pyproject.toml

[build-system]
requires = ["setuptools>=69.1.1"]
build-backend = "setuptools.build_meta"

[project]
name = "instanovo"
authors = [
  { name="InstaDeep Ltd", email="hello@instadeep.com" },
]
keywords = [
    "mass spectrometry",
    "bioinformatics",
    "machine learning",
    "deep learning",
    "transformer",
    "de novo peptide sequencing"
]
description = "De novo sequencing with InstaNovo"
requires-python = ">=3.10"
classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: Apache Software License",
    "Operating System :: OS Independent",
]
dynamic = ["version", "readme", "dependencies"] # , "optional-dependencies"]

[tool.setuptools]
include-package-data = true  # To use MANIFEST.in for including extra files

[tool.setuptools.dynamic]
readme = { file = ["README.md"], content-type = "text/markdown" }
version = { attr = "instanovo.__version__" }
dependencies = {file = ["requirements/requirements.in"]}
optional-dependencies.dev = {file = ["requirements/requirements-dev.txt"]}
optional-dependencies.docs = {file = ["requirements/requirements-dev.txt"]}
optional-dependencies.mlflow = {file = ["requirements/requirements-mlflow.txt"]}

[tool.setuptools.packages.find]
include = ["instanovo*"]

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

[tool.coverage.run]
source = ["instanovo"]
omit = ["*/__init__.py", "*_test.py"]

[tool.coverage.report]
omit = ["__init__.py", "*_test.py"]
exclude_lines = [
    # Don't complain if tests don't hit defensive assertion code:
    "raise AssertionError",
    "raise NotImplementedError",

    # Don't complain if non-runnable code isn't run:
    "if 0:",
    "if __name__ == .__main__.:"]

[tool.coverage.html]
directory = "coverage"

[tool.flake8]
exclude = [".git", "**/__pycache__/", "build/", "dist/", "proto/", "*.pyc", "*.egg-info/", ".cache/", ".eggs/"]
max-line-length = 100
import-order-style = "google"
application-import-names = "instanovo"
doctests = true
docstring-convention = "google"
per-file-ignores = ["__init__.py:F401"]
ignore = ["D107", # Do not require docstrings for __init__
          "W503", # line break before binary operator (not compatible with black)
          "E731"  # do not assign a lambda expression, use a def
        ]
select = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "T", "W"]

[tool.mypy]
python_version = "3.10"
namespace_packages = true
incremental = false
cache_dir = ".mypy_cache"
warn_redundant_casts = true
warn_return_any = true
warn_unused_configs = true
warn_unused_ignores = false
allow_redefinition = true
disallow_untyped_calls = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
check_untyped_defs = true
disallow_untyped_decorators = false
strict_optional = true
strict_equality = true
explicit_package_bases = true
follow_imports = "skip"

[project.urls]
Homepage = "https://github.com/instadeepai/InstaNovo"
Issues = "https://github.com/instadeepai/InstaNovo/issues"