refactor(src): dissolve basic.py, give every module an honest home by cailmdaley · Pull Request #199 · CosmoStat/sp_validation

cailmdaley · 2026-06-20T01:48:19Z

refactor(src): dissolve `basic.py`, give every module an honest home

A behavior-preserving reshape of src/sp_validation/ — no logic changed, only moves, renames, and dead-code removal. The grab-bag basic.py is dissolved, spatial masking gets its own module, and misnamed/dead files are cleaned up. Base: develop.

flowchart LR
    classDef new fill:#d6f5e0,stroke:#2a9d52,color:#0b3d20
    classDef gone fill:#fadbdd,stroke:#c0392b,color:#5b1a1f,stroke-dasharray:5 4

    basic["basic.py"]:::gone
    util["util.py"]
    rjc["run_joint_cat.py"]
    rho["rho_tau.py"]
    cat["cat.py"]

    calib["calibration.py"]
    stats["statistics.py"]:::new
    masks["masks.py"]:::new
    fmt["format.py"]
    cb["catalog_builders.py"]
    plots["plots.py"]
    catalog["catalog.py"]

    basic -->|"metacal + size/SNR cuts"| calib
    basic -->|"math helpers"| stats
    util  -->|rename| fmt
    rjc   -->|rename| cb
    cb    -->|"spatial Mask + algebra"| masks
    rho   -->|"SquareRootScale"| plots
    cat   -->|rename| catalog
    cb -.->|builds on| catalog

statistics.py and masks.py are new; basic.py is deleted. The catalogue layer now reads as a clear pair: catalog.py (data primitives — read/write/access/match) with catalog_builders.py (the runner-class pipeline built on it). Two re-exports keep shared importers working (SquareRootScale via rho_tau, the mask primitives via catalog_builders); the renames preserve each caller's local binding, so no call sites change.

Also folded in: deleted dead info.py, five unused functions, and a shadowed duplicate confusion_matrix; made __init__.__all__ honest and fixed a phantom version-import; and repaired two pre-existing broken imports — a vanished transform_nan, and 6 papers/harmonic files still pointing at the long-gone utils_cosmo_val.

Martin's #197 requests — all ✅

Calibration scripts clustered under scripts/calibration/ · analyse_matched_stars → scratch as a .py · demo_binned_mask / plot_binned_quantities → scratch · all 7 deletions done. (Sacha's namaster_utils and config-space items are reserved for his own next PR.)

— Claude on behalf of Cail

The module named "basic" was a grab-bag: the 546-line `metacal` response class (the heart of shear calibration) plus galaxy-selection masks and a handful of cosmology-independent statistics helpers — none of which "basic" described. Its symbols now live where they belong, and basic.py is deleted. - `metacal` class + `mask_gal_size`/`mask_gal_SNR` (galaxy selection) → calibration.py, joining the m/c routines that already consumed a `gal_metacal` instance. One subsystem, one module. - `jackknif_weighted_average2`, `corr_from_cov`, `chi2_and_pte`, `cov_from_one_covariance` → new statistics.py (a clean leaf: numpy/scipy only; calibration imports the jackknife from it). - Every importer repointed (papers, scripts, the two scratch/guerrini import lines — path-only, his logic untouched); dead `from sp_validation import basic` lines removed from calibration.py and cat.py; `__all__` and the architecture docs updated. - Tests split: metacal + mask pins → test_calibration.py, jackknife pin → test_statistics.py; test_basic.py removed. All moved code is byte-identical to the original (md5-verified); value-drift pins (metacal R-matrix rtol 1e-12) and the full suite pass in-container, except the pre-existing galaxy/cs_util.size old-sandbox gap. No circular imports. Verified by an adversarial multi-agent pass (byte-identity, no-stale-refs, value-pins, no-cycles). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

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>

martinkilbinger · 2026-06-23T13:58:41Z

I am going through the flies; some are (my old ones and) obsolete, I will delete them here.

@sachaguer

#199 (the old PR base, refactor/src-module-layout) was squash-merged into develop (5b8ffdc), so the old base is dead — this brings the ruff work onto current develop instead. Conflicts resolved toward develop's content (the canonical post-#199 code), then `ruff format` + the region-aware policy re-applied on top, so chore/ruff's net contribution over develop stays exactly: the repo-wide format pass, the lint gate (pre-commit + CI), and the behavior-preserving bug fixes. develop's #200 dependency pins are carried in, and the two obsolete scripts #199 deleted (cosmo_val/match_LF_SP.py, scripts/create_joint_shape_cat.py) stay deleted. Verified: `ruff check .` clean except the 5 known undefined names (@sachaguer's, flagged on the PR), `ruff format --check .` clean, every tracked .py compiles. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SkTwLDgicfeoK8Np2bgwp3

* refactor(src): dissolve basic.py into calibration + statistics The module named "basic" was a grab-bag: the 546-line `metacal` response class (the heart of shear calibration) plus galaxy-selection masks and a handful of cosmology-independent statistics helpers — none of which "basic" described. Its symbols now live where they belong, and basic.py is deleted. - `metacal` class + `mask_gal_size`/`mask_gal_SNR` (galaxy selection) → calibration.py, joining the m/c routines that already consumed a `gal_metacal` instance. One subsystem, one module. - `jackknif_weighted_average2`, `corr_from_cov`, `chi2_and_pte`, `cov_from_one_covariance` → new statistics.py (a clean leaf: numpy/scipy only; calibration imports the jackknife from it). - Every importer repointed (papers, scripts, the two scratch/guerrini import lines — path-only, his logic untouched); dead `from sp_validation import basic` lines removed from calibration.py and cat.py; `__all__` and the architecture docs updated. - Tests split: metacal + mask pins → test_calibration.py, jackknife pin → test_statistics.py; test_basic.py removed. All moved code is byte-identical to the original (md5-verified); value-drift pins (metacal R-matrix rtol 1e-12) and the full suite pass in-container, except the pre-existing galaxy/cs_util.size old-sandbox gap. No circular imports. Verified by an adversarial multi-agent pass (byte-identity, no-stale-refs, value-pins, no-cycles). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * felt: reserved-sasha — document Sasha's hands-off zones 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> * test(statistics): pin the extracted helpers; drop dead code in calibration 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> * refactor(src): delete dead info.py, fix cat.py version import 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> * refactor(src): make package __all__ honest 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> * refactor(cosmo_val): hoist b_modes imports to module top level 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> * refactor(run_joint_cat): drop shadowed confusion_matrix def 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> * refactor: remove dead cluster/convergence-map helpers 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> * refactor(src): rename util -> format; drop dead transform_nan import 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> * refactor(src): move SquareRootScale to plots, re-export from rho_tau 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> * fix(papers/harmonic): repoint SquareRootScale off dead utils_cosmo_val 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> * refactor(src): rename run_joint_cat -> catalog_builders 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> * Extract masks.py from catalog_builders.py 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> * Rename cat.py -> catalog.py: catalogue data layer 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> * style(ruff): repo-wide ruff format pass (mechanical, no semantic change) * chore(ruff): wire ruff (pre-commit + CI) + region-aware lint policy * fix(ruff): region-aware lint fixes (behavior-preserving, adversarially verified) * chore(ruff): scope CI lint to library; broaden E402 ignores for per-paper 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). * chore(ruff): pivot lint gate to warn-locally / account-on-develop Flip the lint discipline from "block" to "warn while you work, account when it lands." Pre-commit now auto-applies ruff's SAFE fixes (`ruff format` + `ruff check --fix`: import sorting, unused imports) — a one-time re-stage, not a block — and only WARNS on what ruff won't safely fix (undefined names F821, unused variables F841), which never blocks a commit. That split is ruff's own safe/unsafe-fix taxonomy, not a hand-curated list. Bloat guards (nbstripout, large-files) still block. CI lint now runs only on push to `develop` and PRs targeting `develop`. On failure it goes red (blocks the merge) AND opens/updates a single auto-closing lint-debt issue per committer, @-mentioning + assigning them; a clean run closes it. Fork PRs are covered via pull_request_target, hardened with `uvx --no-config` so an untrusted PR can't redirect ruff's download to a trojaned index. Issue management runs continue-on-error so it can't red a clean run, and a ruff/uvx tooling error reds the gate without filing a committer issue. Settled with Sacha, 2026-06-23. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SkTwLDgicfeoK8Np2bgwp3 * chore(ruff): clear lint baseline to the 5 genuine undefined names Bring the repo-wide ruff baseline from 125 errors down to 5, so the develop gate's first run is honest rather than a wall of false positives: - builtins = ["snakemake"] silences ~110 false F821s — Snakemake injects a `snakemake` object into rule scripts at runtime, so ruff can't see where it's defined. Every other undefined name in those scripts is still caught. - broaden the cosmo_inference E402 ignore from `*.py` to `**` so it also covers `.ipynb` cells (same intentional sys.path / mpl-backend-before- import pattern the .py scripts already get). - normalize mixed tabs/spaces in download_gaia_catalogues.py's SQL f-string to spaces (E101; also unbreaks the surrounding dedent()). Remaining are 5 genuine undefined names (cov_sim_gaussian in papers/harmonic/...validation_cov_cell.py; index/n_contours in the papers/consistency glass-mocks notebook), triaged with their authors. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SkTwLDgicfeoK8Np2bgwp3 * Fix ruff hooks. Removed consistency not book and moved it to my personal scratch. Removed the lines with undefined variable in the harmonic space script. * chore(ruff): PR feedback as a PR comment, issue only for develop pushes Refine the lint gate's feedback surface to fit the event (Cail's call: a separate issue for a PR is disconnected — comment where the author is already looking; issues are for things going straight into develop): - PR against develop → red check (still blocks the merge) + a single auto-updating comment ON the PR with the full violation list, turning green when ruff passes. ruff annotations (--output-format=github) are emitted too (they surface in the run's Checks view; pull_request_target anchors them to the base commit, so not inline on the diff). No issue. - direct push to develop → unchanged: one per-committer auto-closing lint-debt issue (no PR exists to comment on). Adds pull-requests: write for the comment path. Fresh-eyes reviewed (SHIP); the over-promised "inline on Files changed" wording was corrected since the comment's file:line list is the reliable surface. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SkTwLDgicfeoK8Np2bgwp3 --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com> Co-authored-by: Sacha Guerrini <sacha.guerrini@cea.fr>

…licts) #206 (ruff gate) and #199 (basic.py dissolve) squash-merged to develop while #207 still carried their pre-squash commits, so this merge collapses the stack. Resolved by category: - develop's side where it carried fixes #207 lacked: Sacha's cov_sim_gaussian removal in papers/harmonic/2025_09_11_validation_cov_cell.py (21c7d96), the consistency-notebook deletion (moved to scratch), the canonical #206 lint.yml / pre-commit enforcement model, the broader cosmo_inference/** E402 per-file-ignore. - #207's side for its genuine work: the cosmo_val/ package (flat cosmo_val.py deleted), the pseudo_cl primitives, survey.area_from_coords, chi2_and_pte solve+sf (pins re-blessed for it), the glass_mock dedup, the demo hsp_map_logical_or fix; dropped develop's duplicate SquareRootScale. Verified on the fresh container: ruff format+check clean repo-wide; CosmologyValidation imports (75 methods); value-drift + golden pins 32 passed / 1 skipped. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Jmk58xivawGCVFgejJJeDp

* refactor(src): dissolve basic.py into calibration + statistics The module named "basic" was a grab-bag: the 546-line `metacal` response class (the heart of shear calibration) plus galaxy-selection masks and a handful of cosmology-independent statistics helpers — none of which "basic" described. Its symbols now live where they belong, and basic.py is deleted. - `metacal` class + `mask_gal_size`/`mask_gal_SNR` (galaxy selection) → calibration.py, joining the m/c routines that already consumed a `gal_metacal` instance. One subsystem, one module. - `jackknif_weighted_average2`, `corr_from_cov`, `chi2_and_pte`, `cov_from_one_covariance` → new statistics.py (a clean leaf: numpy/scipy only; calibration imports the jackknife from it). - Every importer repointed (papers, scripts, the two scratch/guerrini import lines — path-only, his logic untouched); dead `from sp_validation import basic` lines removed from calibration.py and cat.py; `__all__` and the architecture docs updated. - Tests split: metacal + mask pins → test_calibration.py, jackknife pin → test_statistics.py; test_basic.py removed. All moved code is byte-identical to the original (md5-verified); value-drift pins (metacal R-matrix rtol 1e-12) and the full suite pass in-container, except the pre-existing galaxy/cs_util.size old-sandbox gap. No circular imports. Verified by an adversarial multi-agent pass (byte-identity, no-stale-refs, value-pins, no-cycles). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * felt: reserved-sasha — document Sasha's hands-off zones 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> * test(statistics): pin the extracted helpers; drop dead code in calibration 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> * refactor(src): delete dead info.py, fix cat.py version import 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> * refactor(src): make package __all__ honest 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> * refactor(cosmo_val): hoist b_modes imports to module top level 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> * refactor(run_joint_cat): drop shadowed confusion_matrix def 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> * refactor: remove dead cluster/convergence-map helpers 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> * refactor(src): rename util -> format; drop dead transform_nan import 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> * refactor(src): move SquareRootScale to plots, re-export from rho_tau 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> * fix(papers/harmonic): repoint SquareRootScale off dead utils_cosmo_val 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> * refactor(src): rename run_joint_cat -> catalog_builders 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> * Extract masks.py from catalog_builders.py 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> * Rename cat.py -> catalog.py: catalogue data layer 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> * style(ruff): repo-wide ruff format pass (mechanical, no semantic change) * chore(ruff): wire ruff (pre-commit + CI) + region-aware lint policy * fix(ruff): region-aware lint fixes (behavior-preserving, adversarially verified) * chore(ruff): scope CI lint to library; broaden E402 ignores for per-paper 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). * refactor(cosmo_val): convert module to package (core.py + __init__ re-export) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): extract PseudoClMixin (pseudo_cl) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): extract CatalogCharacterizationMixin (catalog_characterization) * refactor(cosmo_val): extract PSFSystematicsMixin (psf_systematics) * refactor(cosmo_val): extract RealSpaceMixin (real_space) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): extract PureEBMixin (pure_eb) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): extract CosebisMixin (cosebis) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): fix sibling-module imports for package depth 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> * fix(examples): call hsp_map_logical_or from plots, not the cosmo_val 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.) * refactor(cosmo_val): tighten + de-dupe the mixin modules (behavior-preserving) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): drop get_cov_from_onecov, use statistics.cov_from_one_covariance directly Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): _output_path helper for output-path construction Add a private CosmologyValidation._output_path(*parts) that returns os.path.abspath(os.path.join(self.cc["paths"]["output"], *parts)), and route the 29 abspath-wrapped output-path constructions across the mixin modules (catalog_characterization, pseudo_cl, psf_systematics, real_space) through it. Behavior-preserving: only the os.path.abspath(f"{output}/...") sites are converted, where abspath(join(base, suffix)) is byte-identical to abspath(f"{base}/{suffix}") for every suffix shape in the package (verified, incl. embedded subdirs and trailing slashes). Raw f-strings that are not abspath'd (psf_systematics output_dir handoffs to shear_psf_leakage) are intentionally left as-is to avoid changing the string they pass to external tools. Value-drift gate green: 18 passed, 1 skipped. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): _binning helper for treecorr-config overrides Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): collapse print_* color helpers onto _cprint Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(stats): chi2_and_pte uses solve+sf; route B-mode PTE through 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> * refactor(cosmo_val): _calibrated_g / _read_shear_cols for shared shear calibration Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(cosmo_val): keep _calibrated_g strictly behavior-preserving 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. * fix(cosmo_val): aperture-mass uses the DES R11/R22 branch like 2pcf 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. * refactor(cosmo_val): extract survey-stat primitives to survey.py, thin the mixin Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * test(pseudo_cl): pin the pseudo-Cl estimator outputs (golden values) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * refactor(pseudo_cl): extract estimator primitives to top-level pseudo_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> * refactor(glass_mock): use shared pseudo_cl primitives, drop drifted copies 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> * fix(pseudo_cl): make noise-debiasing reproducible (seed the rng) apply_random_rotation called np.random.seed() with no argument, re-seeding from OS entropy on every call, so the pseudo-Cl noise-debiasing realizations were non-reproducible run-to-run. Drop the bare seed; the primitive now uses its rng argument (default_rng() when None), and the debiasing + covariance sampling paths thread a generator seeded from a new CosmologyValidation cell_seed (default 8192). Same numerical scheme, now reproducible. The test_pseudo_cl reproducibility test replaces the old non-determinism guard. --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

cailmdaley and others added 2 commits June 20, 2026 04:50

felt: reserved-sasha — document Sasha's hands-off zones

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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>

cailmdaley force-pushed the refactor/src-module-layout branch from 902377f to 1ff913c Compare June 20, 2026 02:51

cailmdaley mentioned this pull request Jun 20, 2026

Restructuring: top-level layout + workflow/papers/scratch division #197

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cailmdaley changed the base branch from cleanup/restructuring to develop June 20, 2026 12:26

cailmdaley and others added 9 commits June 20, 2026 14:50

cailmdaley changed the title ~~refactor(src): dissolve basic.py into calibration + statistics~~ refactor(src): dissolve basic.py + make the module layout honest Jun 20, 2026

cailmdaley marked this pull request as ready for review June 20, 2026 13:35

cailmdaley changed the title ~~refactor(src): dissolve basic.py + make the module layout honest~~ refactor(src): dissolve basic.py, give every module an honest home Jun 20, 2026

cailmdaley requested review from martinkilbinger and sachaguer June 20, 2026 15:11

This was referenced Jun 20, 2026

sp_validation restructuring & cleanup #202

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chore: ruff format + region-aware lint gate #206

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Deleted obsolete script cosmo_val/match_LF_SP.py

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Deleted old scripts/create_joint_shape_cat.py

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martinkilbinger approved these changes Jun 23, 2026

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cailmdaley merged commit 5b8ffdc into develop Jun 23, 2026
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cailmdaley deleted the refactor/src-module-layout branch June 30, 2026 20:04

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refactor(src): dissolve basic.py, give every module an honest home#199

refactor(src): dissolve basic.py, give every module an honest home#199
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refactor(src): dissolve `basic.py`, give every module an honest home