added more stuff lol

.gitignore

@@ -0,0 +1,194 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+.DS_Store
+
+# Ignore Crew engineering team output
+3_crew/engineering_team/output/
+
+# Ignore memory in sidekick
+memory.db-shm
+memory.db-wal
+memory.db
+
+# Ignore Accounts database in capstone project
+6_mcp/accounts.db
+6_mcp/memory/*.db**/.*env*
+**/*.env*
+
+# New Stuff
+
+data/
+output/

README.md

@@ -0,0 +1,11 @@
+---
+title: omicsfuserx-demo
+emoji: "😊"
+colorFrom: red
+colorTo: green
+sdk: gradio
+sdk_version: 6.3.0
+python_version: 3.13.7
+app_file: mycoder/app.py
+pinned: false
+---

pyproject.toml

@@ -0,0 +1,46 @@
+[project]
+name = "agents"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "anthropic>=0.49.0",
+    "autogen-agentchat>=0.4.9.2",
+    "autogen-ext[grpc,mcp,ollama,openai]>=0.4.9.2",
+    "bs4>=0.0.2",
+    "gradio>=5.22.0",
+    "httpx>=0.28.1",
+    "ipywidgets>=8.1.5",
+    "langchain-anthropic>=0.3.10",
+    "langchain-community>=0.3.20",
+    "langchain-experimental>=0.3.4",
+    "langchain-openai>=0.3.9",
+    "langgraph>=0.3.18",
+    "langgraph-checkpoint-sqlite>=2.0.6",
+    "langsmith>=0.3.18",
+    "lxml>=5.3.1",
+    "mcp-server-fetch>=2025.1.17",
+    "mcp[cli]>=1.5.0",
+    "openai>=1.68.2",
+    "openai-agents>=0.0.15",
+    "playwright>=1.51.0",
+    "plotly>=6.0.1",
+    "polygon-api-client>=1.14.5",
+    "psutil>=7.0.0",
+    "pypdf>=5.4.0",
+    "pypdf2>=3.0.1",
+    "python-dotenv>=1.0.1",
+    "requests>=2.32.3",
+    "semantic-kernel>=1.25.0",
+    "sendgrid>=6.11.0",
+    "setuptools>=78.1.0",
+    "smithery>=0.1.0",
+    "speedtest-cli>=2.1.3",
+    "wikipedia>=1.4.0",
+]
+
+[dependency-groups]
+dev = [
+    "ipykernel>=6.29.5",
+]

requirements.txt

@@ -0,0 +1,690 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml -o requirements.txt
+aiofiles==24.1.0
+    # via
+    #   autogen-ext
+    #   gradio
+aiohappyeyeballs==2.6.1
+    # via aiohttp
+aiohttp==3.12.12
+    # via
+    #   langchain-community
+    #   semantic-kernel
+aioice==0.10.1
+    # via aiortc
+aiortc==1.13.0
+    # via semantic-kernel
+aiosignal==1.3.2
+    # via aiohttp
+aiosqlite==0.21.0
+    # via langgraph-checkpoint-sqlite
+annotated-types==0.7.0
+    # via pydantic
+anthropic==0.53.0
+    # via
+    #   agents (pyproject.toml)
+    #   langchain-anthropic
+anyio==4.9.0
+    # via
+    #   anthropic
+    #   gradio
+    #   httpx
+    #   mcp
+    #   openai
+    #   sse-starlette
+    #   starlette
+asttokens==3.0.0
+    # via stack-data
+attrs==25.3.0
+    # via
+    #   aiohttp
+    #   jsonschema
+    #   referencing
+autogen-agentchat==0.6.1
+    # via agents (pyproject.toml)
+autogen-core==0.6.1
+    # via
+    #   autogen-agentchat
+    #   autogen-ext
+autogen-ext==0.6.1
+    # via agents (pyproject.toml)
+av==14.4.0
+    # via aiortc
+azure-ai-agents==1.0.1
+    # via
+    #   azure-ai-projects
+    #   semantic-kernel
+azure-ai-projects==1.0.0b11
+    # via semantic-kernel
+azure-core==1.34.0
+    # via
+    #   azure-ai-agents
+    #   azure-ai-projects
+    #   azure-identity
+    #   azure-storage-blob
+azure-identity==1.23.0
+    # via semantic-kernel
+azure-storage-blob==12.25.1
+    # via azure-ai-projects
+beautifulsoup4==4.13.4
+    # via
+    #   bs4
+    #   markdownify
+    #   readabilipy
+    #   wikipedia
+bs4==0.0.2
+    # via agents (pyproject.toml)
+certifi==2025.4.26
+    # via
+    #   httpcore
+    #   httpx
+    #   polygon-api-client
+    #   requests
+cffi==1.17.1
+    # via
+    #   aiortc
+    #   cryptography
+    #   pylibsrtp
+chardet==5.2.0
+    # via prance
+charset-normalizer==3.4.2
+    # via requests
+click==8.2.1
+    # via
+    #   typer
+    #   uvicorn
+cloudevents==1.12.0
+    # via semantic-kernel
+colorama==0.4.6
+    # via griffe
+comm==0.2.2
+    # via ipywidgets
+cryptography==45.0.4
+    # via
+    #   aiortc
+    #   azure-identity
+    #   azure-storage-blob
+    #   msal
+    #   pyjwt
+    #   pyopenssl
+dataclasses-json==0.6.7
+    # via langchain-community
+decorator==5.2.1
+    # via ipython
+defusedxml==0.7.1
+    # via semantic-kernel
+deprecation==2.1.0
+    # via cloudevents
+distro==1.9.0
+    # via
+    #   anthropic
+    #   openai
+dnspython==2.7.0
+    # via aioice
+ecdsa==0.19.1
+    # via sendgrid
+executing==2.2.0
+    # via stack-data
+fastapi==0.115.12
+    # via gradio
+ffmpy==0.6.0
+    # via gradio
+filelock==3.18.0
+    # via huggingface-hub
+frozenlist==1.7.0
+    # via
+    #   aiohttp
+    #   aiosignal
+fsspec==2025.5.1
+    # via
+    #   gradio-client
+    #   huggingface-hub
+google-crc32c==1.7.1
+    # via aiortc
+gradio==5.33.1
+    # via agents (pyproject.toml)
+gradio-client==1.10.3
+    # via gradio
+greenlet==3.2.3
+    # via playwright
+griffe==1.7.3
+    # via openai-agents
+groovy==0.1.2
+    # via gradio
+grpcio==1.70.0
+    # via autogen-ext
+h11==0.16.0
+    # via
+    #   httpcore
+    #   uvicorn
+hf-xet==1.1.3
+    # via huggingface-hub
+html5lib==1.1
+    # via readabilipy
+httpcore==1.0.9
+    # via httpx
+httpx==0.28.1
+    # via
+    #   agents (pyproject.toml)
+    #   anthropic
+    #   gradio
+    #   gradio-client
+    #   langgraph-sdk
+    #   langsmith
+    #   mcp
+    #   ollama
+    #   openai
+    #   safehttpx
+httpx-sse==0.4.0
+    # via
+    #   langchain-community
+    #   mcp
+huggingface-hub==0.32.4
+    # via
+    #   gradio
+    #   gradio-client
+idna==3.10
+    # via
+    #   anyio
+    #   httpx
+    #   requests
+    #   yarl
+ifaddr==0.2.0
+    # via aioice
+importlib-metadata==8.7.0
+    # via opentelemetry-api
+ipython==9.3.0
+    # via ipywidgets
+ipython-pygments-lexers==1.1.1
+    # via ipython
+ipywidgets==8.1.7
+    # via agents (pyproject.toml)
+isodate==0.7.2
+    # via
+    #   azure-ai-agents
+    #   azure-ai-projects
+    #   azure-storage-blob
+    #   openapi-core
+jedi==0.19.2
+    # via ipython
+jinja2==3.1.6
+    # via
+    #   gradio
+    #   semantic-kernel
+jiter==0.10.0
+    # via
+    #   anthropic
+    #   openai
+jsonpatch==1.33
+    # via langchain-core
+jsonpointer==3.0.0
+    # via jsonpatch
+jsonref==1.1.0
+    # via autogen-core
+jsonschema==4.24.0
+    # via
+    #   openapi-core
+    #   openapi-schema-validator
+    #   openapi-spec-validator
+jsonschema-path==0.3.4
+    # via
+    #   openapi-core
+    #   openapi-spec-validator
+jsonschema-specifications==2025.4.1
+    # via
+    #   jsonschema
+    #   openapi-schema-validator
+jupyterlab-widgets==3.0.15
+    # via ipywidgets
+langchain==0.3.25
+    # via langchain-community
+langchain-anthropic==0.3.15
+    # via agents (pyproject.toml)
+langchain-community==0.3.24
+    # via
+    #   agents (pyproject.toml)
+    #   langchain-experimental
+langchain-core==0.3.64
+    # via
+    #   langchain
+    #   langchain-anthropic
+    #   langchain-community
+    #   langchain-experimental
+    #   langchain-openai
+    #   langchain-text-splitters
+    #   langgraph
+    #   langgraph-checkpoint
+    #   langgraph-prebuilt
+langchain-experimental==0.3.4
+    # via agents (pyproject.toml)
+langchain-openai==0.3.21
+    # via agents (pyproject.toml)
+langchain-text-splitters==0.3.8
+    # via langchain
+langgraph==0.4.8
+    # via agents (pyproject.toml)
+langgraph-checkpoint==2.0.26
+    # via
+    #   langgraph
+    #   langgraph-checkpoint-sqlite
+    #   langgraph-prebuilt
+langgraph-checkpoint-sqlite==2.0.10
+    # via agents (pyproject.toml)
+langgraph-prebuilt==0.2.2
+    # via langgraph
+langgraph-sdk==0.1.70
+    # via langgraph
+langsmith==0.3.45
+    # via
+    #   agents (pyproject.toml)
+    #   langchain
+    #   langchain-community
+    #   langchain-core
+lazy-object-proxy==1.11.0
+    # via openapi-spec-validator
+lxml==5.4.0
+    # via
+    #   agents (pyproject.toml)
+    #   readabilipy
+markdown-it-py==3.0.0
+    # via rich
+markdownify==1.1.0
+    # via mcp-server-fetch
+markupsafe==3.0.2
+    # via
+    #   gradio
+    #   jinja2
+    #   werkzeug
+marshmallow==3.26.1
+    # via dataclasses-json
+matplotlib-inline==0.1.7
+    # via ipython
+mcp==1.9.3
+    # via
+    #   agents (pyproject.toml)
+    #   autogen-ext
+    #   mcp-server-fetch
+    #   openai-agents
+mcp-server-fetch==2025.1.17
+    # via agents (pyproject.toml)
+mdurl==0.1.2
+    # via markdown-it-py
+more-itertools==10.7.0
+    # via openapi-core
+msal==1.32.3
+    # via
+    #   azure-identity
+    #   msal-extensions
+msal-extensions==1.3.1
+    # via azure-identity
+multidict==6.4.4
+    # via
+    #   aiohttp
+    #   yarl
+mypy-extensions==1.1.0
+    # via typing-inspect
+narwhals==1.42.0
+    # via plotly
+nest-asyncio==1.6.0
+    # via semantic-kernel
+numpy==2.3.0
+    # via
+    #   gradio
+    #   langchain-community
+    #   pandas
+    #   scipy
+    #   semantic-kernel
+ollama==0.5.1
+    # via autogen-ext
+openai==1.85.0
+    # via
+    #   agents (pyproject.toml)
+    #   autogen-ext
+    #   langchain-openai
+    #   openai-agents
+    #   semantic-kernel
+openai-agents==0.0.17
+    # via agents (pyproject.toml)
+openapi-core==0.19.5
+    # via semantic-kernel
+openapi-schema-validator==0.6.3
+    # via
+    #   openapi-core
+    #   openapi-spec-validator
+openapi-spec-validator==0.7.2
+    # via openapi-core
+opentelemetry-api==1.34.1
+    # via
+    #   autogen-core
+    #   opentelemetry-sdk
+    #   opentelemetry-semantic-conventions
+    #   semantic-kernel
+opentelemetry-sdk==1.34.1
+    # via semantic-kernel
+opentelemetry-semantic-conventions==0.55b1
+    # via opentelemetry-sdk
+orjson==3.10.18
+    # via
+    #   gradio
+    #   langgraph-sdk
+    #   langsmith
+ormsgpack==1.10.0
+    # via langgraph-checkpoint
+packaging==24.2
+    # via
+    #   deprecation
+    #   gradio
+    #   gradio-client
+    #   huggingface-hub
+    #   langchain-core
+    #   langsmith
+    #   marshmallow
+    #   plotly
+    #   prance
+pandas==2.3.0
+    # via gradio
+parse==1.20.2
+    # via openapi-core
+parso==0.8.4
+    # via jedi
+pathable==0.4.4
+    # via jsonschema-path
+pexpect==4.9.0
+    # via ipython
+pillow==11.2.1
+    # via
+    #   autogen-core
+    #   gradio
+playwright==1.52.0
+    # via agents (pyproject.toml)
+plotly==6.1.2
+    # via agents (pyproject.toml)
+polygon-api-client==1.14.6
+    # via agents (pyproject.toml)
+prance==25.4.8.0
+    # via semantic-kernel
+prompt-toolkit==3.0.51
+    # via ipython
+propcache==0.3.2
+    # via
+    #   aiohttp
+    #   yarl
+protego==0.4.0
+    # via mcp-server-fetch
+protobuf==5.29.5
+    # via
+    #   autogen-core
+    #   semantic-kernel
+psutil==7.0.0
+    # via agents (pyproject.toml)
+ptyprocess==0.7.0
+    # via pexpect
+pure-eval==0.2.3
+    # via stack-data
+pybars4==0.9.13
+    # via semantic-kernel
+pycparser==2.22
+    # via cffi
+pydantic==2.11.5
+    # via
+    #   anthropic
+    #   autogen-core
+    #   fastapi
+    #   gradio
+    #   langchain
+    #   langchain-anthropic
+    #   langchain-core
+    #   langgraph
+    #   langsmith
+    #   mcp
+    #   mcp-server-fetch
+    #   ollama
+    #   openai
+    #   openai-agents
+    #   pydantic-settings
+    #   semantic-kernel
+pydantic-core==2.33.2
+    # via pydantic
+pydantic-settings==2.9.1
+    # via
+    #   langchain-community
+    #   mcp
+    #   semantic-kernel
+pydub==0.25.1
+    # via gradio
+pyee==13.0.0
+    # via
+    #   aiortc
+    #   playwright
+pygments==2.19.1
+    # via
+    #   ipython
+    #   ipython-pygments-lexers
+    #   rich
+pyjwt==2.10.1
+    # via msal
+pylibsrtp==0.12.0
+    # via aiortc
+pymeta3==0.5.1
+    # via pybars4
+pyopenssl==25.1.0
+    # via aiortc
+pypdf==5.6.0
+    # via agents (pyproject.toml)
+pypdf2==3.0.1
+    # via agents (pyproject.toml)
+python-dateutil==2.9.0.post0
+    # via pandas
+python-dotenv==1.1.0
+    # via
+    #   agents (pyproject.toml)
+    #   mcp
+    #   pydantic-settings
+python-http-client==3.3.7
+    # via sendgrid
+python-multipart==0.0.20
+    # via
+    #   gradio
+    #   mcp
+pytz==2025.2
+    # via pandas
+pyyaml==6.0.2
+    # via
+    #   gradio
+    #   huggingface-hub
+    #   jsonschema-path
+    #   langchain
+    #   langchain-community
+    #   langchain-core
+readabilipy==0.3.0
+    # via mcp-server-fetch
+referencing==0.36.2
+    # via
+    #   jsonschema
+    #   jsonschema-path
+    #   jsonschema-specifications
+regex==2024.11.6
+    # via
+    #   readabilipy
+    #   tiktoken
+requests==2.32.4
+    # via
+    #   agents (pyproject.toml)
+    #   azure-core
+    #   huggingface-hub
+    #   jsonschema-path
+    #   langchain
+    #   langchain-community
+    #   langsmith
+    #   mcp-server-fetch
+    #   msal
+    #   openai-agents
+    #   prance
+    #   requests-toolbelt
+    #   tiktoken
+    #   wikipedia
+requests-toolbelt==1.0.0
+    # via langsmith
+rfc3339-validator==0.1.4
+    # via openapi-schema-validator
+rich==14.0.0
+    # via typer
+rpds-py==0.25.1
+    # via
+    #   jsonschema
+    #   referencing
+ruamel-yaml==0.18.14
+    # via prance
+ruamel-yaml-clib==0.2.12
+    # via ruamel-yaml
+ruff==0.11.13
+    # via gradio
+safehttpx==0.1.6
+    # via gradio
+scipy==1.15.3
+    # via semantic-kernel
+semantic-kernel==1.32.2
+    # via agents (pyproject.toml)
+semantic-version==2.10.0
+    # via gradio
+sendgrid==6.12.3
+    # via agents (pyproject.toml)
+setuptools==80.9.0
+    # via agents (pyproject.toml)
+shellingham==1.5.4
+    # via typer
+six==1.17.0
+    # via
+    #   azure-core
+    #   ecdsa
+    #   html5lib
+    #   markdownify
+    #   python-dateutil
+    #   rfc3339-validator
+smithery==0.1.0
+    # via agents (pyproject.toml)
+sniffio==1.3.1
+    # via
+    #   anthropic
+    #   anyio
+    #   openai
+soupsieve==2.7
+    # via beautifulsoup4
+speedtest-cli==2.1.3
+    # via agents (pyproject.toml)
+sqlalchemy==2.0.41
+    # via
+    #   langchain
+    #   langchain-community
+sqlite-vec==0.1.6
+    # via langgraph-checkpoint-sqlite
+sse-starlette==2.3.6
+    # via mcp
+stack-data==0.6.3
+    # via ipython
+starlette==0.46.2
+    # via
+    #   fastapi
+    #   gradio
+    #   mcp
+tenacity==9.1.2
+    # via
+    #   langchain-community
+    #   langchain-core
+tiktoken==0.9.0
+    # via
+    #   autogen-ext
+    #   langchain-openai
+tomlkit==0.13.3
+    # via gradio
+tqdm==4.67.1
+    # via
+    #   huggingface-hub
+    #   openai
+traitlets==5.14.3
+    # via
+    #   comm
+    #   ipython
+    #   ipywidgets
+    #   matplotlib-inline
+typer==0.16.0
+    # via
+    #   gradio
+    #   mcp
+types-requests==2.32.0.20250602
+    # via openai-agents
+typing-extensions==4.14.0
+    # via
+    #   aiosqlite
+    #   anthropic
+    #   anyio
+    #   autogen-core
+    #   azure-ai-agents
+    #   azure-ai-projects
+    #   azure-core
+    #   azure-identity
+    #   azure-storage-blob
+    #   beautifulsoup4
+    #   fastapi
+    #   gradio
+    #   gradio-client
+    #   huggingface-hub
+    #   langchain-core
+    #   openai
+    #   openai-agents
+    #   openapi-core
+    #   opentelemetry-api
+    #   opentelemetry-sdk
+    #   opentelemetry-semantic-conventions
+    #   pydantic
+    #   pydantic-core
+    #   pyee
+    #   pyopenssl
+    #   referencing
+    #   semantic-kernel
+    #   sqlalchemy
+    #   typer
+    #   typing-inspect
+    #   typing-inspection
+typing-inspect==0.9.0
+    # via dataclasses-json
+typing-inspection==0.4.1
+    # via
+    #   pydantic
+    #   pydantic-settings
+tzdata==2025.2
+    # via pandas
+urllib3==2.4.0
+    # via
+    #   polygon-api-client
+    #   requests
+    #   types-requests
+uvicorn==0.34.3
+    # via
+    #   gradio
+    #   mcp
+wcwidth==0.2.13
+    # via prompt-toolkit
+webencodings==0.5.1
+    # via html5lib
+websockets==14.2
+    # via
+    #   gradio-client
+    #   polygon-api-client
+    #   semantic-kernel
+werkzeug==3.1.1
+    # via
+    #   openapi-core
+    #   sendgrid
+widgetsnbextension==4.0.14
+    # via ipywidgets
+wikipedia==1.4.0
+    # via agents (pyproject.toml)
+xxhash==3.5.0
+    # via langgraph
+yarl==1.20.1
+    # via aiohttp
+zipp==3.23.0
+    # via importlib-metadata
+zstandard==0.23.0
+    # via langsmith