Restructuring: top-level layout + workflow/papers/scratch division#197
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cailmdaley wants to merge 31 commits into
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Restructuring: top-level layout + workflow/papers/scratch division#197cailmdaley wants to merge 31 commits into
cailmdaley wants to merge 31 commits into
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Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Fold Sacha's pending foundation (PR #192 head, sachaguer:develop @ c22f075) onto current develop so the restructuring builds on his foundation without racing his merge gesture (Cail's direction, 2026-06-05). .gitignore conflict resolved in favour of develop: kept the .felt tracking block, rejected sacha's broad cluster bans (*.png *.sh *.fits *.out *.err) — those get narrowed during the restructuring gitignore pass, not adopted wholesale. cosmo_val.py / cat_config.yaml auto-merged cleanly (origin's docstring-RST polish + sacha's functional changes did not collide). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
cosmology.py get_cosmo read planck_defaults["mnu"] but the dict never defined the key, so every bare get_cosmo() call (no ccl_params, no mnu arg) raised KeyError: 'mnu'. Add "mnu": PLANCK18["m_nu"] (0.06 eV). Verified: test_cosmology.py 26/26 pass (was immediate KeyError before). This is the one blocker that kept Sacha's foundation from running clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
docs/source/sp_validation.*.rst are regenerated on every docs build by sphinx-apidoc (deploy-docs.yml: `sphinx-apidoc -feTMo docs/source src/sp_validation`), matching the already-ignored fortuna.*/scripts.* stubs — they should never be committed. uv.lock: the container is the canonical runtime (CLAUDE.md), the lockfile has never been tracked, so ignore it rather than make an unowned pinned-dep commitment. One-line flip to track if we decide to pin. Establishes a clean base for the restructuring branch. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Sacha's branch removed the cosmosis_pipeline_glass_mock_0*.ini and _v0*.ini ignore patterns, which un-ignored ~700 generated glass-mock pipeline configs in cosmo_inference/cosmosis_config/. Restore the two specific patterns (not broad bans) so the tree returns to develop's clean state. These are generated artifacts, never tracked. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
First guard in the restructuring invariant suite (sp-validation-restructuring fiber). A pure file-move must not break imports; this is the first thing to go red on a bad git mv. Two halves, because scripts live OUTSIDE the package and a package-only walk misses them (the gap the ngmix review's test_scripts_import flagged): - Package modules (src/sp_validation/*.py): real import — library code is import-safe, so a broken cross-module reference fails immediately. - Standalone scripts (scripts/*.py): NOT executed (several do work at module level; one isn't a valid module name). Parsed with ast — which also asserts syntactic validity — and every first-party (sp_validation.*) import target resolved via importlib.util.find_spec. Green baseline: 42 passed, 1 xfailed. The xfail is a real find — plot_leakage.py imports `from sp_validation.correlation import *`, a module that never existed (dead LF-leakage script). Marked xfail(strict=True) + KNOWN_BROKEN_SCRIPTS so the baseline is honest and the strict-xfail flips the moment it's fixed/deleted; triage belongs to the scripts/ curation pass. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Restructuring
sp_validationStatus — WIP draft, not yet for review. One organizing principle: the things you run live at the top level, sharing library code in
src/underneath — plus a cleanworkflow/(analysis) ↔papers/(final-figure assembly) ↔scratch/(personal) split.Landed so far (Phase 0–1)
sachaguer:develop(Merge Sacha's fork with fiducial sp_validation #192 head, 120 files: paper plots, harmonic configs, library changes) merged; thecosmology.pyKeyError: 'mnu'blocker fixed (one line) —test_cosmology.py26/26 green. Sacha's broad.gitignorebans were rejected towarddevelop's patterns.scripts/resolution) is green (tests/test_imports.py, 42 passed / 1 xfailed — and it already caught a dead script). Guards ② (snakemake -npasses), ③ (Candide-local config-path existence), ⑤ (symlink integrity), ⑥ (dangling-reference grep) are in progress.developis untouched.Next
Phase 2 — the actual top-level moves (
workflow/,papers/,scratch/) proceed in smallgit mvsteps behind the green guards. The full plan and live state are tracked in thesp-validation-restructuringfiber.— Claude on behalf of Cail