diff --git a/.gitignore b/.gitignore index f1e8d1bb..82fb2697 100644 --- a/.gitignore +++ b/.gitignore @@ -122,7 +122,7 @@ venv.bak/ # and the lockfile has never been tracked. Ignore it rather than commit a # pinned-dep reproducibility promise the project hasn't made. Flip to tracked # if we decide to pin deps via uv. -uv.lock +# uv.lock is committed — it is the reproducible pin the container installs from. # Spyder project settings .spyderproject diff --git a/Dockerfile b/Dockerfile index c791877c..7df622a0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,24 +12,28 @@ RUN apt-get update -y --quiet --fix-missing && \ npm \ tmux -# The base image installs into the system interpreter (/usr/local); use `uv pip` -# so the heavy scientific stack and our deps land where `python` resolves. -RUN uv pip install --no-cache-dir \ - snakemake - -# The base shapepipe image ships cs_util 0.1.9, and `uv pip install -e` does NOT -# upgrade an already-satisfied dependency to meet a *new* lower bound (astral-sh/uv -# #8410). sp_validation now needs `cs_util.size` (cs_util>=0.2.1), so upgrade it -# explicitly here — otherwise the editable install silently keeps 0.1.9 and the -# galaxy import smoke test fails. shear_psf_leakage@develop allows cs-util<0.3, -# so 0.2.x satisfies the whole graph. -RUN uv pip install --no-cache-dir --upgrade 'cs_util>=0.2.1' +# The base shapepipe image provides a uv-managed venv at /app/.venv (exported as +# VIRTUAL_ENV); install sp_validation's deps into that same venv rather than +# spawning a second one under /sp_validation. +ENV UV_PROJECT_ENVIRONMENT=/app/.venv WORKDIR /sp_validation -COPY . /sp_validation -# Install with the test + glass extras so the image can run the unit suite in CI -# *and* the GLASS map-level mock test. `glass` (Generator for Large Scale -# Structure) ships `glass.ext.camb`; `cosmology` provides the `Cosmology` wrapper -# (`Cosmology.from_camb`) GLASS consumes. Both come in via the `[glass]` extra. -RUN uv pip install --no-cache-dir -e '.[test,glass]' +# uv.lock is the SSOT: `uv sync --frozen` installs exactly what it pins, so an +# image build can never silently re-resolve and drift a base-image version (the +# numpy-past-numba drift this lockfile exists to prevent). `--inexact` keeps the +# base image's ShapePipe stack (shapepipe, ngmix, galsim, …) — packages not in +# our lock — instead of pruning them. Copy the lock + manifest first so this +# layer caches independently of source edits. Extras: test (CI unit suite), +# glass (GLASS map-level mock — pulls glass.ext.camb + the cosmology wrapper), +# workflow (Snakemake + mpi4py runners). cs_util 0.2.2 (with cs_util.size) and a +# numba-safe numpy 2.4.6 come straight from the lock, so the old ad-hoc snakemake +# and cs_util `--upgrade` layers are gone. +COPY pyproject.toml uv.lock /sp_validation/ +RUN uv sync --frozen --inexact --no-install-project \ + --extra test --extra glass --extra workflow + +# Install sp_validation itself (editable) into the same venv; deps are already +# satisfied by the sync above. +COPY . /sp_validation +RUN uv pip install --no-deps -e . diff --git a/pyproject.toml b/pyproject.toml index bb1fe413..150aba11 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,10 @@ authors = [ ] license = {text = "MIT"} readme = "README.md" -requires-python = ">=3.11" +# 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", @@ -31,7 +34,27 @@ dependencies = [ # 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", @@ -78,6 +101,13 @@ dependencies = [ [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", @@ -105,6 +135,20 @@ 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]"] @@ -115,7 +159,14 @@ addopts = [ "--cov=sp_validation", "--cov-report=term", "--cov-report=xml", - "--junitxml=pytest.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\"')", @@ -124,7 +175,7 @@ markers = [ [tool.ruff] line-length = 88 -target-version = "py311" +target-version = "py312" # Snakemake injects a `snakemake` object into rule scripts at runtime, so ruff # can't see where it's defined. 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