shapepipe/pyproject.toml at develop · CosmoStat/shapepipe · GitHub

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[project]
name = "shapepipe"
version = "1.1.0"
description = "Galaxy shape measurement pipeline."
readme = "README.rst"
authors = [
    { name = "Samuel Farrens", email = "samuel.farrens@cea.fr" },
    { name = "Axel Guinot", email = "axel.guinot@cea.fr" },
    { name = "Martin Kilbinger", email = "martin.kilbinger@cea.fr" }
]
license = "MIT"
license-files = ["LICENSE"]
requires-python = ">=3.12"
# Dependencies are PINNED to exact versions and kept current by Renovate (see
# renovate.json). shapepipe ships as a container, not a published library, so
# there are no downstream installers to keep flexible — pinning is what lets
# Renovate honor a supply-chain release-age delay before adopting a new release
# (it can't hold uv back to an aged version through a floor range;
# renovatebot/renovate#41624). `uv.lock` is the reproducible manifest generated
# by uv (never hand-edited).
dependencies = [
    "astropy>=7.0",          # major 6 → 7
    "astroquery",
    "canfar",
    "cs_util>=0.2.1",
    "galsim>=2.8",
    "h5py",
    "joblib>=1.4",
    "matplotlib>=3.10",
    "mccd>=1.2.4",
    "modopt>=1.6",
    "mpi4py>=4.1.2",
    "numba>=0.59",           # numpy 2 support
    "numpy>=2.4.6",            # major 1 → 2
    "pandas>=3.0.3",           # major 2 → 3
    "python-dateutil",
    "python-pysap>=0.3",
    "PyQt5",
    "pyqtgraph",
    "reproject>=0.19",
    "sf_tools>=2.0.4",
    "skaha>=1.7",
    "sqlitedict>=2.0",
    "termcolor",
    "tqdm>=4.68.1",
    "vos>=3.6",
    "ngmix>=2.4",
]


[project.optional-dependencies]
doc = [
    "myst-parser",
    "numpydoc",
    "sphinx",
    "sphinxcontrib-bibtex",
    "sphinx-book-theme"
]
jupyter = [
    "ipython>=9.14.1",
    "jupyterlab>=4.5.9",
    "snakemake>=9.22.0",
]
lint = [
    "ruff",
]
release = [
    "build",
    "twine",
]
test = [
    "hypothesis>=6.155.2",
    "pytest>=8.3",
    "pytest-cov>=5.0",
]
fitsio = ["fitsio"]
dev = ["shapepipe[doc,jupyter,lint,release,test,fitsio]"]

[project.scripts]
shapepipe_run       = "shapepipe.shapepipe_run:main"
summary_run         = "shapepipe.summary_run:main"
canfar_submit_job   = "shapepipe.canfar_run:run_job"
canfar_monitor      = "shapepipe.canfar_run:run_log"
canfar_monitor_log  = "shapepipe.canfar_run:run_monitor_log"

[tool.uv]
# shapepipe targets Linux only; skip Windows/macOS wheel resolution
environments = ["sys_platform == 'linux'"]

[tool.uv.sources]
ngmix = { git = "https://github.com/esheldon/ngmix", tag = "v2.4.0" }
# Track cs_util's develop branch (a git ref, not a pinned release) so new
# cs_util.size / cs_util.shape helpers are available without shipping a release
# and rebuilding the image each time. shapepipe's column grammar sources size
# (T = 2*sigma^2) and ellipticity conversions from cs_util.
cs_util = { git = "https://github.com/CosmoStat/cs_util", branch = "develop" }

[build-system]
# Declaring a build backend makes shapepipe an installed package (not a uv
# "virtual" project), so `uv sync` / `pip install -e .` put it on the path
# rather than only its dependencies.
requires = ["setuptools>=61"]
build-backend = "setuptools.build_meta"

[tool.setuptools]
script-files = [
    "scripts/python/update_runs_log_file.py",
    "scripts/sh/init_run_v2.0.sh",
    "scripts/sh/run_job_sp_canfar_v2.0.bash",
    "scripts/sh/job_sp_canfar_v2.0.bash",
]

[tool.setuptools.packages.find]
where = ["src"]

[tool.ruff]
# Ruff is the single lint + format tool, replacing black, isort, and the
# pytest-pycodestyle / pytest-pydocstyle plugins (the latter broke on the
# pytest 9.1 hookspec change). Rules below cover pycodestyle (E/W), Pyflakes
# (F), import sorting (I), and numpydoc-style docstrings (D) — matching the
# project style: PEP 8 + numpydoc.
line-length = 79
target-version = "py312"
src = ["src", "tests"]

[tool.ruff.lint]
select = ["E", "W", "F", "I", "D"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.pytest.ini_options]
# One discovery root: everything lives under `tests/`. Tiers are
# `module/` (per-module unit tests, import package internals directly),
# `unit/` (structural), `science/` (fast guardrails), `cluster/` (candide,
# marked `candide`+`slow`), with shared library code in `helpers/`. See
# tests/README.md.
addopts = "--verbose --strict-markers --cov=shapepipe --cov-report=term-missing"
testpaths = ["tests"]
markers = [
    "slow: heavy compute (minutes); excluded from the fast inner loop.",
    "candide: needs the candide cluster and/or its real data; auto-skipped elsewhere.",
]