pyproject.toml

[project]
name = "mother-ml"
version = "1.0.4"
readme = "README.md"
description = "A ML framework that takes care"
requires-python = ">=3.11, <3.15"
license = { file = "LICENSE" }
authors = [
  { name = "Thomas Wolf" },
  { name = "Florian Huber" },
  { name = "Nicolas Peschke" },
  { name = "Niklas Toetsch" },
  { name = "Satya Kanuri" },
  { name = "Alex Calabrese" },
  { name = "Samantha Martinez" },
  { name = "Hamza Ibrahim" },
  { name = "Agata Zieba" },
  { name = "Yunhee Jeong" },
  { name = "Nesma Mousa" },
  { name = "Lukas Hebing" },
  { name = "Kai Sommer" },
  { name = "Nicolas Arning" },
]

dependencies = [
  "catboost>=1.2.9,<=1.2.10",
  "feature-engine>=1.8.0,<2",
  "numpy>=2.2,<2.3",
  "optuna>=4.2.0,<5",
  "pandas>=2.2,<3.0",
  "pydantic-settings>=2.4.0,<3",
  "rdkit>=2024.9.1",
  "scikit-learn>=1.9.0,<1.10",
  "colorama>=0.4.6,<0.5",
  "boruta>=0.4.3,<0.5",
  "quantile-forest>=1.4.2,<2"
]

[project.urls]
Homepage = "https://github.com/Bayer-Group/MotherML"
Documentation = "https://bayer-group.github.io/MotherML/"
Repository = "https://github.com/Bayer-Group/MotherML"
Issues = "https://github.com/Bayer-Group/MotherML/issues"
Changelog = "https://bayer-group.github.io/MotherML/Changelog/"

[project.optional-dependencies]
### Torch
torch = ["torch>=2.3.0,<3"]

### Report block
report = [
  "matplotlib>3.7.0",
  "seaborn>=0.13.2,<0.14",
  "umap-learn>=0.5.12,<0.6",
  "plotly>=6.0.1,<7",
  "ipywidgets>=8.1.5,<9",
  "igraph>=0.11.8,<0.12",
  "leidenalg>=0.10.2,<0.11",
]

### RNA block
rna = [
  "anndata",
  "scanpy",
]

### Clustering block
clustering = [
  "kmedoids>=0.5.3.1,<0.6",
]

### TabPFN
tabpfn = [
  "tabpfn==8.0.8",
  "torch>=2.3.0,<3",
]


[dependency-groups]
dev = [
  "ipykernel",
  "isort",
  "mypy>0.981",
  "poethepoet",
  "pre-commit",
  "pylint",
  "pytest",
  "pytest-cov",
  "ruff>=0.9.2,<1",
  "types-pyyaml>=6.0.12.20241230",
  "python-semantic-release>=10.2.0,<11",
  "git-changelog>=2.9.4",
]
examples = [
  "polaris-lib>=0.13.0,<0.14",
  "shap>=0.47.2,<0.48",
]
docs = [
  "mkdocs",
  "mkdocs-git-revision-date-localized-plugin",
  "mkdocs-include-markdown-plugin",
  "mkdocs-material",
  "mkdocstrings[python]",
  "markdown-exec[ansi]>=1.7.0,<2",
  "mkdocs-jupyter>=0.25.1,<0.26",
  "mkdocs-git-authors-plugin>=0.9.2,<0.10",
]
test_duration = [
  "pytest-html>=4.0.2,<5",
  "pytest-xdist[psutil]>=3.3.1,<4",
]

[tool.pytest.ini_options]
# Ensure modules are not reloaded between tests
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
# Add this to prevent module reloading
addopts = "--import-mode=importlib"

# Custom markers
markers = [
  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
  "serial: marks tests that should not run in parallel (modifies global state)",
]

log_cli = true
log_cli_level = "INFO"
#log_cli_level = "DEBUG"
# log_cli_format = "%(asctime)s %(levelname)8s %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"
log_cli_format = "%(asctime)s | %(name)30s | %(levelname)8s | %(message)s"
#testpaths = [
#    "test/unit",
#]


[tool.pylint.main]

extension-pkg-allow-list = "rdkit"
# Specify a score threshold under which the program will exit with error.
fail-under = 8

[tool.pylint."MESSAGES CONTROL"]

disable = "too-few-public-methods"

[tool.pylint.basic]
variable-naming-style = "snake_case"
# Naming style matching correct class attribute names.
class-attribute-naming-style = "any"
function-naming-style = "any"

# Naming style matching correct class names.
class-naming-style = "PascalCase"
method-naming-style = "any"
# Naming style matching correct module names.
module-naming-style = "any"

[tool.pylint.format]
# Number of spaces of indent required inside a hanging or continued line.
indent-after-paren = 4

# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
# tab).
indent-string = "    "

# Maximum number of characters on a single line.
max-line-length = 100

[tool.pylint.logging]
# The type of string formatting that logging methods do. `old` means using %
# formatting, `new` is for `{}` formatting.
logging-format-style = "new"

# Logging modules to check that the string format arguments are in logging
# function parameter format.
logging-modules = ["logging"]


[tool.ruff]
# Exclude a variety of commonly ignored directories.
exclude = [
  ".git",
  ".ipynb_checkpoints",
  ".mypy_cache",
  ".pytest_cache",
  ".pytype",
  ".ruff_cache",
  ".venv",
  ".vscode",
  ".scannerwork",
  "__pypackages__",
  "_build",
  "build",
  "dist",
  "site-packages",
  "**qm_transformations.py",
]
indent-width = 4
line-length = 120

# Assume Python 3.11.
target-version = "py311"

[tool.ruff.lint]
# Enable Pyflakes `E` and `F` codes by default.
ignore = []
select = ["E", "F"]

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"

# Like Black, indent with spaces, rather than tabs.
indent-style = "space"

# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false

# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

# Enable auto-formatting of code examples in docstrings. Markdown,
# reStructuredText code/literal blocks and doctests are all supported.
#
# This is currently disabled by default, but it is planned for this
# to be opt-out in the future.
docstring-code-format = true

# Set the line length limit used when formatting code snippets in
# docstrings.
#
# This only has an effect when the `docstring-code-format` setting is
# enabled.
docstring-code-line-length = "dynamic"


[tool.mypy]
disallow_untyped_calls = true
disallow_untyped_defs = true
follow_imports = "skip"
no_implicit_optional = true
show_column_numbers = true
warn_no_return = true

[tool.isort]
extend_skip = [".gitignore", ".pylintrc", "sonar-project.properties"]

[tool.semantic_release]
version_toml = ["pyproject.toml:project.version"] # changelog file
tag_format = "v{version}"
upload_to_vcs_release = true

[tool.semantic_release.changelog]
# Recommended patterns for conventional commits parser that is scope aware
exclude_commit_patterns = [
  '''chore(?:\([^)]*?\))?: .+''',
  '''ci(?:\([^)]*?\))?: .+''',
  '''refactor(?:\([^)]*?\))?: .+''',
  '''style(?:\([^)]*?\))?: .+''',
  '''test(?:\([^)]*?\))?: .+''',
  '''build\((?!deps\): .+)''',
  '''Initial [Cc]ommit.*''',
]
mode = "update"
insertion_flag = "..\n    All versions below are listed in reverse chronological order"

[tool.semantic_release.changelog.default_templates]
changelog_file = "mkdocs/docs/Changelog.md"
output_format = "md"

[tool.semantic_release.branches.main]
match = "(main|master)"
prerelease = false

[tool.semantic_release.commit_parser_options]
minor_tags = ["feat"]
patch_tags = [
  "fix",
  "perf",
  "refactor",
  "docs",
  "style",
  "test",
  "chore",
  "ci",
  "build",
]
other_allowed_tags = [
  "build",
  "chore",
  "ci",
  "docs",
  "style",
  "refactor",
  "test",
]
allowed_tags = [
  "feat",
  "fix",
  "perf",
  "build",
  "chore",
  "ci",
  "docs",
  "style",
  "refactor",
  "test",
]
default_bump_level = 0
parse_squash_commits = true
ignore_merge_commits = true



[tool.poe.tasks]
analyse-coverage = [
  "coverage",
  { shell = "coverage xml -o coverage-report.xml", help = "Generate coverage for sonar qube" },
]
build = "uv build"
check-format = { cmd = "ruff format --check src test examples", help = "Check code format compliance" }
check-hook = "pre-commit run --all-files"
check-lint = { cmd = "ruff check src test ", help = "run static analysis checks" }
check-sort-imports = { cmd = "isort . --sg=old --check-only --profile black", help = "check imports are sorted" }
check-static-analysis = ["check-lint", "check-types"]
check-style = ["check-sort-imports", "check-format"]
check-types = { cmd = "mypy -p src --ignore-missing-imports", help = "check type hint annotations" }
coverage = { shell = "pytest test -m 'not slow and not serial' -n auto --cov-report xml --cov=mother test --junit-xml=xunit-test.xml", help = "Generate coverage report (xml)" }
dist-test = [
  "build",
  { shell = "cd dist && ../test/test-dist.bash `uv run --with tomli python -c \"import tomli; print('mother_ml-' + tomli.load(open('../pyproject.toml','rb'))['project']['version'] + '-py3-none-any.whl')\"`", help = "check build package in its own environment" },
]
docs = { shell = "cd mkdocs; mkdocs build", help = "Build documentation" }
docs-python-fences = { cmd = "python scripts/check_docs_python_fences.py", help = "Execute python fenced code blocks in docs markdown" }
format = { cmd = "ruff format src test examples", help = "Perform code style format" }
install-hook = "pre-commit install"
lint = { cmd = "ruff check src test --fix", help = "Run linter on src and test folder" }
serve-coverage = [
  "coverage",
  { shell = "coverage html -d coverage-html && cd coverage-html; python -m http.server --bind 127.0.0.1", help = "Generate coverage html report" },
]
serve-docs = { shell = "cd mkdocs; JUPYTER_PLATFORM_DIRS=1 mkdocs serve", help = "Serve project html documentation" }
sort-imports = { cmd = "isort . --sg=old --profile black", help = "apply import sort ordering" }
style = ["sort-imports", "format"]
test-unit = { shell = "pytest test -m 'not slow and not serial' -n auto && pytest test -m 'serial and not slow' -n 0" }
test-slow = { shell = "pytest test -m 'slow' -n auto" }


[tool.uv.build-backend]
module-name = "mother"

[build-system]
requires = ["uv_build>=0.11.1,<0.12.0","setuptools>=76.0.0"]
build-backend = "uv_build"