pyproject.toml

[project]
name = "ptmdiscoverer"
version = "0.1.0"
description = "PTMdiscoverer leverages generative AI to accelerate the discovery of post-translational modifications (PTMs) in proteomics experiments. It identifies delta masses in peptide fragmentation patterns from mass spectrometry (MS) data and utilizes a large language model (LLM) for their annotation and interpretation across various phenotypes or experimental conditions."
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "matplotlib>=3.10.6",
    "openai>=1.106.1",
    "pandas>=2.3.2",
]

[project.optional-dependencies]
# Standalone PTMdiscoverer MCP server (lightweight, no agentic framework)
mcp = [
    "mcp[cli]>=1.6.0",
]
# Jupyter notebook extras for data exploration
notebook = [
    "h5py>=3.14.0",
    "hdf5plugin>=5.1.0",
    "jupyterlab>=4.4.7",
    "matplotlib>=3.10.6",
    "numpy>=2.2.6",
    "ipykernel>=6.29.5",
]
# Full ADEPT agentic framework — MCP server, LangChain agent, Streamlit UI.
# Install with:  uv pip install -e ".[adept]"
adept = [
    "fastmcp>=2.6.0",
    "mcp",
    "litellm>=1.83.0",
    "langchain>=0.3.0",
    "langchain-openai",
    "langchain-community",
    "streamlit>=1.20.0",
    "aiosqlite>=0.17.0",
    "chromadb>=1.0.12",
    "uvicorn[standard]>=0.20.0",
    "python-dotenv>=1.0.0",
    "numpy>=1.20.0",
    "fastapi",
    "biopython",
    "rdkit",
    "chembl_webresource_client",
    "meeko",
    "selenium",
    "webdriver_manager",
    "watchdog",
    "PyMuPDF>=1.23.0",
    "openpyxl",
    "python-docx",
    "pubchempy",
    "gemmi",
]

[project.scripts]
# Standalone PTMdiscoverer CLI
ptmdiscoverer = "ptmdiscoverer.cli:main"
# PTMdiscoverer standalone MCP server
ptmdiscoverer-mcp = "ptmdiscoverer.mcp_server:main"
# ADEPT agentic framework servers
run-mcp-server = "agentic_framework_pkg.mcp_server.main:start_server_cli"
run-streamlit-harness = "agentic_framework_pkg.streamlit_app.main:start_harness_cli"

[tool.setuptools.packages.find]
where = ["src"]

[build-system]
requires = ["setuptools>=64", "wheel"]
build-backend = "setuptools.build_meta"

[dependency-groups]
dev = [
    "mypy>=1.19.1",
    "pdoc>=15.0.0",
    "pip-audit>=2.5.0",
    "pytest>=8.3.0",
    "pytest-asyncio>=1.0.0",
    "pytest-cov>=7.0.0",
    "pytest-mock>=3.0.0",
    "ruff>=0.5.0",
]

[tool.ruff]
line-length = 120
target-version = "py311"
fix = true
show-fixes = true

[tool.ruff.lint]
select = ["E", "F", "I", "N", "UP", "B", "S", "W"]
ignore = [
    "E501",  # long lines allowed
    "S101",  # allow assert in tests
    "S105",  # ignore hardcoded password false positive
]

[tool.ruff.lint.isort]
known-first-party = ["ptmdiscoverer", "agentic_framework_pkg"]
combine-as-imports = true

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
check_untyped_defs = true
ignore_missing_imports = true

[tool.coverage.run]
# Scope: ptmdiscoverer core + its ADEPT interface adapter files only.
# All other ADEPT framework files (Streamlit, BLAST, RAG, LangChain agent, etc.)
# are excluded because they require live services or are out of scope for this sweep.
source = ["ptmdiscoverer", "agentic_framework_pkg"]
omit = [
    # ADEPT framework — out of scope for this sweep
    "*/streamlit_app/*",
    "*/core/*",
    "*/mcp_server/main.py",
    "*/mcp_server/server.py",
    "*/mcp_server/tools/blastq_tool.py",
    "*/mcp_server/tools/csv_rag_tool.py",
    "*/mcp_server/tools/pubchem_tool.py",
    "*/mcp_server/tools/uniprot_tool.py",
    "*/mcp_server/tools/websearch_tool.py",
    "*/mcp_server/tools/general_tools.py",
    "*/mcp_server/vector_store_manager.py",
    "*/mcp_server/state_manager.py",
    "*/scientific_workflow/langchain_agent.py",
    "*/scientific_workflow/mcp_langchain_tools.py",
]

[tool.coverage.report]
fail_under = 90
show_missing = true
skip_empty = true

[tool.pytest.ini_options]
asyncio_mode = "auto"
testpaths = ["tests"]
addopts = "-m 'not integration and not llm'"
markers = [
    "unit: fast isolated unit tests",
    "integration: slower end-to-end tests",
    "slow: slow-running tests (deselect with -m 'not slow')",
    "llm: live LLM API call tests (requires OPENAI_API_KEY; run with: pytest -m llm)",
]