/backends.py,sha256=yKI5fofVd3sDxJp5BEaqPsXjIOrKrpge1KnFG-X7gzU,12321
+EvoScientist/cli.py,sha256=-7iL6NUjW5CmLKx1BLd0d-Y2DtcXPcoMOCdOgA6X-_E,59946
+EvoScientist/middleware.py,sha256=ai2SZjSNtGCMQdFiMELPJ1t0uKPDZ199Lp5dEr5EnTo,931
 EvoScientist/prompts.py,sha256=ni-qHoEoM703xtfD4J3IlvwAWPcW8gcNiCBVjRJoy3g,10692
-EvoScientist/skills_manager.py,sha256=r1ZCnZkFij-uRwj09FmT67VFR5eRgd3ynzKWmykQJeI,12205
 EvoScientist/subagent.yaml,sha256=yoFlMJWitLlYuOe4_44EPG6vjpNP_txHBlqr-kNX2GM,6130
-EvoScientist/tools.py,sha256=7rCq3Sy74qAKEKnttvy9H7-LB8moXeYK0h7xRJnZJGk,6772
+EvoScientist/tools.py,sha256=oYaJN8tl_NCw6PLFFNRZbjPB9-VriVcpVb6Zp-d_xVQ,4223
 EvoScientist/utils.py,sha256=GuWMRMkPHYgUOtoPZA0ErIt4FUBE4NMkz_OZluxYyRo,6801
-EvoScientist/llm/__init__.py,sha256=A3nQPKGP6qqh2K72_NZlUozNNwfD4jcEMyBerne9IGc,363
-EvoScientist/llm/models.py,sha256=3AhHG__OLbnQlgB3kIM3Ejf9kU2Cv6rDzc7uT5eKzYk,3335
 EvoScientist/skills/accelerate/SKILL.md,sha256=Ju_xLlGW3bZBWQO_8FWThkP155jE2atq9Ww0Zn8XwEs,8328
 EvoScientist/skills/accelerate/references/custom-plugins.md,sha256=Gy8c9dcKFV93ksrRKkZr5DFbeH_iHgGzbTK_N0aTwCA,11781
 EvoScientist/skills/accelerate/references/megatron-integration.md,sha256=ad7cw8eMGX3vqGUxQSVBuWpiQJDAr9eHqWfPhlEXJz0,11252
@@ -23,11 +16,14 @@ EvoScientist/skills/bitsandbytes/SKILL.md,sha256=3VM2RakwcfyTM6Yul6MwgDnUqHPV-3F
 EvoScientist/skills/bitsandbytes/references/memory-optimization.md,sha256=a8y1Mt5qkEeFylaRRPuGSKGnBXIL2JT6xFDdW-qBBWc,12642
 EvoScientist/skills/bitsandbytes/references/qlora-training.md,sha256=E2Nrxy-_gLz6nEgA30MQ_RQ4mdRX3w-aJO7f16RJriQ,12015
 EvoScientist/skills/bitsandbytes/references/quantization-formats.md,sha256=U1nvDKjlg305DaYvlyJW2SS5NMNVI2XHD__m1YEErH4,10258
+EvoScientist/skills/clip/SKILL.md,sha256=n8rPHAQdce8eYcfKwrt6LELD0Z1sKg_C5fWjyWQbej4,6884
+EvoScientist/skills/clip/references/applications.md,sha256=aC_DE-Y8775GbtDv30gEiUajq7KS5fMs9AWPz1lpKuk,5360
 EvoScientist/skills/find-skills/SKILL.md,sha256=fvjNEIEVsOauW_LuEKshYkbvd19pRdVV-rXcQqfFeKo,4169
 EvoScientist/skills/find-skills/scripts/install_skill.py,sha256=sbLrZeY887LeiKcvA7f3AuxJI98PwGeAVyttVXxs_eA,6332
 EvoScientist/skills/flash-attention/SKILL.md,sha256=3GL1xP6jFkjZhs9ZcE-61FbkB5d4p7NvVXm9MvxTG58,10190
 EvoScientist/skills/flash-attention/references/benchmarks.md,sha256=Jk_zBgr4JMMvem48DgIIw4ZGxyiyKS-zXt6SOjjWC2s,7129
 EvoScientist/skills/flash-attention/references/transformers-integration.md,sha256=ievo4gdW7iGBA6EUTUaC6WCg-qB4cMJYhTC8jSbEQaE,7427
+EvoScientist/skills/langgraph-docs/SKILL.md,sha256=8Whxox7qKnNti7ijSJlDtscsk2dPXeNFFdr8dKWHAfY,1054
 EvoScientist/skills/llama-cpp/SKILL.md,sha256=10yqRUg_Wzxr1iZ-ObREYnmJ_5D9uEtsLnw9pN3xQ-8,5912
 EvoScientist/skills/llama-cpp/references/optimization.md,sha256=TomBHAgn9eud65_GCc1EHrGX-w-oXnndjB8nKxSmaf0,1659
 EvoScientist/skills/llama-cpp/references/quantization.md,sha256=x2hqhok9Tg4FLMczti6hvA5dro8bF0Q2zCk6RqSGiT0,4956
@@ -101,17 +97,23 @@ EvoScientist/skills/skill-creator/references/workflows.md,sha256=70hGh31dq0dRGgG
 EvoScientist/skills/skill-creator/scripts/init_skill.py,sha256=C7olC5TKpMsrKLFdrSb9zzca7aTJeXuBIOVcLjPgxzw,10863
 EvoScientist/skills/skill-creator/scripts/package_skill.py,sha256=sx-8s-Ni1cUwjpklX_joPN46UT4GNpU5ZKZISUyhCTE,3288
 EvoScientist/skills/skill-creator/scripts/quick_validate.py,sha256=OBqy09H9XsMjcQFkEwY-_5nQ1IxBV0cIXGFRfpZ9u4c,3523
-EvoScientist/stream/__init__.py,sha256=_mdc88i75D3qlfuIBWpNm4-W5xMYIvM39vERgb53Bkk,1933
-EvoScientist/stream/display.py,sha256=jCyohjfulwgyV-gOa5g5HXsepNLNLjdMdfQE9bt1-ZA,22565
+EvoScientist/skills/tensorboard/SKILL.md,sha256=cXxLBfiLvIiNVMxR-jkK4iXWh7O4b7YW42zH_CYQgCA,15276
+EvoScientist/skills/tensorboard/references/integrations.md,sha256=pkfUfpWJ63q7vLSU_CyPIcK4yrH-46WeMMq0uBAUzUo,16205
+EvoScientist/skills/tensorboard/references/profiling.md,sha256=FHEwLVicAMO9nQJHAI1zLk9EaEJpKy3EWH7IJ4rNM9g,13337
+EvoScientist/skills/tensorboard/references/visualization.md,sha256=Dl72GAjcC7HTggoGlaqGpK9mWfG6IyQgSVO4TdpvOBU,14897
+EvoScientist/skills/vllm/SKILL.md,sha256=j4Yt6lbZa9jQvBlUa92hYWYwZCVQeWFBxI17_4zs4DI,9013
+EvoScientist/skills/vllm/references/optimization.md,sha256=D4YNM3rbHQcj1AcNizFEUX8RGtf2U2BpJ7xnp6AZsaw,5769
+EvoScientist/skills/vllm/references/quantization.md,sha256=X7MOqej77Ep_MEfzfRDAkA0QzS32ZVWBj_1CWjspsnA,6746
+EvoScientist/skills/vllm/references/server-deployment.md,sha256=fbYY7EC4Zf4u-s9GwEw9XcIz_GSjxj0mRRr7l7eVET4,5252
+EvoScientist/skills/vllm/references/troubleshooting.md,sha256=MHrNkI5gZ0AXvSNjcm5rm-GUEAYuPbBkUpCmmAKXYoM,9037
+EvoScientist/stream/__init__.py,sha256=cO30Ujs7mVB1pZjI0AXgaggmPeV6jXgBjt6AKYH42kQ,1219
 EvoScientist/stream/emitter.py,sha256=zmdn8vIXNgkgoWRtanrMtPN2GlsHmZtdFmoqCry3o_o,2978
-EvoScientist/stream/events.py,sha256=dSnHsDGl_HEBbfmQYv40YZVR-RDZPLZFsjlwmO46ch4,17251
 EvoScientist/stream/formatter.py,sha256=vyv89NGoTzxjsWt0teBXX38MZzFLhzMDBUcIH6-slDo,5532
-EvoScientist/stream/state.py,sha256=RX7JOBJLYXu7tdtDx71QR2U8JDHHTsB4GM877z9UKLM,12961
 EvoScientist/stream/tracker.py,sha256=cVWmiTCiwzOh84I7sAXXfgr_HXxOCCCzTvli-XJhthQ,3670
-EvoScientist/stream/utils.py,sha256=yQXhPIzOYzpNUUyDvkQDv1K-Yo0ePkXMtU7fHhRoG64,7718
-evoscientist-0.0.1.dev4.dist-info/licenses/LICENSE,sha256=NsYFy5JSm90lmXcPNQuthVTCVaVcbT4XZ9h5HpAoGIo,1069
-evoscientist-0.0.1.dev4.dist-info/METADATA,sha256=Hi6nET3VH8m2uv_JIcCNrQZJz4jL1OfbMd6jM5tGEY0,13901
-evoscientist-0.0.1.dev4.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-evoscientist-0.0.1.dev4.dist-info/entry_points.txt,sha256=mGxz9_-jfGhwkdiiVGTQ9IQEhzLixWJoPNU39_boWMM,154
-evoscientist-0.0.1.dev4.dist-info/top_level.txt,sha256=XBZouSd9lQfNn0Fus6jQb9nqdXzAbKyzh987Jt3A2-A,13
-evoscientist-0.0.1.dev4.dist-info/RECORD,,
+EvoScientist/stream/utils.py,sha256=36e5aaEZVpwTZnqO1qlVs2QTr04JbmWuvHMSbor49xM,7278
+evoscientist-0.1.0rc2.dist-info/licenses/LICENSE,sha256=NsYFy5JSm90lmXcPNQuthVTCVaVcbT4XZ9h5HpAoGIo,1069
+evoscientist-0.1.0rc2.dist-info/METADATA,sha256=2a_6L4t6tuldTQEvLYZFyoNgOeOFxFq5Pr0hdO0YxOY,8581
+evoscientist-0.1.0rc2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+evoscientist-0.1.0rc2.dist-info/entry_points.txt,sha256=AQTfRSD-9-fgD1ViOdbGcvhsNeaUNgvmNqLkNY7o7Zw,55
+evoscientist-0.1.0rc2.dist-info/top_level.txt,sha256=XBZouSd9lQfNn0Fus6jQb9nqdXzAbKyzh987Jt3A2-A,13
+evoscientist-0.1.0rc2.dist-info/RECORD,,

evoscientist-0.1.0rc2.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+evoscientist = EvoScientist.cli:main

EvoScientist/config.py

@@ -1,274 +0,0 @@
-"""Configuration management for EvoScientist.
-
-Handles loading, saving, and merging configuration from multiple sources
-with the following priority (highest to lowest):
-    CLI arguments > Environment variables > Config file > Defaults
-"""
-
-from __future__ import annotations
-
-import os
-from dataclasses import dataclass, asdict, fields
-from pathlib import Path
-from typing import Any, Literal
-
-import yaml
-
-
-# =============================================================================
-# Configuration paths
-# =============================================================================
-
-def get_config_dir() -> Path:
-    """Get the configuration directory path.
-
-    Uses XDG_CONFIG_HOME if set, otherwise ~/.config/evoscientist/
-    """
-    xdg_config = os.environ.get("XDG_CONFIG_HOME")
-    if xdg_config:
-        return Path(xdg_config) / "evoscientist"
-    return Path.home() / ".config" / "evoscientist"
-
-
-def get_config_path() -> Path:
-    """Get the path to the configuration file."""
-    return get_config_dir() / "config.yaml"
-
-
-# =============================================================================
-# Configuration dataclass
-# =============================================================================
-
-@dataclass
-class EvoScientistConfig:
-    """EvoScientist configuration settings.
-
-    Attributes:
-        anthropic_api_key: Anthropic API key for Claude models.
-        openai_api_key: OpenAI API key for GPT models.
-        tavily_api_key: Tavily API key for web search.
-        provider: Default LLM provider ('anthropic' or 'openai').
-        model: Default model name (short name or full ID).
-        default_mode: Default workspace mode ('daemon' or 'run').
-        default_workdir: Default workspace directory (empty = use ./workspace).
-        max_concurrent: Maximum concurrent sub-agents.
-        max_iterations: Maximum delegation iterations.
-        show_thinking: Whether to show thinking panels in CLI.
-    """
-
-    # API Keys
-    anthropic_api_key: str = ""
-    openai_api_key: str = ""
-    nvidia_api_key: str = ""
-    tavily_api_key: str = ""
-
-    # LLM Settings
-    provider: str = "anthropic"
-    model: str = "claude-sonnet-4-5"
-
-    # Workspace Settings
-    default_mode: Literal["daemon", "run"] = "daemon"
-    default_workdir: str = ""
-
-    # Agent Parameters
-    max_concurrent: int = 3
-    max_iterations: int = 3
-
-    # UI Settings
-    show_thinking: bool = True
-
-
-# =============================================================================
-# Config file operations
-# =============================================================================
-
-def load_config() -> EvoScientistConfig:
-    """Load configuration from file.
-
-    Returns:
-        EvoScientistConfig instance with values from file, or defaults if
-        file doesn't exist.
-    """
-    config_path = get_config_path()
-
-    if not config_path.exists():
-        return EvoScientistConfig()
-
-    try:
-        with open(config_path) as f:
-            data = yaml.safe_load(f) or {}
-
-        # Filter to only valid fields
-        valid_fields = {f.name for f in fields(EvoScientistConfig)}
-        filtered_data = {k: v for k, v in data.items() if k in valid_fields}
-
-        return EvoScientistConfig(**filtered_data)
-    except Exception:
-        # On any error, return defaults
-        return EvoScientistConfig()
-
-
-def save_config(config: EvoScientistConfig) -> None:
-    """Save configuration to file.
-
-    Args:
-        config: EvoScientistConfig instance to save.
-    """
-    config_path = get_config_path()
-    config_path.parent.mkdir(parents=True, exist_ok=True)
-
-    data = asdict(config)
-
-    # Save all fields including empty API keys (users can set them via env vars instead)
-    with open(config_path, "w") as f:
-        yaml.safe_dump(data, f, default_flow_style=False, sort_keys=False)
-
-
-def reset_config() -> None:
-    """Reset configuration to defaults by deleting the config file."""
-    config_path = get_config_path()
-    if config_path.exists():
-        config_path.unlink()
-
-
-# =============================================================================
-# Config value operations
-# =============================================================================
-
-def get_config_value(key: str) -> Any:
-    """Get a single configuration value.
-
-    Args:
-        key: Configuration key name.
-
-    Returns:
-        The value, or None if key doesn't exist.
-    """
-    config = load_config()
-    return getattr(config, key, None)
-
-
-def set_config_value(key: str, value: Any) -> bool:
-    """Set a single configuration value.
-
-    Args:
-        key: Configuration key name.
-        value: New value.
-
-    Returns:
-        True if successful, False if key is invalid.
-    """
-    valid_fields = {f.name for f in fields(EvoScientistConfig)}
-    if key not in valid_fields:
-        return False
-
-    config = load_config()
-
-    # Type coercion based on field type
-    field_info = next(f for f in fields(EvoScientistConfig) if f.name == key)
-    field_type = field_info.type
-
-    try:
-        if field_type == "bool" or field_type is bool:
-            if isinstance(value, str):
-                value = value.lower() in ("true", "1", "yes", "on")
-            else:
-                value = bool(value)
-        elif field_type == "int" or field_type is int:
-            value = int(value)
-        elif field_type == "str" or field_type is str:
-            value = str(value)
-    except (ValueError, TypeError):
-        return False
-
-    setattr(config, key, value)
-    save_config(config)
-    return True
-
-
-def list_config() -> dict[str, Any]:
-    """List all configuration values.
-
-    Returns:
-        Dictionary of all configuration key-value pairs.
-    """
-    return asdict(load_config())
-
-
-# =============================================================================
-# Effective configuration (merging sources)
-# =============================================================================
-
-# Environment variable mappings
-_ENV_MAPPINGS = {
-    "anthropic_api_key": "ANTHROPIC_API_KEY",
-    "openai_api_key": "OPENAI_API_KEY",
-    "nvidia_api_key": "NVIDIA_API_KEY",
-    "tavily_api_key": "TAVILY_API_KEY",
-    "default_mode": "EVOSCIENTIST_DEFAULT_MODE",
-    "default_workdir": "EVOSCIENTIST_WORKSPACE_DIR",
-}
-
-
-def get_effective_config(cli_overrides: dict[str, Any] | None = None) -> EvoScientistConfig:
-    """Get effective configuration by merging all sources.
-
-    Priority (highest to lowest):
-        1. CLI arguments (cli_overrides)
-        2. Environment variables
-        3. Config file
-        4. Defaults
-
-    Args:
-        cli_overrides: Dictionary of CLI argument overrides.
-
-    Returns:
-        EvoScientistConfig with merged values.
-    """
-    # Start with file config (includes defaults for missing values)
-    config = load_config()
-    data = asdict(config)
-
-    # Apply environment variable overrides
-    for config_key, env_key in _ENV_MAPPINGS.items():
-        env_value = os.environ.get(env_key)
-        if env_value:
-            # Type coercion
-            field_info = next(f for f in fields(EvoScientistConfig) if f.name == config_key)
-            field_type = field_info.type
-            if field_type == "bool" or field_type is bool:
-                data[config_key] = env_value.lower() in ("true", "1", "yes", "on")
-            elif field_type == "int" or field_type is int:
-                try:
-                    data[config_key] = int(env_value)
-                except ValueError:
-                    pass
-            else:
-                data[config_key] = env_value
-
-    # Apply CLI overrides (highest priority)
-    if cli_overrides:
-        for key, value in cli_overrides.items():
-            if value is not None and key in data:
-                data[key] = value
-
-    return EvoScientistConfig(**data)
-
-
-def apply_config_to_env(config: EvoScientistConfig) -> None:
-    """Apply config API keys to environment variables if not already set.
-
-    This allows the config file to provide API keys that downstream
-    libraries (like langchain-anthropic) can pick up.
-
-    Args:
-        config: Configuration to apply.
-    """
-    if config.anthropic_api_key and not os.environ.get("ANTHROPIC_API_KEY"):
-        os.environ["ANTHROPIC_API_KEY"] = config.anthropic_api_key
-    if config.openai_api_key and not os.environ.get("OPENAI_API_KEY"):
-        os.environ["OPENAI_API_KEY"] = config.openai_api_key
-    if config.nvidia_api_key and not os.environ.get("NVIDIA_API_KEY"):
-        os.environ["NVIDIA_API_KEY"] = config.nvidia_api_key
-    if config.tavily_api_key and not os.environ.get("TAVILY_API_KEY"):
-        os.environ["TAVILY_API_KEY"] = config.tavily_api_key

EvoScientist/llm/__init__.py

@@ -1,21 +0,0 @@
-"""LLM module for EvoScientist.
-
-Provides a unified interface for creating chat model instances
-with support for multiple providers.
-"""
-
-from .models import (
-    MODELS,
-    DEFAULT_MODEL,
-    get_chat_model,
-    list_models,
-    get_model_info,
-)
-
-__all__ = [
-    "MODELS",
-    "DEFAULT_MODEL",
-    "get_chat_model",
-    "list_models",
-    "get_model_info",
-]