pyproject.toml

[build-system]
requires = ["setuptools>=69", "setuptools-scm>=8", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "assembly-designer"
dynamic = ["version"]  # via setuptools-scm
description = "Design and workflow tools for (MoClo/Golden Gate) assemblies and in-silico plasmid design"
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
authors = [{ name = "Tim Stoltmann", email = "t.stoltmann@fz-juelich.de" }]
keywords = ["moclo", "golden-gate", "synthetic-biology", "cloning", "plasmid", "bioinformatics"]
classifiers = [
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
  "Operating System :: OS Independent",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "Typing :: Typed",
]

# ---------------- Runtime Dependencies ----------------
dependencies = [
  "biopython>=1.83,<2.0",
  "pandas>=2.1,<3.0",
  "numpy>=1.26,<3.0",
  "pydantic>=2.6,<3.0",
  "matplotlib>=3.0",
  "seaborn>=0.11",
  "networkx>=2.5",
  "ipython>=7.0",
  "openpyxl>=3.0",
  "textwrap3>=0.9.2",
  "robotools>=1.0",
  "fastprogress>=1.0.3",
  "Pillow>=10.0",
  # --- Notebook-Stack directly integrated ---
  "ipykernel>=6.29",
  "notebook>=7",
  "jupyterlab>=4",
  "ipywidgets>=8",
]

# ---------------- Optional Dependencies ----------------
[project.optional-dependencies]
# Dev-Stack
dev = [
  "pytest>=8.0",
  "pytest-cov>=5.0",
  "black>=24.3",
  "ruff>=0.5",
  "mypy>=1.10",
  "pre-commit>=3.6",
  "build>=1.2",
  "twine>=5.0",
]

# In-silico: DnaCauldron + SnapGene
insilico = [
  "dnacauldron>=2.0,<3.0",
  "snapgene_reader>=0.1.20,<1.0",
]

# OPTIONAL: aliases
reports = ["dnacauldron>=2.0,<3.0"]
snapgene = ["snapgene_reader>=0.1.20,<1.0"]
excel = ["xlsxwriter>=3.1"]

# S1 documentation helpers (Word export + plasmid map rendering via Matplotlib)
# Install with:  pip install -e ".[s1doc]"
s1doc = [
  "python-docx>=1.1.0",
  "dna-features-viewer>=3.1.0",
]

# Meta extra that installs *all* useful stacks in one go (no self-references)
all-local = [
  # dev
  "pytest>=8.0",
  "pytest-cov>=5.0",
  "black>=24.3",
  "ruff>=0.5",
  "mypy>=1.10",
  "pre-commit>=3.6",
  "twine>=5.0",
  # nb (now redundant, but retained for compatibility)
  "ipykernel>=6.29",
  "notebook>=7",
  "jupyterlab>=4",
  "ipywidgets>=8",
  # insilico
  "dnacauldron>=2.0,<3.0",
  "snapgene_reader>=0.1.20,<1.0",
  # excel/reports
  "xlsxwriter>=3.1",
  # s1doc (ohne cairosvg)
  "python-docx>=1.1.0",
  "dna-features-viewer>=3.1.0",
  "edlib>=1.3.9",
]

# ---------------- CLI Entry Point ----------------
[project.scripts]
assembly-designer = "assembly_designer.workflow:main"

# ---------------- Project URLs ----------------
[project.urls]
Homepage   = "https://github.com/JuBiotech/AssemblyDesigner"
Repository = "https://github.com/JuBiotech/AssemblyDesigner"
Issues     = "https://github.com/JuBiotech/AssemblyDesigner/issues"
Documentation = "https://github.com/JuBiotech/AssemblyDesigner#readme"

# ---------------- setuptools Configuration ----------------
[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
where = ["."]
include = ["assembly_designer*"]
exclude = ["tests*", "docs*", "examples*", "reports*", "build*", "dist*"]

[tool.setuptools.package-data]
assembly_designer = ["py.typed"]

# ---------------- setuptools-scm (Version from Git) ----------------
[tool.setuptools_scm]
version_scheme = "guess-next-dev"
local_scheme = "node-and-date"
fallback_version = "0.0.0"

# ---------------- Code Style: Black ----------------
[tool.black]
line-length = 88
target-version = ["py310", "py311"]
skip-string-normalization = false
include = '\.pyi?$'
exclude = '''
/(
    \.git
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''

# ---------------- Linting: Ruff ----------------
[tool.ruff]
target-version = "py310"
line-length = 88

[tool.ruff.lint]
select = ["E", "F", "I", "B", "UP", "N"]
ignore = [
  "E501",  # long lines ok in docstrings
  "UP038",
  "UP007",
]

[tool.ruff.lint.per-file-ignores]
"assembly_designer/workflow/__init__.py" = ["F401"]

# ---------------- Type Checking: mypy ----------------
[tool.mypy]
python_version = "3.11"
ignore_missing_imports = true
no_implicit_optional = false
strict_optional = true
warn_unused_ignores = true

# ---------------- Coverage ----------------
[tool.coverage.run]
branch = true
source = ["assembly_designer"]
omit = ["*/tests/*"]

[tool.coverage.report]
show_missing = true
skip_covered = true
precision = 2
fail_under = 90

# ---------------- Pytest ----------------
[tool.pytest.ini_options]
addopts = "-q --strict-markers"
testpaths = ["tests"]