Remove dead scripts and fix stale doc paths

CLAUDE.md

@@ -18,7 +18,7 @@ Tests live in `src/sp_validation/tests/` and import the full scientific stack,
 so run them inside the container.
 - Run all tests: `pytest` (collects from `src/sp_validation/tests`; coverage on by default)
 - Skip the slow tests: `pytest -m "not slow"`
-- Run a single test: `pytest src/sp_validation/tests/test_cosmology.py::test_function_name`
+- Run a single test: `pytest src/sp_validation/tests/test_cosmo_val.py::test_function_name`
 
 CI runs this same suite inside the freshly-built image before publishing it
 (see `.github/workflows/deploy-image.yml`).
@@ -57,11 +57,13 @@ is the container (full scientific stack pre-built). For a local dev environment:
 - **Healpy/HealSparse**: Sky map handling
 
 ### Cosmology Inference Pipeline (`cosmo_inference/`)
-Run via `./pipeline.sh` with flags:
-- `--pcf`: Calculate 2-point correlation functions
-- `--covmat`: Calculate covariance matrix with CosmoCov
-- `--inference`: Run CosmoSIS inference
-- `--mcmc_process`: Analyze MCMC chains
+Orchestrated through Snakemake, not a standalone driver; see
+`cosmo_inference/README.md`. From the repository root:
+
+```bash
+snakemake --profile workflow/profiles/candide -s workflow/Snakefile \
+    inference_fiducial --configfile <run config>
+```
 
 ### Configuration
 Main configuration in `scripts/calibration/params.py` with parameters:

CONTRIBUTING.md

@@ -74,7 +74,7 @@ toolchain (`autoconf`, `automake`, `libtool`, `pkg-config`) available.
 ```bash
 pytest                       # full suite
 pytest -m "not slow"         # skip the slow tests
-pytest src/sp_validation/tests/test_cosmology.py::test_name   # a single test
+pytest src/sp_validation/tests/test_cosmo_val.py::test_name   # a single test
 ```
 
 Tests live in `src/sp_validation/tests/`. The default options (configured in

README.md

@@ -5,7 +5,7 @@ Validation of weak-lensing catalogues (galaxy and star shapes and other paramete
 [![docs](https://img.shields.io/badge/docs-sphinx-blue)](https://cosmostat.github.io/sp_validation/)
 [![CI](https://github.com/CosmoStat/sp_validation/actions/workflows/deploy-image.yml/badge.svg)](https://github.com/CosmoStat/sp_validation/actions/workflows/deploy-image.yml)
 [![container](https://img.shields.io/badge/container-ghcr.io-2496ED?logo=docker&logoColor=white)](https://github.com/CosmoStat/sp_validation/pkgs/container/sp_validation)
-[![python](https://img.shields.io/badge/python-3.11%2B-blue?logo=python&logoColor=white)](https://www.python.org/downloads/)
+[![python](https://img.shields.io/badge/python-3.12%2B-blue?logo=python&logoColor=white)](https://www.python.org/downloads/)
 [![license](https://img.shields.io/badge/license-MIT-blue)](https://github.com/CosmoStat/sp_validation/blob/develop/LICENCE.txt)
 [![code style: ruff](https://img.shields.io/badge/code%20style-ruff-261230?logo=ruff&logoColor=white)](https://github.com/astral-sh/ruff)
 [![contribute](https://img.shields.io/badge/contribute-read-lightgrey)](https://github.com/CosmoStat/sp_validation/blob/develop/CONTRIBUTING.md)

docs/source/installation.rst

@@ -82,6 +82,6 @@ For a narrower install, ``.[test]`` adds only the test extras and ``.[docs]`` on
 
 .. note::
 
-   ``sp_validation`` requires Python 3.11 or newer and pulls in a large scientific stack: ``treecorr``, ``pyccl``, ``healpy``, ``pymaster``, and others.
+   ``sp_validation`` requires Python 3.12 or newer and pulls in a large scientific stack: ``treecorr``, ``pyccl``, ``healpy``, ``pymaster``, and others.
    A bare development install builds these from source, which is slow and platform-sensitive.
    For most users the container is the more reliable path.

papers/bmodes/Snakefile

@@ -2,7 +2,7 @@
 # compute workflow at ../../workflow/.
 
 configfile: "config/config.yaml"
-configfile: "/n17data/cdaley/unions/pure_eb/code/sp_validation/cosmo_val/cat_config.yaml"
+configfile: "/n17data/cdaley/unions/code/sp_validation/cosmo_val/cat_config.yaml"
 
 envvars:
     "PYTHONUNBUFFERED",

papers/bmodes/config/ecut_spec.md

@@ -32,7 +32,7 @@ DES-Y3 used e < 0.8 to remove stars.
 
 ### How versions flow through the pipeline
 
-Everything is driven by `config["versions"]` in `workflow/config/config.yaml`. Adding a
+Everything is driven by `config["versions"]` in `papers/bmodes/config/config.yaml`. Adding a
 version there (plus its `cat_config.yaml` entry) makes it flow through all existing rules:
 `xi`, `covariance`, `pure_eb_data_vector`, `cosebis_data_vector`, `cl_data_vector`.
 The 2PCF and covariance are independent and can run in parallel.
@@ -43,7 +43,7 @@ Key resolution functions in `workflow/Snakefile`:
 - `resolve_covariance_version()` — identity function (each version gets its own covariance)
 - Wildcard constraint: `version=r"SP_v[\d.]+(_w_iv)?(_leak_corr)?"` — needs `_ecut\d+`
 
-Version comparison rules in `workflow/rules/claims.smk` (lines 131, 271, 386) use
+Version comparison rules in `papers/bmodes/rules/claims.smk` (lines 131, 271, 386) use
 `VERSIONS_LEAK_CORR` for inputs and derive version lists from config in the scripts.
 These should be parameterized to accept a version list via `snakemake.params`, so the
 same rules serve both paper and ecut comparisons.
@@ -71,10 +71,10 @@ uncorrected columns can't be consistently filtered to guarantee the same rows.
 
 | What | Where |
 |------|-------|
-| Workflow config | `workflow/config/config.yaml` (search `ecut`) |
-| Catalog config | `code/sp_validation/cosmo_val/cat_config.yaml` (search `ecut07`) |
+| Workflow config | `papers/bmodes/config/config.yaml` (search `ecut`) |
+| Catalog config | `cosmo_val/cat_config.yaml` (search `ecut07`) |
 | Pipeline orchestration | `workflow/Snakefile` (wildcard constraints, version resolution functions) |
-| Version comparison rules | `workflow/rules/claims.smk` lines 131, 271, 386 |
+| Version comparison rules | `papers/bmodes/rules/claims.smk` lines 131, 271, 386 |
 | Version comparison scripts | `workflow/scripts/{pure_eb,cosebis,cl}_version_comparison.py` |
 | Covariance params | `workflow/rules/covariance.smk` line 4 (`get_cat_params`) |
 

papers/bmodes/scripts/update_survey_stats.py

@@ -5,7 +5,7 @@
 memory usage.
 
 Usage:
-    python workflow/scripts/update_survey_stats.py \
+    python papers/bmodes/scripts/update_survey_stats.py \
         --mask-standard <path> --mask-starhalo <path>
 """
 

papers/cosmo_val/Snakefile

@@ -7,7 +7,7 @@
 # isolation or as the whole suite via the default `cosmo_val_all` target.
 
 configfile: "config/config.yaml"
-configfile: "/n17data/cdaley/unions/pure_eb/code/sp_validation/cosmo_val/cat_config.yaml"
+configfile: "/n17data/cdaley/unions/code/sp_validation/cosmo_val/cat_config.yaml"
 
 envvars:
     "PYTHONUNBUFFERED",

pyproject.toml

@@ -159,8 +159,8 @@ glass = [
 # Snakemake workflow and cross-validation runners are available.
 workflow = [
     "snakemake",
-    # run_2pcf_highres.py drives the MPI convergence run; the container ships
-    # OpenMPI under /opt/ompi so mpi4py builds against it.
+    # Optional MPI runners (the container ships OpenMPI at /opt/ompi, so mpi4py
+    # builds against it).
     "mpi4py",
     # CosmoSIS drives the cosmo_inference sampling step. Sdist-only, so this is a
     # source build (~2 min) against the base image's gfortran/GSL/cfitsio/OpenMPI —

workflow/rules/twopoint.smk

@@ -24,55 +24,6 @@ rule xi:
         "../scripts/run_2pcf.py"
 
 
-# PARKED: xi_highres (high-resolution xi for COSEBIS integration). Not runnable
-# as written -- the shell invokes run_2pcf_highres.py bare, but the script has
-# required --cat-config and --out arguments. Revive it with those supplied.
-#
-# The MPI reasoning below is hard-won and must survive the revival:
-#
-#   Exception to the profile-driven container model: this is multi-node MPI, one
-#   `apptainer exec` per rank. Snakemake's own container wrapping puts the
-#   *whole* shell command -- `mpiexec` included -- inside a single container
-#   instance, so only rank 0's node would run inside it; the other ranks,
-#   spawned by SLURM/PMI on their own nodes, would land bare on the host.
-#   `container: None` plus an explicit `mpiexec -n N apptainer exec ...`
-#   per-rank is therefore required.
-#   Snakemake's slurm-jobstep plugin deliberately does NOT prepend `srun` to a
-#   job carrying an `mpi` resource, which is what lets the rule's own launcher
-#   run on the host, outside the container.
-#   Because this rule builds its own apptainer call, reaching the source-cache
-#   copy of the script relies on our `--bind /home` rather than on Snakemake's
-#   automatic mount -- and on a concrete image file, since `apptainer exec`
-#   takes no `docker://` URI. Take that path from `resolve_image()[0]` rather
-#   than naming a second image path that can drift.
-#
-# rule xi_highres:
-#     container: None
-#     params:
-#         image=resolve_image()[0],
-#     input:
-#         script=workflow.source_path("../scripts/run_2pcf_highres.py"),
-#     output:
-#         txt=str(COSMO_VAL / f"{FIDUCIAL['version']}_xi_minsep={FIDUCIAL['min_sep_int']}_maxsep={FIDUCIAL['max_sep_int']}_nbins=10000_npatch=1.txt"),
-#         xi_plus=str(COSMO_VAL / f"xi_plus_{FIDUCIAL['version']}_minsep={FIDUCIAL['min_sep_int']}_maxsep={FIDUCIAL['max_sep_int']}_nbins=10000_npatch=1.fits"),
-#         xi_minus=str(COSMO_VAL / f"xi_minus_{FIDUCIAL['version']}_minsep={FIDUCIAL['min_sep_int']}_maxsep={FIDUCIAL['max_sep_int']}_nbins=10000_npatch=1.fits"),
-#     resources:
-#         tasks=30,
-#         cpus_per_task=12,
-#         nodes=6,
-#         mem_mb_per_cpu=2000,
-#         runtime=2880,
-#         slurm_extra="'--exclude=n17,n09,n36 --partition=pscomp'",
-#         mpi="/softs/openmpi/5.0.5-slurm-CentOS8/bin/mpiexec",
-#     shell:
-#         "{resources.mpi} -n {resources.tasks} "
-#         "apptainer exec "
-#         "--bind /home,/n09data,/n17data,/n23data1,/softs "
-#         "--env LD_LIBRARY_PATH=/softs/openmpi/5.0.5-slurm-CentOS8/lib "
-#         "{params.image} "
-#         "python {input.script} --cat-config <...> --out <...>"
-
-
 rule rho_tau_stats:
     output:
         rho_stats=str(COSMO_VAL / "rho_tau_stats/rho_stats_{version}_minsep={min_sep}_maxsep={max_sep}_nbins={nbins}_npatch={npatch}.fits"),