Helpers that operate on pipeline inputs and outputs but are not pipeline modules: nothing here is run by shapepipe_run, and nothing here is part of the Snakemake workflow's rule graph (that is workflow/scripts/).

Everything under scripts/*/ with a .py, .sh or .bash extension is symlinked onto $PATH inside the container image under its bare name, so cfis_field_select and python scripts/python/cfis_field_select.py are the same command.

Each script's own --help and module docstring is the reference; this file is only a map. Run any of them with -h first.

• cfis_field_select.py — select CFIS tiles or exposures by sky coordinates or by name, and emit the ID list. This is how a tile list for workflow/config.yaml is made.
• check_tile_coverage.py — flag input simulation tiles whose weight maps are mostly empty, as a YAML exclude list. Called from sp_validation's image-sims orchestration, not from here.

• collate_star_cat.py — collate the per-exposure PSF validation catalogues into the input merge_starcat wants for the rho/tau statistics.
• create_final_cat.py — merge per-tile final catalogues into one HDF5 file for sp_validation.
• stats_global.py — histograms and tables from the SETools per-CCD summary statistics of a whole run.

The image-simulation chain is still driven by the pre-Snakemake bash layer, which sp_validation's image_sims.smk calls into. These exist for it and are not used by real-data runs.

• init_run_v2.0.py — lay out a run directory for that layer.
• update_runs_log_file.py — rebuild log_run_sp.txt from the run directories on disk, which that layer needs because it deletes run dirs.
• test_tile_det.py + test_tile_det.cfg — drive tile detection over it.

Orthogonal to everything above: build_status.py, build_history.py, plot_trends.py, run_breakdown_grid.py, plot_breakdown_grid.py and plot_s4_ablations.py build the shape-measurement status page and its trend/ablation figures.

• shapepipe_run_example.sh — run the bundled example pipeline against a writable copy of /app/example. This is the container's CI smoke test.
• apptainer_noslurm.sh — apptainer exec with the SLURM/PMI/PMIX/OMPI environment stripped, for MPI inside a SLURM job.
• run_job_sp_canfar_v2.0.bash, job_sp_canfar_v2.0.bash, job_list_help.bash, functions.sh — the bit-coded bash job layer. Kept only for image simulations (above); real-data runs go through workflow/.

Scratch notebooks: wcs.ipynb, test_centroid_shift.py.

centroid/ — the metacalibration multiplicative-bias validation of the ngmix centroid handling: run_all.sh drives centroid_bias_v2.py over the three cases in configs/.