pyproject.toml

[project]
name = "sp_validation"
version = "0.6.0"
description = "Validation of weak-lensing catalogues (galaxy and star shapes and other parameters) produced by ShapePipe"
authors = [
    {name = "Martin Kilbinger", email = "martin.kilbinger@cea.fr"},
    {name = "Cail Daley", email = "cail.daley@cea.fr"},
    {name = "Sacha Guerrini", email = "sacha.guerrini@cea.fr"},
]
license = {text = "MIT"}
readme = "README.md"
# 3.12 floor: cosmo-numba (a hard dependency below) requires >=3.12, and the
# production container is Python 3.12 (shapepipe base image). Keeping the floor
# in sync with the container is what makes `uv lock` resolvable.
requires-python = ">=3.12"
classifiers = [
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Operating System :: Unix",
    "Operating System :: MacOS"
]
dependencies = [
    "adjustText",
    "astropy>=5.0",
    # Floor at the current latest release; do not cap — we want the eventual
    # scipy-1.18 fix release. Revisit the scipy cap below when camb ships
    # > 1.6.6 with the scipy-1.18 / BBN fix.
    "camb>=1.6",
    "clmm",
    "colorama",
    # Track cs_util's develop branch directly (git dependency) rather than a
    # PyPI pin: the two repos are iterating together heavily and cs_util
    # releases are infrequent. This PR's cosmology repoint needs get_cosmo /
    # get_theo_c_ell / get_theo_xi / PLANCK18 in cs_util.cosmo, which land via
    # CosmoStat/cs_util#76 — so this goes green once #76 merges into develop.
    "cs_util @ git+https://github.com/CosmoStat/cs_util.git@develop",
    # Fast numba B-mode kernels (Schneider et al. 2022): the Schneider E/B split
    # and COSEBIS live here, imported in b_modes.py. Tracks aguinot/cosmo-numba
    # main (not published on PyPI). main carries the numpy-2 FFT fix via its
    # rocket-fft dependency (which teaches numba's nopython mode to handle
    # np.fft), and declares numba/numpy/rocket-fft from its requirements.txt so
    # those constraints reach the resolver.
    "cosmo-numba @ git+https://github.com/aguinot/cosmo-numba.git@main",
    "emcee",
    # numba is the load-bearing pin of this whole environment: its numpy ceiling
    # (numba 0.66 -> numpy<2.5) is what keeps the resolver from drifting numpy
    # forward and breaking numba/ngmix — the failure this lockfile exists to
    # prevent. cosmo-numba above also carries this constraint, but we pin numba
    # ourselves too: it makes the one critical constraint visible and resilient
    # to cosmo-numba's dependency metadata (which has silently emptied out
    # between refs before). We pin numba, never numpy directly.
    "numba",
    # Imported directly across src/ (calibration, plots) alongside seaborn —
    # declared explicitly rather than leaned on as a seaborn transitive.
    "matplotlib",
    "pandas",
    "pyyaml",
    # SHA-pinned snapshot of getdist branch `upper_triangle_whisker`.
    "getdist @ git+https://github.com/benabed/getdist.git@113cd22a9a0d013b6f72fe734be81f260f3d3be5",
    "h5py",
    "healpy",
    "healsparse",
    "importlib_metadata",
    "joblib>=0.13",
    "jupyter",
    "jupyterlab",
    "jupytext>=1.15",
    "lenspack",
    "lmfit",
    "numpy>=2.0",
    "opencv-python-headless",
    "pyccl",
    "pyarrow",
    "pymaster",
    "regions",
    "reproject",
    # scipy 1.18 ported FITPACK from Fortran to C, changing the return shape of
    # RectBivariateSpline(scalar, scalar, grid=False) from 0-d `array(x)` to
    # shape-(1,) `array([x])`. camb's BBN Y_He predictor (bbn.py) wraps the
    # result in np.float64(), which collapses a 0-d array to a scalar but leaves
    # a (1,) array as (1,); set_cosmology then fails at the ctypes float
    # assignment `self.YHe = YHe` with `TypeError: only 0-dimensional arrays can
    # be converted to Python scalars`, failing all get_cosmo-backed tests. camb
    # 1.6.6 (latest on PyPI) and current master are both unfixed. Lift this cap
    # when camb ships > 1.6.6 with the scipy-1.18 fix.
    "scipy<1.18",
    "seaborn",
    # Intentionally tracks the mutable `develop` branch (NOT SHA-pinned):
    # shear_psf_leakage is actively co-developed CosmoStat code we want to stay
    # current with, so freezing it would only create bump-churn. (Contrast the
    # getdist feature-branch below, which is an external fork we pin for repro.)
    "shear_psf_leakage @ git+https://github.com/CosmoStat/shear_psf_leakage.git@develop",
    "skyproj",
    "statsmodels",
    "treecorr>=5.0",
    "tqdm",
    "uncertainties"
]

[project.urls]
Homepage = "https://github.com/CosmoStat/sp_validation"

[tool.uv]
# The reproducibility target is the Linux container; scope the lock to Linux
# (mirrors shapepipe) so `uv lock` resolves the linux-centric stack (pymaster,
# mpi4py) without hunting for macOS/Windows wheels. macOS dev installs still
# work via `uv pip install -e .` (unlocked), just not `uv sync` from the lock.
environments = ["sys_platform == 'linux'"]

[project.optional-dependencies]
test = [
    "pytest",
    "pytest-cov",
    "ruff"
]
docs = [
    "sphinx>=8.0",
    "myst-parser>=4.0",
    "numpydoc>=1.8",
    "sphinxcontrib-bibtex>=2.6",
    # 6.0.3 is a broken wheel on PyPI (dist-info only, no python module)
    "sphinxawesome-theme>=5.3,!=6.0.3"
]
# GLASS mock generation (sp_validation.glass_mock). Kept optional: the core
# library and its import guard resolve without GLASS, and the production
# container does not yet ship it. Pinned set (verified 2026-06-13, fiber
# glass-cosmology-api-pin): glass 2025.1 is the unique version with the flat API
# the map path uses AND the legacy ``cosmo.dc``/``xm``/``ef`` interface that
# ``cosmology`` 2022.10.9 (its newest release) provides — newer glass calls
# ``comoving_distance``, which no ``cosmology`` release exposes. ``matter_cls``
# lives in the separate ``glass.ext.camb`` package (absent from glass core
# >=2024.2), so it is pinned explicitly.
glass = [
    "glass==2025.1",
    "glass.ext.camb==2023.6",
    "cosmology==2022.10.9",
    # fitsio: make_unions_glass_sim.py writes the mock catalogue as FITS.
    "fitsio",
]
# Cosmo-inference workflow runners (workflow/scripts/*). Kept optional: the core
# library resolves without them, but the container installs this extra so the
# Snakemake workflow and cross-validation runners are available.
workflow = [
    "snakemake",
    # run_2pcf_highres.py drives the MPI convergence run; the container ships
    # OpenMPI (/opt/ompi) so mpi4py builds against it.
    "mpi4py",
    # NOTE: workflow/scripts/cv_*.py also import `cv_runner`, which is not
    # published or resolvable (no public repo found) — left undeclared pending
    # its source. Same for `unions_wl` (scripts/check_footprint.py).
]
develop = ["sp_validation[test,docs]"]

[tool.pytest.ini_options]
testpaths = ["src/sp_validation/tests"]
addopts = [
    "--verbose",
    "--cov=sp_validation",
    "--cov-report=term",
    "--cov-report=xml",
    "--junitxml=pytest.xml",
    # The base ShapePipe image's test extra ships old pytest-pydocstyle /
    # pytest-pycodestyle, whose pytest_collect_file hooks use the `path` arg the
    # newer pytest our lock installs has removed — they crash collection.
    # sp_validation lints with ruff, not these, so don't load them. Harmless if
    # absent (`-p no:` just skips an unregistered plugin).
    "-p", "no:pydocstyle",
    "-p", "no:pycodestyle"
]
markers = [
    "fast: marks tests as fast (deselect with '-m \"not fast\"')",
    "slow: marks tests as slow (deselect with '-m \"not slow\"')"
]

[tool.ruff]
line-length = 88
target-version = "py312"

# Snakemake injects a `snakemake` object into rule scripts at runtime, so ruff
# can't see where it's defined. Declaring it a builtin silences the false
# `F821 undefined-name` it raises in `workflow/scripts/*` (~110 hits) while
# still catching every other undefined name in those scripts.
builtins = ["snakemake"]

[tool.ruff.lint]
select = [
    "E",  # pycodestyle errors
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    "I",  # isort
]
ignore = [
    "E712",  # comparison to True should be 'if cond is True:' or 'if cond:'
    "E501",  # line-too-long: the formatter owns line width (ruff's own guidance)
]

# Region-aware relaxations. src/ stays strict (no ignores). The peripheral
# trees — workflow scripts, per-paper analysis scripts, top-level scripts, and
# scratch — legitimately do sys.path manipulation before importing (E402) and
# pull names in via `from x import *` (F403/F405); enforcing those there would
# be noise, not signal.
[tool.ruff.lint.per-file-ignores]
"workflow/scripts/*" = ["E402"]
"papers/*/scripts/*" = ["E402", "F403", "F405"]
"papers/*/*.py" = ["E402", "F403", "F405"]  # per-paper analysis scripts live at this level too
"scripts/*" = ["E402", "F403", "F405"]
"scratch/*" = ["E402", "F403", "F405"]
"cosmo_inference/**" = ["E402"]  # notebooks + scripts do sys.path + mpl-backend setup before imports (covers .ipynb cells, not just .py)