Verifying prepared outputs (manifests, jobs, scripts)

Purpose

Quick reference for the helper scripts that print and inspect files produced by valska-bayeseor-prepare.
Two helper files:
- bash_scripts/check_bayeseor_manifests.sh — runnable checker: runs a prepare into a (temporary by default) results-root, prints selected prepared files and performs basic checks (e.g. manifest["tool"] == "bayeseor").
- bash_scripts/print_example_prepared_file_outputs.sh — documentation/example file containing a copy‑pasteable invocation and illustrative sample output.

Prerequisites

valska-bayeseor-prepare on PATH (in your ValSKA environment).
Optional: jq and yq for nicer pretty-printing (the scripts fall back to Python / sed).

Quick copy‑paste examples

Default (print manifest only, keep the temporary results-root):

./bash_scripts/check_bayeseor_manifests.sh --keep \
  --beam chromatic_Gaussian \
  --sky GLEAM \
  --data "gsm_plus_gleam-158.30-167.10-MHz-nf-38-fov-19.4deg-circ-field-1_quentin.uvh5" \
  --template validation_chromatic_Gaussian.yaml \
  --run-id sweep

Show everything (manifest, jobs.json, submit scripts, YAML templates, artefacts):

./bash_scripts/check_bayeseor_manifests.sh --show-all --keep \
  --beam chromatic_Gaussian \
  --sky GLEAM \
  --data "gsm_plus_gleam-158.30-167.10-MHz-..." \
  --template validation_chromatic_Gaussian.yaml \
  --run-id sweep

Reproduce the repo example output:

# example output is stored in:
# bash_scripts/print_example_prepared_file_outputs.sh
# to reproduce, run the checker with the same args used in that file:
./bash_scripts/check_bayeseor_manifests.sh --show-all --keep <same-args-as-example>

What the checker prints (sections)

manifest — the generated manifest.json (pretty-printed).
jobs — jobs.json (if present).
scripts — SLURM submit scripts / submit*.sh / *.sbatch (heads).
yaml — rendered template YAMLs (heads).
artefacts — files referenced by manifest (heads, textual or marked binary).

CLI options (summary)

--keep : keep the temporary results-root (default temporary dir is removed on exit).
--show <list> : comma-separated list of sections to print (valid: manifest, jobs, scripts, yaml, artefacts). Default: manifest.
--show-all : show all sections.
--results-root <dir> : provide a specific directory to write prepared outputs to (useful for reproducible runs).

Example minimal output (illustrative)

Running: valska-bayeseor-prepare --beam chromatic_Gaussian --sky GLEAM --data ... --template validation_chromatic_Gaussian.yaml --run-id sweep --results-root /tmp/valska-bayeseor-manifests-XXXX

==== Manifest: /tmp/.../sweep/manifest.json ====
{
  "tool": "bayeseor",
  "created_utc": "20260125T123456Z",
  "valska_version": "0.1.0",
  "beam_model": "chromatic_Gaussian",
  "sky_model": "GLEAM",
  "run_id": "sweep",
  "run_dir": "/tmp/.../sweep",
  "template_name": "validation_chromatic_Gaussian.yaml",
  ...
}
OK: manifest tool is 'bayeseor'

---- jobs.json ----
{ "jobs": [ {"name":"precompute"}, {"name":"fit"} ] }

---- submit.sh (head) ----
#!/bin/sh
#SBATCH --time=1-11:00:00
#SBATCH --mem=64G
srun ./run.sh

---- template YAML (head) ----
priors:
  - name: fwhm

---- artefacts (from manifest) ----
run_script: /tmp/.../run.sh
  #!/bin/sh
  echo "ok"

Checked 1 manifest(s) — all OK
Temporary results-root kept at: /tmp/valska-bayeseor-manifests-XXXX

Exit codes

0 : all manifests checked OK
2 : no manifest.json files found under the results-root
3 : one or more manifests failed checks (e.g., wrong tool)

Troubleshooting

No manifest found:
- Ensure --data is a valid runtime_paths key or an absolute path to the .uvh5.
- The checker uses a temporary --results-root unless you pass --results-root <dir> or --keep. Use --keep to inspect generated files.
Wrong tool field:
- Manifest tool should be "bayeseor". If it differs, inspect src/valska/external_tools/bayeseor/setup.py.
Pretty printing not working:
- Install jq / yq; the scripts fall back to Python / sed.
Binary artefacts:
- Artefacts are printed head-first and binary files are marked unreadable.

Notes and tips

bash_scripts/print_example_prepared_file_outputs.sh is informational and contains a concrete invocation + sample output — use it to see expected output shape.
Make the checker executable if needed:

chmod +x bash_scripts/check_bayeseor_manifests.sh

Consider adding a small CI job that runs the checker with a tiny prepare and verifies manifest["tool"] == "bayeseor".