pyproject.toml

[project]
name = "scientific-writer"
version = "2.21.0"
description = "Deep research and writing tool - combines AI-driven deep research with well-formatted written outputs. Generates publication-ready scientific documents with verified citations."
readme = "README.md"
requires-python = ">=3.10"
license = "MIT"
authors = [
    { name = "K-Dense Inc.", email = "contact@k-dense.ai" },
]
keywords = ["scientific-writing", "research", "latex", "citations", "claude"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Topic :: Scientific/Engineering",
]
dependencies = [
    # The code imports the 0.2.x hook/types surface (StopHookInput, HookContext);
    # cap below 0.3 since the SDK API is still evolving pre-1.0.
    "claude-agent-sdk>=0.2.126,<0.3",
    "python-dotenv>=1.0.0",
    # requests and pymupdf are not imported by scientific_writer itself, but the
    # bundled skill scripts (web lookup, pdf_to_images) rely on them at runtime.
    "requests>=2.31.0",
    "pymupdf>=1.24.0",
]

[project.urls]
Homepage = "https://github.com/K-Dense-AI/claude-scientific-writer"
Repository = "https://github.com/K-Dense-AI/claude-scientific-writer"
Issues = "https://github.com/K-Dense-AI/claude-scientific-writer/issues"
Changelog = "https://github.com/K-Dense-AI/claude-scientific-writer/blob/main/CHANGELOG.md"

# System Dependencies (must be installed separately):
# 
# LaTeX Distribution (required for PDF compilation):
#   - macOS: MacTeX (https://www.tug.org/mactex/) or BasicTeX
#     Install: brew install --cask mactex-no-gui
#   - Linux: TeX Live
#     Install: sudo apt-get install texlive-full (Ubuntu/Debian)
#              sudo dnf install texlive-scheme-full (Fedora)
#   - Windows: MiKTeX (https://miktex.org/) or TeX Live
#
# Required LaTeX packages (usually included in full distributions):
#   - pdflatex, bibtex, latexmk
#   - Common packages: amsmath, graphicx, hyperref, natbib, geometry
#
# PDF to Image Conversion:
#   PyMuPDF is included as a dependency - no external software needed!
#   PDF to image conversion works out of the box.
#
# Optional but recommended:
#   - Ghostscript (for PDF manipulation)
#   - ImageMagick (for image processing)
#   - LibreOffice (for Office rendering and recalculation helpers)
#   - FFmpeg (for audio/video conversion through MarkItDown)

[project.scripts]
scientific-writer = "scientific_writer.cli:cli_main"

[project.optional-dependencies]
analysis = [
    "lifelines>=0.30.0",
    "matplotlib>=3.10.9",
    "numpy>=2.2.6",
    "pandas>=2.3.3",
    "scipy>=1.15.3",
]
office = [
    "defusedxml>=0.7.1",
    # 0.1.6 currently requires an unavailable Azure prerelease on a supported split.
    "markitdown[all]>=0.1.5,!=0.1.6",
    "openai>=2.47.0",
    "openpyxl>=3.1.5",
    "pillow>=12.3.0",
]

[build-system]
requires = ["hatchling>=1.31,<2"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["scientific_writer"]

[tool.hatch.build.targets.sdist]
exclude = [
    "/.claude",
    "/docs/examples",
    "/extensions",
    "/skills",
]

[dependency-groups]
dev = [
    "pytest>=8.0",
    "ruff>=0.4",
    "mypy>=1.10",
    "codespell>=2.4.3",
    "pre-commit>=4.6.1",
]

[tool.ruff]
line-length = 110
target-version = "py310"
# The bundled/mirrored skill trees and vendored extensions carry their own scripts;
# lint only the package, scripts, and tests.
extend-exclude = [
    "skills",
    ".claude",
    "scientific_writer/.claude",
    "extensions",
    "templates",
]

[tool.ruff.lint]
select = ["E", "F", "W", "B"]
ignore = ["E501"]

[tool.mypy]
python_version = "3.10"
files = ["scientific_writer"]
exclude = "scientific_writer/\\.claude"
ignore_missing_imports = true


[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git,.gitignore,.gitattributes,.claude,skills,scientific_writer/.claude,extensions,docs/examples,*.pdf,*.svg,*.css,*.xsd'
check-hidden = true
# Ignore camelCase/PascalCase identifiers, and word fragments from bold formatting
# (**S**pecific, \textbf{F}requency, etc.)
ignore-regex = '\b[a-z]+[A-Z]\w*\b|\b[A-Z][a-z]+[A-Z]\w*\b|\*\*.\*\*\w+|\\textbf\{.\}\w+'
# Domain-specific terms:
#  theses - plural of thesis (BibTeX entry type)
#  infarction - medical term (myocardial infarction)
#  ser - XML series element
#  pres - presentation abbreviation
#  commun - as in "Nature Communications" journal
#  stard - STARD reporting guideline (Standards for Reporting Diagnostic Accuracy)
#  ehr - Electronic Health Record
#  anc - Absolute Neutrophil Count
#  ot - Occupational Therapy
#  som - Serviceable Obtainable Market
#  caf/cafs - Cancer-Associated Fibroblasts
#  promis - PROMIS patient-reported outcome measures
#  slac - SLAC National Accelerator Laboratory
#  als - Amyotrophic Lateral Sclerosis / Advanced Light Source
#  abd - abbreviation for abdomen/abdominal
#  rouge - ROUGE metric (NLP evaluation)
#  nd - shorthand for 2nd
#  reacher - Functional Reach test (rehabilitation)
#  fallow - Gutenberg diagram layout term (fallow area)
#  trough - Gartner Hype Cycle term (Trough of Disillusionment)
#  childs - surname
#  recuse - legitimate word (to recuse oneself)
#  inh - medical abbreviation (inhalation)
#  ois - Optimal Information Size (statistics)
#  re-use - valid hyphenation
#  edn - abbreviation for "edition" (Nature citation style: "10th edn")
#  bu - Business Unit abbreviation
#  vermillion - valid alternate spelling of vermilion
ignore-words-list = 'theses,infarction,ser,pres,commun,stard,ehr,anc,ot,som,caf,cafs,promis,slac,als,abd,rouge,nd,reacher,fallow,trough,childs,recuse,inh,ois,re-use,edn,bu,vermillion'