Quick Reference

This page collects the main commands and tracked example config files used by the single-pulsar manual.

Tracked Example Files

The repository now includes example files that mirror the playbook:

  • configs/catalogs/ingest/single_pulsar_mapping.example.json

  • configs/runs/ingest/single_pulsar_ingest.example.toml

  • configs/runs/fixdataset/single_pulsar_step1_fix.example.toml

  • configs/runs/pqc/single_pulsar_pqc_detect.example.toml

  • configs/runs/fixdataset/single_pulsar_pqc_apply.example.toml

  • configs/rules/pqc/single_pulsar_backend_profiles.example.toml

  • configs/workflows/single_pulsar_3pass.example.toml

These files use placeholder paths and names. Copy them to project-specific files and replace the placeholders before running.

Main Commands

Ingest:

pleb ingest --config configs/runs/ingest/single_pulsar_ingest.example.toml

Step 1 FixDataset:

pleb --config configs/runs/fixdataset/single_pulsar_step1_fix.example.toml

Step 2 PQC detect:

pleb --config configs/runs/pqc/single_pulsar_pqc_detect.example.toml

Step 3 QC apply:

pleb --config configs/runs/fixdataset/single_pulsar_pqc_apply.example.toml

Three-pass workflow:

pleb workflow --file configs/workflows/single_pulsar_3pass.example.toml

Useful Inspection Commands

Inspect the current git state:

git status

Inspect branch differences after Step 1:

git diff raw_ingest..step1_fix_flags_variants -- J1909-3744

Inspect branch differences after Step 3:

git diff step2_pqc_balanced_detect..step3_apply_qc_comments -- J1909-3744

Find a pulsar directory inside the canonical dataset:

rg --files /data/canonical/EPTA-DR3/epta-dr3-data | rg 'J1909-3744'

Inspect the latest resolved config inside a run directory:

sed -n '1,240p' results/j1909_pqc_detect/run_settings/pipeline_config.resolved.toml

Checklist By Stage

Before ingest:

  • confirm the raw source roots,

  • confirm the canonical backend names,

  • confirm pulsar aliases,

  • confirm the intended ingest branch names.

Before Step 1:

  • confirm fix_base_branch points to the ingest branch,

  • confirm the pulsar exists in the canonical dataset,

  • confirm the variant catalogs point to readable files,

  • confirm the jump grouping flag is the intended one.

Before Step 2:

  • confirm Step 1 completed and wrote the expected branch,

  • confirm tempo2/container paths are valid,

  • confirm pqc_backend_col is the intended grouping column,

  • confirm QC is enabled and action is still disabled.

Before Step 3:

  • confirm the Step-2 QC outputs exist,

  • confirm fix_qc_results_dir points to the Step-2 run directory,

  • confirm fix_qc_branch matches the Step-2 branch,

  • confirm the action policy is still comment-first unless there is a clear reason otherwise.