pyproject.toml

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

[project]
dynamic= ["version"]
name = "picasso_workflow"
description = "Automation and documentation of DNA-PAINT analysis workflows"
license = {'file' = "LICENSE"}
requires-python = ">=3.10"
dependencies = [
    "matplotlib",
    "seaborn",
    "numpy",
    "pandas",
    "tables",
    "numba",
    "openpyxl==3.1.2",
    "picassosr>=0.11.0a1",
    # GUI uses PyQt6 directly; keep in sync with picasso's constraint
    "PyQt6>=6.10.2,<7",
    # Embedded HTML report viewer in the GUI Results tab (QWebEngineView);
    # keep the major/minor in sync with PyQt6.
    "PyQt6-WebEngine>=6.10,<7",
    # NVML bindings for GPU CUDA-core count in analysis_documentation
    # (nvidia-smi cannot report cores). Harmless without an NVIDIA driver.
    "nvidia-ml-py>=12.0.0",
    "moviepy==1.0.3",
    "python-dotenv==1.0.1",
    "pre-commit>=3.5.1",
    "bandit==1.7.8",
    # "coverage>=6.5,<6.6",
    "pytest==8.1.1",
    "isort==5.13.2",
    "aicspylibczi>=3.1.1",
    "fsspec>=2022.8.0",
    "aicsimageio",
    "psutil",
    "atlassian-python-api",
    "memory-profiler>=0.61.0",
    "loguru>=0.7.3",
    "h5py",
    "memory_profiler",
    # "mpi4py",
    # "openmpi"
]
keywords = ["picasso"]

[project.scripts]
picasso-workflow-gui = "picasso_workflow._launcher:main"

[project.optional-dependencies]
cluster = [
    "mpi4py>=4.0.2",
]

[tool.setuptools]
packages = ["picasso_workflow"]

[tool.setuptools_scm]
# Writes the version into a file that is importable at runtime, even when
# installed from a wheel or sdist (i.e. without a .git directory).
write_to = "picasso_workflow/_version.py"
# Shown when the package is imported outside a git repository and no tag
# is reachable (e.g. a fresh checkout with no tags yet).
fallback_version = "0.3.3.dev0"

[tool.setuptools.package-data]
picasso_workflow = ["picasso-workflow.ico"]

[tool.black]
line-length = 79
include = "\\.pyi?$"
exclude = '''
/(
    \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | buck-out
  | build
  | dist
)/
'''

[tool.mypy]
strict = true

[tool.flake8]
# Stock flake8 only (E/W = pycodestyle, F = pyflakes, C90 = complexity). Line
# length is owned by black, so E501 is ignored here (black already wraps code;
# long strings/comments/HTML it can't split are intentional). E203/W503 are
# the standard black-compatibility ignores.
max-line-length = 88  # informational; E501 is ignored
extend-ignore = "E203,E501,W503"
# extend-exclude keeps flake8's sensible defaults and additionally skips the
# generated/snapshot test fixtures and the isolated experimental modules
# (not imported by the package) that still carry WIP F-codes.
extend-exclude = "docs,picasso_workflow/spinna_mle.py,picasso_workflow/spinna_mle_2.py,picasso_workflow/nn_redistribution.py,picasso_workflow/tests/TestData"

[tool.bandit]
exclude = "/tests"
skips = "B105,B404"
baseline = "bandit-baseline.json"
format = "txt"

[tool.pytest-cov]
[pytest-cov.run]
branch = "True"
[pytest-cov.report]
fail_under = 80

[tool.pytest.ini_options]
minversion = "6.0"
# Local default: run only the fast unit tests. The heavy `integration`
# tests (synthetic pipeline + template smoke) are deselected here so a bare
# `pytest -v` stays quick during development. Opt back in explicitly with
# `pytest -m integration` (or run them on the cluster via
# tools/cluster_tests/submit_all.sh). The cluster tier sbatch scripts pass
# their own `-m ...`, which overrides this default (last `-m` wins).
addopts = "-ra -q -m 'not integration'"
testpaths = ["picasso_workflow/tests"]
markers = [
    "integration: tests that run the real picasso pipeline (run with '-m integration'; deselected by default)",
    "real_data: tests that require acquired datasets from the lab network volumes (set PW_TEST_DATA_DIR)",
]
# picasso announces API changes (a default flipping, a function going private)
# via DeprecationWarning, which Python hides by default -- so a picassosr bump
# silently breaks the workflow at runtime on the cluster instead of here. Fail
# the test run on them. Scoped to `picasso.*` so unrelated third-party
# deprecations stay warnings; the pattern is a regex matched against the
# emitting module's __name__, and "picasso\." excludes our own
# "picasso_workflow.*" modules.
filterwarnings = [
    'error::DeprecationWarning:picasso\..*',
]