pyproject.toml

[project]
name = "xai4mri"
version = "0.0.1"
description = "xai4mri is designed for advanced MRI analysis using deep learning combined with explainable A.I. (XAI)."
readme = "README.md"
requires-python = ">=3.9, <3.12"  # TODO: to update to 3.12, but first iNNvestigate would need to be updated
license = { file = "LICENSE" }
keywords = [
    "transfer-learning",
    "xai",
    "explainable-ai",
    "explanation",
    "interpretation",
    "prediction",
    "MRI",
    "sMRI",
    "3D-conv",
    "deep-learning",
    "structure",
    "brain",
    "t1w",
    "flair",
    "swi",
    "dwi",
]
authors = [{ name = "Simon M. Hofmann", email = "simon.hofmann@pm.me" }]
maintainers = [{ name = "Simon M. Hofmann", email = "simon.hofmann@pm.me" }]
classifiers = [
    "Development Status :: 2 - Pre-Alpha",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]

dependencies = [
    "antspyx>=0.4.2, <0.5.0",  # TODO: to update to 0.5.* solve issue with ants.from_nibabel()
    "innvestigate>=2.1.1, <3.0.0",
    "nilearn>=0.10, <1.0",
    "tensorflow>=2.6, <2.15", # TODO: 2.15 not tested yet, iNNvestigate would need to be updated
    "tqdm>=4.66.5, <5.0",
]

[project.optional-dependencies]
develop = [
    "bumpver==2023.1129",
    "ruff>=0.6.8, <1.0.0",        # including format
    "tox>=4.20.0, <5.0.0",
    "pre-commit>=3.8.0, <4.0.0",
    "pytest>=8.3.3, <9.0.0",
    "pytest-cov>=5.0.0, <6.0.0",
]

docs = [
    "blacken-docs>=1.16, <2.0",
    "docutils>=0.21.1, <1.0.0",
    "markdown-callouts>=0.3.0, <1.0.0",
    "markdown-exec[ansi]>=1.7.0, <2.0.0",
    "mkdocs>=1.5, <2.0",
    "mkdocs-autorefs>=0.5.0, <1.0.0",
    "mkdocs-bibtex>=2.11.0, <3.0.0",
    "mkdocs-coverage>=1.0.0, <2.0.0",
    "mkdocs-gen-files>=0.5.0, <1.0",
    # "mkdocs-git-committers-plugin-2>=1.1",
    "mkdocs-jupyter>=0.24.6, <1.0.0",
    "mkdocs-literate-nav>=0.6.1, <1.0",
    "mkdocs-material>=9.4.8, <10.0.0",
    "mkdocs-material-extensions>=1.3, <2.0",
    "mkdocs-minify-plugin>=0.7.1, <1.0.0",
    "mkdocs-redirects>=1.2.1, <2.0.0",
    "mkdocstrings[python]",                # add language-specific extensions
    "pypandoc>=1.13, <2.0",                # if issue: install via conda install -c conda-forge pypandoc
]

[project.urls]
homepage = "https://shescher.github.io/xai4mri/"
documentation = "https://shescher.github.io/xai4mri/"
repository = "https://github.com/SHEscher/xai4mri"
changelog = "https://github.com/SHEscher/xai4mri/blob/main/CHANGELOG.md"

[build-system]
requires = ["setuptools>=65", "wheel"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
platforms = ["unix", "linux", "osx", "cygwin", "win32"]
zip-safe = false

# # To automatically find the package(s) (Beta feature (Oct, 2022)):
[tool.setuptools.packages.find]
where = ["src"]
include = ["xai4mri", "xai4mri.*"]
exclude = ["tests"]

# ALL ABOVE IS ADAPTATION OF THE FORMER setup.cfg
# ALL BELOW WAS ALREADY PART OF pyproject.toml [Oct, 2022]

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.mypy]
mypy_path = "src"
check_untyped_defs = true
disallow_any_generics = true
ignore_missing_imports = true
no_implicit_optional = true
show_error_codes = true
strict_equality = true
warn_redundant_casts = true
warn_return_any = true
warn_unreachable = true
warn_unused_configs = true
no_implicit_reexport = true

[tool.coverage.run]
data_file = "tests/.coverage"

[tool.coverage.report]
exclude_lines = ["if __name__ == .__main__.:", "if TYPE_CHECKING:", "@abstract"]

[tool.coverage.html]
directory = "tests/coverage_html_report"

[tool.ruff]
# Select rules / linters to apply
lint.select = [ # add /comment-out rules (the list below does not contain all rulles)
    # "ALL", # all rules
    "D",   # pydocstyle
    "E",   # pycodestyle [default]
    "F",   # Pyflakes [default]
    "I",   # isort imports
    "RUF", # ruff specific
    "UP",  # pyupgrade [default]
    "W",   # pycodestyle: warning
    "C90", # mccabe
    "N",   # pep8-naming
    "ANN", # flake8-annotations (toggle on if you intend to work with type annotations)
    "S",   # flake8-bandit
    "BLE", # flake8-blind-except
    "B",   # flake8-bugbear
    "A",   # flake8-builtins
    "COM", # flake8-commas
    "C4",  # flake8-comprehensions
    # "EM", # flake8-errmsg
    "FA",  # flake8-future-annotations (see ANN above)
    "ISC", # flake8-implicit-str-concat
    # "ICN", # flake8-import-conventions
    "G",   # flake8-logging-format
    "INP", # flake8-no-pep420
    "PT",  # flake8-pytest-style
    "Q",   # flake8-quotes
    "RET", # flake8-return
    "SIM", # flake8-simplify
    "TCH", # flake8-type-checking
    "ARG", # flake8-unused-arguments
    "PTH", # flake8-use-pathlib
    "TD",  # flake8-todos
    "FIX", # flake8-fixme
    "ERA", # eradicate
    "PD",  # pandas-vet
    "PL",  # Pylint
    "NPY", # NumPy-specific rules
] # run `ruff linter` to see all rules
fix = false # true: Ruff will try to fix errors automatically
# List of rules to consider non-autofix-able.
lint.unfixable = [ # either with fix = true or when `ruff . --fix` is executed
    "ERA001", # found commented-out code
    "F401",   # unused imports
    # "RUF100", # `noqa` directives that are no longer applicable
]
# Ignore specific rules or the whole set of a rule
lint.ignore = [
    "ANN003", # flake8-annotations: Missing type annotation for **kwargs
    "ANN101", # flake8-annotations: Missing type annotation for self in method
    "ANN102", # flake8-annotations: Missing type annotation for cls in classmethod
    "ANN401", # flake8-annotations: Any
    "COM812", # Trailing comma missing
    "D203",   # 1 blank line required before class docstring: incompatible with D211 (=no blank line required)
    "D212",   # multi-line-summary-first-line incompatible with D213 (=should start at second line)
    "DTZ005", # timezone-naive datetime
    "E402",   # Module level import not at the top of file (covert by ISORT)
    # "E501", # Ignore line-length since we use 119
    # "ERA001", # Found commented-out code
    "ISC001", # single-line-implicit-string-concatenation [is in conflict with `ruff format`]
    "S301",   # suspicious-pickle-usage
    "TD002",  # Missing author in To-Do
    "TD003",  # Missing issue link on the line following a To-Do
]
# lint.ignore-init-module-imports = true # void automatically removing unused imports in __init__.py [deprecated]
respect-gitignore = true       # files and folder ignored in gitignore are ignore by ruff as well [default: true]
src = ["src/xai4mri", "tests"]

# Exclude a variety of commonly ignored directories.
include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
extend-exclude = ["data"]
line-length = 119                                           # Same as flake8 and black
target-version = "py39"                                     # assume Python >= 3.9
output-format = "concise"                                   # "full" or "concise"
preview = false                                             # true: Ruff will use unstable rules and fixes

[tool.ruff.lint.extend-per-file-ignores]
# Ignore specific rules in specific files
"__init__.py" = ["F401", "D104"]
"*.ipynb" = ["D100"] # ignore docsstring in notebooks
"tests/*.py" = [
    "S101",
    "D103",
    "PLC2701",
] # ignore assert statements, and private objects in tests
"prune_image.py" = ["RUF002"]

[tool.ruff.format]
docstring-code-format = true # default: false
preview = true               # true: Ruff will use unstable rules and fixes

[tool.ruff.lint.flake8-annotations]
allow-star-arg-any = true
ignore-fully-untyped = true
suppress-none-returning = true

[tool.ruff.lint.flake8-comprehensions]
allow-dict-calls-with-keyword-arguments = true

[tool.ruff.lint.isort]
known-local-folder = ["src/xai4mri"]
# known-first-party = ...

[tool.ruff.lint.mccabe]
# Flag errors (`C901`) whenever the complexity level exceeds x.
max-complexity = 20 # default x: 10

[tool.ruff.lint.pep8-naming]
ignore-names = [] # fill with specific class, function, variable names

[tool.ruff.lint.pydocstyle]
# convention = "google"  # "numpy", "pep257"

[tool.ruff.lint.pylint]
# Flag errors (`PLR*`) w.r.t. complexity levels
max-args = 15       # default: 5
max-branches = 20   # default: 12
max-returns = 6     # default: 6
max-statements = 70 # default: 50
max-locals = 19
# allow-magic-value-types = ["int"]

[tool.black]
line-length = 119
target-version = ["py38", "py39", "py310", "py311"]
include = '(\.pyi?|\.ipynb)$'
exclude = '''  # A regex preceded with ^/ will apply only to files and directories in the root of the project.
(
  ^/models
  | ^/data
  | /*/\..*  # ignore (hidden) files in hidden directories
)
'''

# For instance, run in shell: bumpver update --patch --no-fetch --dry
[tool.bumpver]
current_version = "0.0.1"
version_pattern = "MAJOR.MINOR.PATCH"
pre_commit_hook = "scripts/badge.sh"
commit_message = "bump version {old_version} -> {new_version}"
commit = true
tag = true
push = false

[tool.bumpver.file_patterns]
"pyproject.toml" = ['^version = "{version}"', 'current_version = "{version}"']
"src/xai4mri/__init__.py" = ['^__version__ = "{version}"']
"README.md" = ['version-v.{version}']