[LisaGoh]

Replaces CosmoCov with OneCovariance for the real-space cosmic-shear ξ± covariance, and adds a tomographic variant. This PR only touches the covariance. The tomographic data vector, and putting this covariance into SACC, are in #306.

Brought up to date with develop (merged, not rebased; T is retired since #402).

What changes

• workflow/rules/covariance.smk
  • covariance_ini writes the OneCovariance .ini; covariance_run runs it and writes a dense ξ± matrix (.dat, np.savetxt): G+NG for ng, G only for g.
  • Survey parameters come from the catalogue entry (cov_th: sigma_e, n_e, A). The n(z) comes from shear.redshift_path, and the mask Cℓ from MASK_CLS_FILES; both are split into directory and file, as OneCovariance expects.
  • Targets: covariance, covariance_masked, covariance_unmasked (NG on the reporting grid, G on the integration grid), and the new covariance_tomo.
  • Removed: the CosmoCov rules (covariance_ini/covariance_cosmocov/covariance_cat/covariance_process) and workflow/scripts/cosmocov_process.py.
• workflow/common.py
  • One naming scheme, COV_BASE_TEMPLATE, used for rule outputs through cov_output() and filled in by covariance_base():
    covariance_{version}_{gaussian}_minsep=…_maxsep=…_nbins=…{mask_suffix}{tomo_suffix}
  • covariance_base / covariance_dir / covariance_path take tomo_suffix. covariance_path() now returns the .dat by default, so inference, the glass mocks, cosmo_val (pure-E/B, COSEBIs, assemble_sacc) and the bmodes figures read the OneCovariance matrix without changes of their own.
  • Wildcard constraints for tomo_suffix ((_tomo)?) and npatch.
• workflow/rules/masks.smk: removed prepare_mask_for_cosmocov.
• Paper configs: tools.cosmocov_executable is replaced by tools.onecov_executable.
• Tests: removed the CosmoCov post-processing regression test; the tau-sampling and glass-covariance checks stay.

Tested

• Dry runs resolve for covariance, covariance_tomo and the whole cosmo_val paper DAG. For the fiducial catalogue, the rendered .ini matches its cov_th and n(z).
• pytest: covariance-rule regression, assemble_sacc, xi-grid and cv-params tests pass.

Heads-up for reviewers

• OneCovariance products use the same directory and file names CosmoCov used. Launch with your own COSMO_INFERENCE; on the shared tree the new .ini would overwrite CosmoCov's.
• No .dat exists yet, so anything that needs a covariance triggers OneCovariance runs. The non-Gaussian ones are slow.
• The bmodes paper scripts that hard-code _processed.txt still read the published CosmoCov files, so the paper's numbers are unchanged.
• To check before merging: the element order of OneCovariance's matrix output (expected: ξ+ then ξ−, by θ; for tomography, bin pairs (1,1), (1,2), …, (n,n)) against an existing _processed.txt.
• Tomographic inputs: an n(z) file with one column per bin, and comma-separated per-bin values in cov_th. With today's non-tomographic fiducial catalogue, covariance_tomo only renames the single-bin covariance.

Out of scope

• ggl / 3x2pt covariances: deferred until there is a lens sample.

🤖 Generated with Claude Code

[github-actions]

🤖 autofix pushed 74caf77, ruff is clean — formatting and safe lint fixes were applied for you; nothing else to do.

[cailmdaley]

thank you Lisa this looks great, please continue to take liberties! review incoming.

for the n(z) format, i'm proposing we migrate to SACC (see #241 for motivation, #246 for what this would mean for the OneCovariance interface). but i think it's fine to go ahead with what you've assumed for now so this PR can be merged quickly, and we can do the switch to SACC later.

[cailmdaley]

Thanks Lisa — this is a really nice move. The CosmoCov→OneCovariance swap is much cleaner than the old block/cat/process chain, and the COV_BASE_TEMPLATE consolidation plus workflow.source_path fix are genuine improvements to common.py, liberties happily taken. A few things to sort before merge, one of which I think breaks the workflow as-is:

Blocker: build_redshift_path is deleted but still called. workflow/rules/inference.smk line 66 and (worse) line 138 still call build_redshift_path — line 138 is evaluated at parse time, so any snakemake invocation on this branch should die with a NameError, not just covariance targets. Simplest fix: keep build_redshift_path as it was (it's exactly build_redshift_dir(version) + build_redshift_path_lens(version, blind)) alongside the new helpers, or update inference.smk in this PR. (If the covariance run worked for you, I suspect it was against a locally-edited inference.smk — worth double-checking what state that was in.)

Personal-path defaults — let's fix the pattern, not the username. To be fair, the previous defaults were no more neutral: they were Cail's personal tree. Rather than swapping one username for another, let's use this PR to drop personal defaults entirely — make COSMO_VAL / COSMO_INFERENCE / CAT_CONFIG required (env var or config key, loud error if unset), so each of us sets our own and the repo carries nobody's paths. Happy for that to be a small follow-up if you'd rather keep this PR focused. The one that genuinely needs reverting here is COSMOLOGY_PARAMS — inline comment explains why (it's about the generating rule, not whose disk).

Rest is inline — mostly small. On n(z) formats and area/sigma_e specification: as in my comment above, fine to keep your assumed formats for now and revisit with the SACC migration (#241/#246).

— Fable on behalf of Cail

[cailmdaley]

Rather than these defaults carrying anyone's personal tree (the old values were Cail's, so this is a fix-the-pattern note, not a revert request): suggest requiring COSMO_VAL / COSMO_INFERENCE / CAT_CONFIG explicitly — env var or config key, loud error if unset — so each of us sets our own and the repo carries nobody's paths. Fine as a small follow-up if you'd rather keep this PR focused.

[cailmdaley]

This one does need to stay relative (independent of the defaults question above): the cosmology_params rule generates this file at the relative path results/cosmology/planck18.json in the run directory, so pointing the constant at an absolute path decouples the reader from the generator — the rule would write one file and everything else would read another.

[cailmdaley]

Three copies of the same version-normalization regex block now — worth one _nz_base_version(version) helper that the three functions share.

Also a naming/semantics check to resolve with the TO-DO: in the ini, zlens_file gets build_redshift_path_lens (the existing source-galaxy n(z)) and zclust_file gets ..._source.txt. OneCov's zlens is the lensing source sample and zclust the clustering lens sample — so a file suffixed _source feeding zclust reads inverted. If the intent is _lens.txt for the clustering sample, let's fix the suffix before anyone generates files against this convention.

Minor: build_redshift_dir returns a trailing-slash dir which the rule then passes through os.path.dirname, and the _lens/_source helpers return bare filenames that go through os.path.basename. Both round-trips can go — return dir and filenames and use them directly.

[cailmdaley]

This branches on the global config["probe_3x2pt"] while everything else in the rule branches on the {probe} wildcard — if they disagree (config says 3x2pt, someone requests a wl target, or vice versa) you get an ini with mismatched survey-spec lines. Suggest get_cat_params(version, probe) taking the wildcard, and dropping the global key entirely: then covariance_3x2pt (line 391) can just say probe="3x2pt", which also fixes the slightly bewildering probe_3x2pt: wl in the test config.

[cailmdaley]

Hardcoded 8 here has to match threads: 8 on covariance_onecov by hand (the ini is written by a different rule, so {threads} can't be used directly). Worth a single shared constant (e.g. ONECOV_CORES = 8) used by both, so they can't drift.

[cailmdaley]

Stale comment — the ini's file = is now the full covariance base name, not cov_tmp_onecov.dat.

[cailmdaley]

Making this config-overridable is a nice touch. The default uses the deprecated pure_eb/ compat symlink though — canonical path is now /automnt/n17data/cdaley/unions/analyses/shear_2d/bmodes_2d/results/covariance/glass_mock_v1.4.6.

[cailmdaley]

probe=DEFAULT_PROBE binds the default at function-definition time — it happens to work because configure() runs before the includes, but it's fragile ordering. Safer: probe=None and resolve inside (which is also the pattern covariance_base already uses). Relatedly, DEFAULT_PROBE = "wl" hardcoded inside configure() could just be a module-level constant, or read from config if we ever want a non-wl default.

[LisaGoh]

@cailmdaley I think this is ready to be merged! I updated the PR description, rebased it to merge into develop and proposed an updated workflow (see the latest comment in #375). Once this is merged, we can merge #306 as well!