Add tomographic and 3x2pt covariance realspace measurement

[LisaGoh]

Hello, I've updated the Snakemake workflow to run on OneCovariance for the real space probe, and included tomographic and 3x2pt formats! I've also taken the liberty to clean up the common.py script >.<

I've ran the covariance workflow and it works, now we just have to decide what kind of format we want our nz distributions to be (I've assumed a single file with i columns, i being the number of tomographic bins), and how we want to specify the area and sigma_e (I've assumed a comma-separated string).

The output is compatible with the previous Cosmocov-processed file. I'll update the Cosmosis fitting script as a next step in the other issue!

[github-actions]

✅ ruff is clean — nothing to fix here.

[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.