Scripts¶

The repository ships with a set of CLI drivers and bash wrappers under scripts/. They cover the whole pipeline from reformatting the raw .DAT files through measurements to plots.

The authoritative index is scripts/bookkeeping.md. The summary below mirrors it; consult that file for the full per-script flag list.

Python drivers¶

Script	Purpose
`reformat_catalogues.py`	`CatshortV.*.DAT → halo.hdf5` (read-only on the source).
`measure_hmf.py`	Batch HMF measurement loop (load-or-measure).
`load_hmf.py`	Single-record or `--grid` summary inspector for `hmf.hdf5`.
`plot_hmf.py`	One-panel HMF plot, one line per imodel, mean over iboxes.
`measure_xi_hh.py`	Batch `xi_hh` measurement loop. Reads `config_xi_hh.yaml` by default.
`load_xi_hh.py`	Single-record or `--grid` inspector for `xi_hh.hdf5`.
`plot_xi_hh.py`	`r²ξ` plot in one panel, one line per mass-bin pair.
`example_load_halo.py`	Worked example: load a `halo.hdf5`, summarise columns, demo a mass cut.

Bash drivers¶

Run from the repository root. They use set -euo pipefail and forward extra flags via EXTRA_ARGS / MEASURE_EXTRA_ARGS.

Script	Wraps	Sub-grid
`reformat_catalogues_LCDM_z0.25.sh`	`reformat_catalogues.py`	LCDM, z=0.25, m=1..64, b=1..5
`reformat_catalogues_fRn1_z0.25.sh`	`reformat_catalogues.py`	fRn1 variant of the above
`load_hmf_LCDM_z0.25.sh`	`load_hmf.py`	per-realisation loop
`load_hmf_fRn1_z0.25.sh`	`load_hmf.py`	fRn1 variant
`measure_xi_hh_LCDM_z0.25.sh`	`measure_xi_hh.py`	LCDM, m=1..9, b=1..5
`measure_xi_hh_fRn1_z0.25.sh`	`measure_xi_hh.py`	fRn1 variant
`load_xi_hh_LCDM_z0.25.sh`	`load_xi_hh.py`	per-realisation loop

Conventions¶

All Python drivers run under micromamba run -n cosemu python3 ….
Measurement drivers default to load-or-measure via the HMFLoader / XiHHLoader classes — missing files are produced on demand, existing files are left alone unless --overwrite is passed.
2PCF measurements read binning from scripts/config_xi_hh.yaml unless --no-config is given.
The raw CatshortV.*.DAT files are read-only: if halo.hdf5 is missing, the source is reformatted into a fresh HDF5 mirror; the .DAT is never modified.

Notebooks¶

A worked walkthrough lives at notebooks/example_load.ipynb — loads halo + HMF + xi_hh + velocity moments + sub-grid stacking on a single realisation. Open it locally with Jupyter against the cosemu kernel.