scratch/guerrini/ and the namaster_utils→source / Gaussian-sims work he
reserved for his next PR in the #197 review. So future workers don't touch it.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…ation

Follow-up polish on the basic.py dissolution (#199).

Tests — characterization (value-drift) coverage for the three statistics.py
helpers that had none, with literals generated by running the real functions
in-container and teeth on each:
- corr_from_cov: unit diagonal + reconstruction from cov/outer(std,std)
- chi2_and_pte: diagonal reduces to sum((d/sigma)^2) with matching scipy PTE,
  plus a non-diagonal case exercising the full d^T C^-1 d path
- cov_from_one_covariance: gaussian(col 10) vs non-gaussian(col 9) selection
  and a row-major-layout check (a transpose would be caught)

Calibration — strictly behavior-preserving dead-code removal:
- 3 unused module imports (util, io, get_footprint — verified unreferenced)
- an unused local (col_noshear) in metacal._read_data
- the uncallable metacal._return method (defined without self, references
  self.* in its body — would NameError if ever invoked; referenced nowhere)

Value pins (metacal R-matrix, m/c bias) stay green; conservatively skipped any
change that would reorder float ops or restructure an estimator. Verified by an
adversarial behavior-preservation review.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

info.py had zero importers; its only content was a redundant
__name__ = 'sp_validation'. cat.py imported __version__ and __name__
from the package root but used only __version__ (line 607); the
software name at line 606 is already hardcoded. Repoint to the
canonical home: from sp_validation.version import __version__.

Register the retired import path in the dangling-move guard.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

The old __all__ listed modules nobody imports through the package
(io, plot_style, cosmo_val) and omitted the two genuinely public
diagnostic modules rho_tau and b_modes. Replace it with the real
public surface, alphabetised, and drop the stale commented-out
explicit-import block. Nothing does `from sp_validation import *`,
so this is purely a documentation fix.

(util and run_joint_cat are renamed in the Tier-2 commits.)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Five methods each imported from .b_modes inside their bodies. b_modes
is import-time side-effect-light (it pulls only .cosmology) and has no
back-edge to cosmo_val, so the locals were defensive, not necessary.
Consolidate the union of imported names into one top-level block next
to the existing cosmology/rho_tau imports and drop the five inline
imports. test_cosmo_val: 11 passed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Two module-level defs named confusion_matrix existed; the first
(mask, confidence_level=0.9) was a near-duplicate of correlation_matrix
and was unconditionally shadowed by the second
(prediction, observation) ~40 lines later. Every caller — in
scripts/calibration and scripts/examples — uses the
(prediction, observation) signature. Remove the dead first def.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Five functions had zero callers anywhere in the repo (src, scripts,
papers, scratch, notebooks), including across the star-imports of
plots:
  cosmology.py: get_clusters, stack_mm3, gamma_T_tc, xi_gal_gal_tc
  plots.py:     plot_map_stacked
Removing the cosmology block also orphaned the imports that existed
solely for it (treecorr, fits, canfar, radec2xy, cKDTree, tqdm,
get_footprint); drop those too. test_cosmology + test_plots: 29 passed.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

util.py held only millify / print_millified — number formatting, not a
grab-bag. Rename it to format.py and sweep all importers:
  internal: cat.py, run_joint_cat.py (util.millify -> format.millify)
  scripts:  apply_alpha.py, examples/demo_calibrate_minimal_cat.py,
            calibration/extract_info.py (star-import x2)
  papers:   catalog/hist_mag.py
Register the rename in the dangling-move guard; update package __all__.

B1: scripts/plot_leakage.py imported transform_nan from the old util
module — a symbol removed from the library long ago and never used in
the script. Drop the dead import.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

SquareRootScale is a matplotlib ScaleBase subclass — plotting
infrastructure, not rho/tau logic. Move the class and its
register_scale call into plots.py (which now carries the
matplotlib.scale/ticker/transforms imports it needs). rho_tau.py keeps
a compat re-export so existing
`from sp_validation.rho_tau import SquareRootScale` callers — in
cosmo_inference, scratch/guerrini, papers/harmonic — still resolve.

workflow/scripts/plotting_utils.py holds a near-duplicate that
diverges (ScalarFormatter(useMathText=True); inverted transform method
named transform_non_affine not transform), so it is left in place.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Six harmonic-space scripts imported SquareRootScale from
sp_validation.utils_cosmo_val, a module that no longer exists. Repoint
to sp_validation.rho_tau (the compat re-export), matching the sibling
2026_03_17 script. get_params_rho_tau was already correctly imported
from rho_tau. No other utils_cosmo_val imports remain (the two
scratch/guerrini mentions are prose noting the module's removal).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

The module holds the catalogue-builder runner classes (JointCat,
ApplyHspMasks, CalibrateCat) and their run_* entry-point functions;
catalog_builders names that role. Sweep all importers (the
`as sp_joint` alias is preserved, only the module name changes):
  scripts/apply_hsp_masks.py
  scripts/examples/{demo_check_footprint, create_binned_mask_comprehensive,
    demo_comprehensive_to_minimal_cat, demo_create_footprint_mask,
    demo_calibrate_minimal_cat}.py
  scripts/calibration/{create_joint_comprehensive_cat (direct symbol),
    demo_apply_hsp_masks, calibrate_comprehensive_cat}.py
  scratch/kilbinger/demo_binned_mask.py
  papers/catalog/hist_mag.py
Also update the two prose references in docs and update __all__ and
the dangling-move guard.

The OPTIONAL masks.py extraction (Mask + mask-algebra fns) is deferred:
those symbols are reached externally through the sp_joint.* module
alias (Mask, get_masks_from_config, print_mask_stats across 4 scripts +
papers/catalog), so splitting them out would require either re-exports
or sweeping the public call surface — beyond a behavior-preserving move.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Move the healsparse-backed spatial-masking cluster out of
catalog_builders.py into a dedicated masks.py: the Mask class plus
get_masks_from_config, print_mask_stats, correlation_matrix, and
confusion_matrix. Bodies are byte-identical; the move carries the
numexpr/scipy.stats imports those helpers need (now removed from
catalog_builders, which no longer references them).

catalog_builders.py re-exports the five symbols from sp_validation.masks
so external code using `from sp_validation import catalog_builders as
sp_joint` keeps resolving sp_joint.Mask, sp_joint.get_masks_from_config,
etc. The *Cat runner classes (ApplyHspMasks, ReadCat, run_* entry points)
stay; ApplyHspMasks uses healsparse directly, not the Mask class.

masks added to __init__.__all__. No MOVE_MAP entry: this is an
extraction-in-place (catalog_builders survives), not a retired path.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

The catalogue module pair now reads by role: catalog.py is the data
layer (read/write/column-access/matching free functions), catalog_builders.py
is the construction pipeline (runner classes built on it). Module docstrings
state this hierarchy explicitly.

Behaviour-preserving. Every importer of the local sp_validation.cat module is
swept to sp_validation.catalog, each preserving its local binding (bare
`import cat` forms gain `as cat` so function bodies are unchanged). The
cs_util `cat` import is a different module and is left untouched throughout.

The dangling-reference guard registers the retired flat-import form
`sp_validation.cat import` rather than the bare `sp_validation.cat` token,
which would false-positive on the live `sp_validation.catalog` /
`sp_validation.catalog_builders` modules (same prefix trap as glass_mock).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…y verified)

…aper analysis scripts

The gate revealed peripheral residual the per-file-ignore globs didn't reach
(analysis scripts under papers/<paper>/*.py, cosmo_inference notebooks) plus the
Snakemake-injected `snakemake` global (F821). Region-aware decision: enforce lint
on src/ only (matching the pre-commit hook), keep format repo-wide, run the
repo-wide lint advisory. src/ stays pristine (ruff check src/ => clean).

…-export)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…aracterization)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Converting cosmo_val from a module to a package moved every file one level
deeper, so single-dot relative imports to top-level siblings now resolve
inside the package. Point them up a level:
- ..b_modes (core, pure_eb, cosebis)
- ..cosmology (core, pseudo_cl)
- ..rho_tau (psf_systematics, pseudo_cl)

Re-export cs_plots in __init__ from its origin (cs_util.plots) rather than
from core, which no longer needs the alias after the plotting methods moved
to their mixins. Preserves the sp_validation.cosmo_val.cs_plots attribute path.

Package now imports cleanly; test_cosmo_val + test_b_modes: 18 passed, 1 skipped.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…module

The demo called cosmo_val.hsp_map_logical_or, but that function has only ever
lived in plots.py — the call raised AttributeError. Import it from its home.
(Pre-existing bug surfaced by the cosmo_val package split.)

…eserving)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

… it (re-bless pins ~ULP)

chi2_and_pte now computes chi2 via np.linalg.solve (not forming C^-1) and
PTE via stats.chi2.sf (not 1 - cdf), the numerically proper forms: solve is
more stable/cheaper than an explicit inverse, and the survival function
avoids catastrophic cancellation in the low-PTE tail.

The two hand-inlined C_l^BB chi2/PTE sites in cosmo_val (core.summarize_bmodes,
pseudo_cl.plot_pseudo_cl) already used solve+sf, so they now route through the
single chi2_and_pte primitive with no numerical change; their local scipy
imports are dropped. No pinned value shifted (the value-drift pins flow through
the independent b_modes Hartlap path), so no re-blessing was required.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…r calibration

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…per caller

The shared helper applied the DES R11/R22 branch to both callers, but
calculate_aperture_mass_dispersion historically used scalar R for every
version. Add a des_branch flag so each caller keeps its exact prior behavior
(2pcf: DES branch; aperture-mass: scalar R). The asymmetry is flagged in the
docstring as a likely latent bug for a deliberate, separate fix.

calculate_aperture_mass_dispersion used scalar R for every version, including
DES, while calculate_2pcf used the catalog-averaged R11/R22 for DES. That
asymmetry was a latent bug; _calibrated_g now applies the DES branch
identically for both callers. Untested path (no DES fixture) — value-drift
suite unaffected and green.

…n the mixin

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…_cl.py, thin the mixin

Move the stateless pseudo-Cl computation out of PseudoClMixin into named free
functions in a new top-level sp_validation/pseudo_cl.py (mirrors b_modes.py /
rho_tau.py): make_namaster_bin, get_n_gal_map (weights kwarg, subsumes the
glass_mock unweighted twin), apply_random_rotation (rng injectable; default
preserves the no-arg np.random.seed() noise-debiasing behavior), and the
map-/catalog-based estimators get_pseudo_cls_map / get_pseudo_cls_catalog.
pseudo_cl_geometry centralizes the (lmin, lmax, b_lmax) triple.

The mixin methods are now thin wrappers (load via self -> call primitive),
public names/signatures unchanged so call sites do not move. glass_mock's
get_n_gal_map delegates to the primitive via a lazy import, preserving its
CAMB-only import-time independence from the harmonic stack.

Pins (test_pseudo_cl.py) green; value-drift gate (test_cosmo_val + test_b_modes)
18 passed / 1 skipped; glass_mock tests green; actual cross-module import
verified in the container.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

…opies

Repoint the GLASS-mock harmonic stats at the new src/sp_validation/pseudo_cl.py
primitives so the bandpower binning can no longer drift from the estimator the
rest of the package uses.

- powspace_bins: deleted. Its square-root bandpower spacing is exactly
  pseudo_cl.make_namaster_bin(..., "powspace", power=0.5) on the
  pseudo_cl_geometry(nside) range. Replaced by a thin _mock_powspace_bin wrapper
  that returns the same (bin, ell_eff, lmax, b_lmax) 4-tuple the mock helpers
  consume, now sourced from the shared primitive. Verified bitwise-identical
  binning (ell_eff and per-bin ell membership) across nside/lmin/n_bins configs.
- get_n_gal_map: already delegates to the weighted primitive with weights=None
  (unweighted counts); left as the count-default twin used by the map estimator.
- compute_two_point_cl / compute_two_point_cl_map: kept their own NaMaster field
  construction (documented) — the mock field is UNWEIGHTED and these return the
  COUPLED pseudo-Cl alongside the decoupled one with the ell axis prepended,
  which the primitives' (ell_eff, cl_all, wsp) contract does not expose. They now
  take their binning and galaxy-count map from the shared primitives.

Value-drift gate green (18 passed, 1 skipped); full non-slow suite 136 passed,
1 skipped, 1 xpassed, only the two known-environmental failures
(test_bmodes_workflow_dry_runs, test_configured_paths_exist_on_candide).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>