pyproject.toml

[build-system]
# pdm
requires = ["pdm-backend"]
build-backend = "pdm.backend"
# hatch
#requires = ["hatchling"]
#build-backend = "hatchling.build"

[project]
name = "mammoth"
authors = [
  { name = "Raymond Ehlers", email = "raymond.ehlers@cern.ch" },
]
description = "Mostly columnar based physics analyses"
readme = "README.md"
license.file = "LICENSE"
requires-python = ">=3.10"
classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Science/Research",
  "Intended Audience :: Developers",
  "License :: OSI Approved :: BSD License",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering",
  "Typing :: Typed",
]
dynamic = ["version"]
dependencies = [
    "awkward >=2.0.8",
    "uproot >=4.2",
    "numpy >=1.21",
    "scipy >=1.11.3",
    "pyarrow >=4",
    "pyhepmc >=2.12.0",
    "pandas >=2.0",
    "attrs >=21.2.0",
    "particle >=0.15.1",
    "numba >=0.56.0",
    "boost-histogram >=1.5",
    "hist[plot] >=2.8",
    "seaborn >=0.11.2",
    "vector >=0.8.5",
    "parsl[monitoring] >=2023.10.23",
    "rich >=v13.4.0",
    # My packages last:
    # - mammoth_cpp
    # For general:
    #"mammoth_cpp >=0.1",
    # For pdm:
    "mammoth_cpp @ file:///${PROJECT_ROOT}/mammoth-cpp",
    # For hatch:
    #"mammoth_cpp @ file://{root:uri}/mammoth-cpp",
    # - pachyderm
    # For pdm: it's in the dev dependencies since we want it to be editable, but we can
    # copy it twice, see here: https://github.com/pdm-project/pdm/discussions/1479
    "pachyderm >= 3.0",
    # For hatch: we can install it locally (but not editable) with:
    #"pachyderm @ file://{root:uri}/external/pachyderm",
    "dask[distributed,diagnostics]>=2022.12.0",
    "dask-jobqueue>=0.8.1",
    "rich-argparse>=1.4.0",
    "strenum>=0.4.15; python_version < \"3.11\"",
]

[project.optional-dependencies]
test = [
    "pytest >=6.2.4",
    "pytest-cov >=3",
    "pytest-sugar >=0.9.5",
]
docs = [
    "sphinx>=7.0",
    "myst_parser>=0.13",
    "sphinx_copybutton",
    "sphinx_autodoc_typehints",
    "furo>=2023.08.17",
]

# NOTE: We use this for the dev dependencies because we need the PDM support for local
#       editable repositories. If we ever don't need that, we can just move it to the
#       standard compliant groups in `[project.optional-dependencies]` (eg. if moving to hatch)
[tool.pdm.dev-dependencies]
dev = [
    "ruff >=0.0.209",
    "mypy >=0.931",
    "ipython >=8.0",
    "ipykernel >=6.15.1",
    "pytest >=6.2.4",
    "pytest-cov >=3",
    "pytest-sugar >=0.9.5",
    "pytest-xdist >=3.1.0",
    # Included so we can grab the headers for vscode (also so that we can build in the env if we want)
    "pybind11 >=2.10",
    # pachyderm
    # pdm requires editable dependencies to be in the dev dependencies
    "-e file:///${PROJECT_ROOT}/external/pachyderm#egg=pachyderm",
]

[project.scripts]
shadd = "mammoth.framework.io.output_utils:shit_hadd"
handle_files_from_failed_jobs = "mammoth.job_file_management_utils:steer_handle_files_from_failed_jobs_entry_point"
count_events_in_track_skim = "mammoth.framework.io.track_skim_utils:count_events_in_track_skim_entry_point"

[project.urls]
Homepage = "https://github.com/raymondEhlers/mammoth"
"Bug Tracker" = "https://github.com/raymondEhlers/mammoth/issues"
Discussions = "https://github.com/raymondEhlers/mammoth/discussions"
Changelog = "https://github.com/raymondEhlers/mammoth/releases"

[tool.hatch]
version.path = "src/mammoth/__init__.py"

[tool.pdm.version]
source = "scm"
write_to = "mammoth/_version.py"
write_template = "version = '{}'"

[tool.pdm.build]
excludes = [
    "tests/track_skim_validation/input/alice",
    "tests/track_skim_validation/**/*.root",
    "tests/track_skim_validation/**/*.parquet",
    "tests/track_skim_validation/**/*.pdf",
    "**/.mypy_cache/",
]


[tool.pytest.ini_options]
minversion = "6.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
filterwarnings = [
  "error",
  # Temporarily until this is resolved: https://github.com/dateutil/dateutil/issues/1314
  # NOTE: It is coming from dateutil, which is used by matplotlib + pandas
  "ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:dateutil.tz.tz",
]
#log_level = "INFO"
#log_cli_level = "DEBUG"
testpaths = [
  "tests",
]


[tool.coverage]
run.source = ["mammoth"]
report.exclude_also = [
  '\.\.\.',
  'if typing.TYPE_CHECKING:',
]


[tool.mypy]
files = ["src", "tests"]
python_version = "3.10"
warn_unused_configs = true
strict = true
show_error_codes = true
enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
warn_unreachable = true
no_implicit_reexport = false
disallow_untyped_defs = false
disallow_incomplete_defs = false
exclude = [".venv*"]

[[tool.mypy.overrides]]
module = "mammoth.*"
disallow_untyped_defs = true
disallow_incomplete_defs = true

[[tool.mypy.overrides]]
module = [
    "boost_histogram",
    "coloredlogs",
    "cycler",
    "dask.*",
    "enlighten",
    "jet_substructure.*",
    "IPython",
    "matplotlib.*",
    "mplhep",
    "networkx.*",
    "numba",
    "numpy",
    "pandas",
    "pyarrow.*",
    "parsl.*",
    "ROOT",
    "seaborn",
    "scipy.interpolate",
    "scipy",
    "strenum",  # Only for python 3.10 and below
    "uproot",
    "pyhepmc",
    "awkward",
    "ruamel.*",
    "dask_jobqueue",
    "rich_argparse",
    # NOTE: Many of these are not direct dependencies, but implicit dependencies of actual dependencies.
    #       For some reason, this fails occasionally, and the easiest response is just to ignore.
    #       pre-commit + mypy really is extraordinarily painful...
    "traitlets.*",
    "tornado.*",
    "paramiko",
    "jupyter",
    "jupyter_server",
]
ignore_missing_imports = true


[tool.ruff]
src = ["src"]
line-length = 120
exclude = [
    '.git',
    '.env',
    '.env3',
    '.venv',
    '.venv*',
    'env',
    '__pycache__',
    'bak',
    'build',
    'dist',
    "src/*/_version.py",
    "projects/jetscape/summer_school_2022",
]

[tool.ruff.lint]
extend-select = [
  "B",        # flake8-bugbear
  "I",        # isort
  "C901",     # mccabe
  "ARG",      # flake8-unused-arguments
  "C4",       # flake8-comprehensions
  "EM",       # flake8-errmsg
  "ICN",      # flake8-import-conventions
  "G",        # flake8-logging-format
  "PGH",      # pygrep-hooks
  "PIE",      # flake8-pie
  "PL",       # pylint
  "PT",       # flake8-pytest-style
  "PTH",      # flake8-use-pathlib
  "RET",      # flake8-return
  "RUF",      # Ruff-specific
  "SIM",      # flake8-simplify
  "T20",      # flake8-print
  "UP",       # pyupgrade
  "YTT",      # flake8-2020
  "EXE",      # flake8-executable
  "NPY",      # NumPy specific rules
  "PD",       # pandas-vet
]
ignore = [
  "PLR09",    # Too many <...>
  "PLR2004",  # Magic value used in comparison
  "ISC001",   # Conflicts with formatter
  "ISC003",   # Force string to be implicitly concatenated. However, I find this structure to be useful for better
              # readability due to consistent spacing with plotting labels.
  "G004",     # Logging format string. This isn't best practices, but I use it too much to change for now
  "PLC0414",  # Messes with the re-export of imports needed from mypy
  "PD011",    # Calls to `.values` are usually for histograms, not pandas. This is getting picked up as a false positive
]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["T20"]
"noxfile.py" = ["T20"]
"projects/**" = [
  "T20",      # Print statements are fairly common in jupyter notebooks
  "E402",     # Module level import not at top of file are fairly common in notebooks
  "F841",     # Again, unused variables are common in notebooks
  "B018",     # For useless variables. Sometimes we have useless statements to print them
]

[tool.ruff.lint.mccabe]
max-complexity = 12

[tool.ruff.lint.isort]
required-imports = ["from __future__ import annotations"]
known-first-party = ["mammoth", "mammoth_cpp"]


[tool.pylint]
py-version = "3.10"
ignore-paths = [".*/_version.py"]
reports.output-format = "colorized"
similarities.ignore-imports = "yes"
messages_control.disable = [
  "design",
  "fixme",
  "line-too-long",
  "missing-module-docstring",
  "wrong-import-position",
]


[tool.codespell]
ignore-words-list = "subjet, gaus, fpt, slac"


[tool.check-manifest]
ignore = [
  ".github/**",
  "docs/**",
  ".pre-commit-config.yaml",
  ".readthedocs.yml",
  "src/*/_version.py",
  "noxfile.py",
]