Full Settings Catalog

This chapter documents all PipelineConfig keys with practical TOML and CLI examples. Use it as an operator handbook when tuning large configuration files.

Example conventions

• TOML examples are single-key snippets for clarity.

• CLI examples use --set key=value.

• Paths are illustrative; adapt to your environment.

Core pipeline

home_dir

Type: Path Default: <required> Meaning: Root of the data repository containing pulsar folders. Example TOML:

home_dir = "/data/epta"

Example CLI:

pleb --config pipeline.toml --set home_dir="/data/epta"

singularity_image

Type: Path Default: <required> Meaning: Singularity/Apptainer image with tempo2. Example TOML:

singularity_image = "/images/tempo2.sif"

Example CLI:

pleb --config pipeline.toml --set singularity_image="/images/tempo2.sif"

dataset_name

Type: Optional[str] Default: None Meaning: Dataset name or path (see resolved()). Example TOML:

dataset_name = "DR3full"

Example CLI:

pleb --config pipeline.toml --set dataset_name="DR3full"

results_dir

Type: Path Default: Path('.') Meaning: Output directory for pipeline reports. Example TOML:

results_dir = "results"

Example CLI:

pleb --config pipeline.toml --set results_dir="results"

branches

Type: List[str] Default: ['main', 'EPTA'] Meaning: Git branches to run/compare. Example TOML:

branches = ["main","raw_ingest"]

Example CLI:

pleb --config pipeline.toml --set branches=["main","raw_ingest"]

reference_branch

Type: str Default: 'main' Meaning: Branch used as change-report reference. Example TOML:

reference_branch = "main"

Example CLI:

pleb --config pipeline.toml --set reference_branch="main"

pulsars

Type: PulsarSelection Default: 'ALL' Meaning: “ALL” or an explicit list of pulsar names. Example TOML:

pulsars = ["J1713+0747","J1022+1001"]

Example CLI:

pleb --config pipeline.toml --set pulsars=["J1713+0747","J1022+1001"]

outdir_name

Type: Optional[str] Default: None Meaning: Optional output subdirectory name. Example TOML:

outdir_name = "run_pqc_balanced"

Example CLI:

pleb --config pipeline.toml --set outdir_name="run_pqc_balanced"

cleanup_output_tree

Type: bool Default: True Meaning: Pipeline setting. Example TOML:

cleanup_output_tree = false

Example CLI:

pleb --config pipeline.toml --set cleanup_output_tree=false

cleanup_work_dir

Type: bool Default: False Meaning: Pipeline setting. Example TOML:

cleanup_work_dir = true

Example CLI:

pleb --config pipeline.toml --set cleanup_work_dir=true

epoch

Type: str Default: '55000' Meaning: Tempo2 epoch used for fitting. Example TOML:

epoch = "55000"

Example CLI:

pleb --config pipeline.toml --set epoch="55000"

force_rerun

Type: bool Default: False Meaning: Re-run tempo2 even if outputs exist. Example TOML:

force_rerun = true

Example CLI:

pleb --config pipeline.toml --set force_rerun=true

jobs

Type: int Default: 1 Meaning: Parallel workers per branch. Example TOML:

jobs = 8

Example CLI:

pleb --config pipeline.toml --set jobs=8

run_tempo2

Type: bool Default: True Meaning: Whether to run tempo2. Example TOML:

run_tempo2 = false

Example CLI:

pleb --config pipeline.toml --set run_tempo2=false

make_toa_coverage_plots

Type: bool Default: True Meaning: Generate coverage plots. Example TOML:

make_toa_coverage_plots = false

Example CLI:

pleb --config pipeline.toml --set make_toa_coverage_plots=false

make_change_reports

Type: bool Default: True Meaning: Generate change reports. Example TOML:

make_change_reports = false

Example CLI:

pleb --config pipeline.toml --set make_change_reports=false

make_covariance_heatmaps

Type: bool Default: True Meaning: Generate covariance heatmaps. Example TOML:

make_covariance_heatmaps = false

Example CLI:

pleb --config pipeline.toml --set make_covariance_heatmaps=false

make_residual_plots

Type: bool Default: True Meaning: Generate residual plots. Example TOML:

make_residual_plots = false

Example CLI:

pleb --config pipeline.toml --set make_residual_plots=false

make_outlier_reports

Type: bool Default: True Meaning: Generate outlier tables. Example TOML:

make_outlier_reports = false

Example CLI:

pleb --config pipeline.toml --set make_outlier_reports=false

make_plots

Type: Optional[bool] Default: None Meaning: Convenience toggle to disable all plotting outputs. Example TOML:

make_plots = true

Example CLI:

pleb --config pipeline.toml --set make_plots=true

make_reports

Type: Optional[bool] Default: None Meaning: Convenience toggle to disable report outputs. Example TOML:

make_reports = true

Example CLI:

pleb --config pipeline.toml --set make_reports=true

make_covmat

Type: Optional[bool] Default: None Meaning: Convenience toggle to control covariance heatmaps. Example TOML:

make_covmat = true

Example CLI:

pleb --config pipeline.toml --set make_covmat=true

testing_mode

Type: bool Default: False Meaning: If True, skip change reports (useful for CI). Example TOML:

testing_mode = true

Example CLI:

pleb --config pipeline.toml --set testing_mode=true

run_pqc

Type: bool Default: False Meaning: Enable optional pqc stage. Example TOML:

run_pqc = true

Example CLI:

pleb --config pipeline.toml --set run_pqc=true

qc_report

Type: bool Default: False Meaning: Generate pqc report artifacts after the run. Example TOML:

qc_report = true

Example CLI:

pleb --config pipeline.toml --set qc_report=true

run_fix_dataset

Type: bool Default: False Meaning: Enable FixDataset stage. Example TOML:

run_fix_dataset = true

Example CLI:

pleb --config pipeline.toml --set run_fix_dataset=true

make_binary_analysis

Type: bool Default: False Meaning: Enable binary analysis table. Example TOML:

make_binary_analysis = true

Example CLI:

pleb --config pipeline.toml --set make_binary_analysis=true

PQC detector settings

pqc_backend_col

Type: str Default: 'group' Meaning: Backend grouping column for pqc. Example TOML:

pqc_backend_col = "sys"

Example CLI:

pleb --config pipeline.toml --set pqc_backend_col="sys"

pqc_drop_unmatched

Type: bool Default: False Meaning: Drop unmatched TOAs in pqc. Example TOML:

pqc_drop_unmatched = true

Example CLI:

pleb --config pipeline.toml --set pqc_drop_unmatched=true

pqc_merge_tol_seconds

Type: float Default: 2.0 Meaning: Merge tolerance in seconds for pqc. Example TOML:

pqc_merge_tol_seconds = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_merge_tol_seconds=1.0

pqc_tau_corr_minutes

Type: float Default: 30.0 Meaning: OU correlation time for pqc. Example TOML:

pqc_tau_corr_minutes = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_tau_corr_minutes=1.0

pqc_fdr_q

Type: float Default: 0.01 Meaning: False discovery rate for pqc. Example TOML:

pqc_fdr_q = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_fdr_q=1.0

pqc_mark_only_worst_per_day

Type: bool Default: True Meaning: Mark only worst TOA per day. Example TOML:

pqc_mark_only_worst_per_day = false

Example CLI:

pleb --config pipeline.toml --set pqc_mark_only_worst_per_day=false

pqc_tau_rec_days

Type: float Default: 7.0 Meaning: Recovery time for transient scan. Example TOML:

pqc_tau_rec_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_tau_rec_days=1.0

pqc_window_mult

Type: float Default: 5.0 Meaning: Window multiplier for transient scan. Example TOML:

pqc_window_mult = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_window_mult=1.0

pqc_min_points

Type: int Default: 6 Meaning: Minimum points for transient scan. Example TOML:

pqc_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_min_points=4

pqc_delta_chi2_thresh

Type: float Default: 25.0 Meaning: Delta-chi2 threshold for transients. Example TOML:

pqc_delta_chi2_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_delta_chi2_thresh=1.0

pqc_exp_dip_min_duration_days

Type: float Default: 21.0 Meaning: Minimum duration (days) for exp dips. Example TOML:

pqc_exp_dip_min_duration_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_exp_dip_min_duration_days=1.0

pqc_step_enabled

Type: bool Default: True Meaning: PQC detector/feature threshold. Example TOML:

pqc_step_enabled = false

Example CLI:

pleb --config pipeline.toml --set pqc_step_enabled=false

pqc_step_min_points

Type: int Default: 20 Meaning: PQC detector/feature threshold. Example TOML:

pqc_step_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_step_min_points=4

pqc_step_delta_chi2_thresh

Type: float Default: 25.0 Meaning: PQC detector/feature threshold. Example TOML:

pqc_step_delta_chi2_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_step_delta_chi2_thresh=1.0

pqc_step_scope

Type: str Default: 'both' Meaning: PQC detector/feature threshold. Example TOML:

pqc_step_scope = "both"

Example CLI:

pleb --config pipeline.toml --set pqc_step_scope="both"

pqc_dm_step_enabled

Type: bool Default: True Meaning: PQC detector/feature threshold. Example TOML:

pqc_dm_step_enabled = false

Example CLI:

pleb --config pipeline.toml --set pqc_dm_step_enabled=false

pqc_dm_step_min_points

Type: int Default: 20 Meaning: PQC detector/feature threshold. Example TOML:

pqc_dm_step_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_dm_step_min_points=4

pqc_dm_step_delta_chi2_thresh

Type: float Default: 25.0 Meaning: PQC detector/feature threshold. Example TOML:

pqc_dm_step_delta_chi2_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_dm_step_delta_chi2_thresh=1.0

pqc_dm_step_scope

Type: str Default: 'both' Meaning: PQC detector/feature threshold. Example TOML:

pqc_dm_step_scope = "both"

Example CLI:

pleb --config pipeline.toml --set pqc_dm_step_scope="both"

pqc_robust_enabled

Type: bool Default: True Meaning: PQC detector/feature threshold. Example TOML:

pqc_robust_enabled = false

Example CLI:

pleb --config pipeline.toml --set pqc_robust_enabled=false

pqc_robust_z_thresh

Type: float Default: 5.0 Meaning: PQC detector/feature threshold. Example TOML:

pqc_robust_z_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_robust_z_thresh=1.0

pqc_robust_scope

Type: str Default: 'both' Meaning: PQC detector/feature threshold. Example TOML:

pqc_robust_scope = "backend"

Example CLI:

pleb --config pipeline.toml --set pqc_robust_scope="backend"

pqc_add_orbital_phase

Type: bool Default: True Meaning: Add orbital-phase feature. Example TOML:

pqc_add_orbital_phase = false

Example CLI:

pleb --config pipeline.toml --set pqc_add_orbital_phase=false

pqc_add_solar_elongation

Type: bool Default: True Meaning: Add solar elongation feature. Example TOML:

pqc_add_solar_elongation = false

Example CLI:

pleb --config pipeline.toml --set pqc_add_solar_elongation=false

pqc_add_elevation

Type: bool Default: False Meaning: Add elevation feature. Example TOML:

pqc_add_elevation = true

Example CLI:

pleb --config pipeline.toml --set pqc_add_elevation=true

pqc_add_airmass

Type: bool Default: False Meaning: Add airmass feature. Example TOML:

pqc_add_airmass = true

Example CLI:

pleb --config pipeline.toml --set pqc_add_airmass=true

pqc_add_parallactic_angle

Type: bool Default: False Meaning: Add parallactic-angle feature. Example TOML:

pqc_add_parallactic_angle = true

Example CLI:

pleb --config pipeline.toml --set pqc_add_parallactic_angle=true

pqc_add_freq_bin

Type: bool Default: False Meaning: Add frequency-bin feature. Example TOML:

pqc_add_freq_bin = true

Example CLI:

pleb --config pipeline.toml --set pqc_add_freq_bin=true

pqc_freq_bins

Type: int Default: 8 Meaning: Number of frequency bins if enabled. Example TOML:

pqc_freq_bins = 4

Example CLI:

pleb --config pipeline.toml --set pqc_freq_bins=4

pqc_observatory_path

Type: Optional[str] Default: None Meaning: Optional observatory file path. Example TOML:

pqc_observatory_path = "value"

Example CLI:

pleb --config pipeline.toml --set pqc_observatory_path="value"

pqc_structure_mode

Type: str Default: 'none' Meaning: Feature-structure mode (none/detrend/test/both). Example TOML:

pqc_structure_mode = "both"

Example CLI:

pleb --config pipeline.toml --set pqc_structure_mode="both"

pqc_structure_detrend_features

Type: Optional[List[str]] Default: ['solar_elongation_deg', 'orbital_phase'] Meaning: Features to detrend against. Example TOML:

pqc_structure_detrend_features = ["solar_elongation_deg","orbital_phase"]

Example CLI:

pleb --config pipeline.toml --set pqc_structure_detrend_features=["solar_elongation_deg","orbital_phase"]

pqc_structure_test_features

Type: Optional[List[str]] Default: ['solar_elongation_deg', 'orbital_phase'] Meaning: Features to test for structure. Example TOML:

pqc_structure_test_features = ["solar_elongation_deg","orbital_phase"]

Example CLI:

pleb --config pipeline.toml --set pqc_structure_test_features=["solar_elongation_deg","orbital_phase"]

pqc_structure_nbins

Type: int Default: 12 Meaning: Bin count for structure tests. Example TOML:

pqc_structure_nbins = 4

Example CLI:

pleb --config pipeline.toml --set pqc_structure_nbins=4

pqc_structure_min_per_bin

Type: int Default: 3 Meaning: Minimum points per bin. Example TOML:

pqc_structure_min_per_bin = 4

Example CLI:

pleb --config pipeline.toml --set pqc_structure_min_per_bin=4

pqc_structure_p_thresh

Type: float Default: 0.01 Meaning: p-value threshold for structure detection. Example TOML:

pqc_structure_p_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_structure_p_thresh=1.0

pqc_structure_circular_features

Type: Optional[List[str]] Default: ['orbital_phase'] Meaning: Circular features in [0,1). Example TOML:

pqc_structure_circular_features = ["orbital_phase"]

Example CLI:

pleb --config pipeline.toml --set pqc_structure_circular_features=["orbital_phase"]

pqc_structure_group_cols

Type: Optional[List[str]] Default: None Meaning: Grouping columns for structure tests. Example TOML:

pqc_structure_group_cols = ["sys"]

Example CLI:

pleb --config pipeline.toml --set pqc_structure_group_cols=["sys"]

pqc_outlier_gate_enabled

Type: bool Default: False Meaning: Enable hard sigma gate for outlier membership. Example TOML:

pqc_outlier_gate_enabled = true

Example CLI:

pleb --config pipeline.toml --set pqc_outlier_gate_enabled=true

pqc_outlier_gate_sigma

Type: float Default: 3.0 Meaning: Sigma threshold for outlier gate. Example TOML:

pqc_outlier_gate_sigma = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_outlier_gate_sigma=1.0

pqc_outlier_gate_resid_col

Type: Optional[str] Default: None Meaning: Residual column to gate on (optional). Example TOML:

pqc_outlier_gate_resid_col = "post"

Example CLI:

pleb --config pipeline.toml --set pqc_outlier_gate_resid_col="post"

pqc_outlier_gate_sigma_col

Type: Optional[str] Default: None Meaning: Sigma column to gate on (optional). Example TOML:

pqc_outlier_gate_sigma_col = "err"

Example CLI:

pleb --config pipeline.toml --set pqc_outlier_gate_sigma_col="err"

pqc_event_instrument

Type: bool Default: False Meaning: Enable per-event membership diagnostics. Example TOML:

pqc_event_instrument = true

Example CLI:

pleb --config pipeline.toml --set pqc_event_instrument=true

pqc_solar_events_enabled

Type: bool Default: False Meaning: Enable solar event detection. Example TOML:

pqc_solar_events_enabled = true

Example CLI:

pleb --config pipeline.toml --set pqc_solar_events_enabled=true

pqc_solar_approach_max_deg

Type: float Default: 30.0 Meaning: Max elongation for solar approach region. Example TOML:

pqc_solar_approach_max_deg = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_approach_max_deg=1.0

pqc_solar_min_points_global

Type: int Default: 30 Meaning: Min points for global fit. Example TOML:

pqc_solar_min_points_global = 4

Example CLI:

pleb --config pipeline.toml --set pqc_solar_min_points_global=4

pqc_solar_min_points_year

Type: int Default: 10 Meaning: Min points for per-year fit. Example TOML:

pqc_solar_min_points_year = 4

Example CLI:

pleb --config pipeline.toml --set pqc_solar_min_points_year=4

pqc_solar_min_points_near_zero

Type: int Default: 3 Meaning: Min points near zero elongation. Example TOML:

pqc_solar_min_points_near_zero = 4

Example CLI:

pleb --config pipeline.toml --set pqc_solar_min_points_near_zero=4

pqc_solar_tau_min_deg

Type: float Default: 2.0 Meaning: Min elongation scale for exponential. Example TOML:

pqc_solar_tau_min_deg = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_tau_min_deg=1.0

pqc_solar_tau_max_deg

Type: float Default: 60.0 Meaning: Max elongation scale for exponential. Example TOML:

pqc_solar_tau_max_deg = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_tau_max_deg=1.0

pqc_solar_member_eta

Type: float Default: 1.0 Meaning: Per-point membership SNR threshold. Example TOML:

pqc_solar_member_eta = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_member_eta=1.0

pqc_solar_freq_dependence

Type: bool Default: True Meaning: Fit 1/f^alpha dependence. Example TOML:

pqc_solar_freq_dependence = false

Example CLI:

pleb --config pipeline.toml --set pqc_solar_freq_dependence=false

pqc_solar_freq_alpha_min

Type: float Default: 0.0 Meaning: Lower bound for alpha. Example TOML:

pqc_solar_freq_alpha_min = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_freq_alpha_min=1.0

pqc_solar_freq_alpha_max

Type: float Default: 4.0 Meaning: Upper bound for alpha. Example TOML:

pqc_solar_freq_alpha_max = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_freq_alpha_max=1.0

pqc_solar_freq_alpha_tol

Type: float Default: 0.001 Meaning: Optimization tolerance for alpha. Example TOML:

pqc_solar_freq_alpha_tol = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_solar_freq_alpha_tol=1.0

pqc_solar_freq_alpha_max_iter

Type: int Default: 64 Meaning: Max iterations for alpha optimizer. Example TOML:

pqc_solar_freq_alpha_max_iter = 4

Example CLI:

pleb --config pipeline.toml --set pqc_solar_freq_alpha_max_iter=4

pqc_orbital_phase_cut_enabled

Type: bool Default: False Meaning: Enable orbital-phase based flagging. Example TOML:

pqc_orbital_phase_cut_enabled = true

Example CLI:

pleb --config pipeline.toml --set pqc_orbital_phase_cut_enabled=true

pqc_orbital_phase_cut_center

Type: float Default: 0.25 Meaning: Eclipse center phase (0..1). Example TOML:

pqc_orbital_phase_cut_center = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_orbital_phase_cut_center=1.0

pqc_orbital_phase_cut

Type: Optional[float] Default: None Meaning: Fixed orbital-phase cutoff (0..0.5), or None for auto. Example TOML:

pqc_orbital_phase_cut = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_orbital_phase_cut=1.0

pqc_orbital_phase_cut_sigma

Type: float Default: 3.0 Meaning: Sigma threshold for automatic cutoff estimation. Example TOML:

pqc_orbital_phase_cut_sigma = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_orbital_phase_cut_sigma=1.0

pqc_orbital_phase_cut_nbins

Type: int Default: 18 Meaning: Number of bins for cutoff estimation. Example TOML:

pqc_orbital_phase_cut_nbins = 4

Example CLI:

pleb --config pipeline.toml --set pqc_orbital_phase_cut_nbins=4

pqc_orbital_phase_cut_min_points

Type: int Default: 20 Meaning: Minimum points for cutoff estimation. Example TOML:

pqc_orbital_phase_cut_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_orbital_phase_cut_min_points=4

pqc_eclipse_events_enabled

Type: bool Default: False Meaning: Enable eclipse event detection. Example TOML:

pqc_eclipse_events_enabled = true

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_events_enabled=true

pqc_eclipse_center_phase

Type: float Default: 0.25 Meaning: Eclipse center phase (0..1). Example TOML:

pqc_eclipse_center_phase = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_center_phase=1.0

pqc_eclipse_min_points

Type: int Default: 30 Meaning: Min points for global fit. Example TOML:

pqc_eclipse_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_min_points=4

pqc_eclipse_width_min

Type: float Default: 0.01 Meaning: Min eclipse width in phase. Example TOML:

pqc_eclipse_width_min = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_width_min=1.0

pqc_eclipse_width_max

Type: float Default: 0.5 Meaning: Max eclipse width in phase. Example TOML:

pqc_eclipse_width_max = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_width_max=1.0

pqc_eclipse_member_eta

Type: float Default: 1.0 Meaning: Per-point membership SNR threshold. Example TOML:

pqc_eclipse_member_eta = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_member_eta=1.0

pqc_eclipse_freq_dependence

Type: bool Default: True Meaning: Fit 1/f^alpha dependence. Example TOML:

pqc_eclipse_freq_dependence = false

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_freq_dependence=false

pqc_eclipse_freq_alpha_min

Type: float Default: 0.0 Meaning: Lower bound for alpha. Example TOML:

pqc_eclipse_freq_alpha_min = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_freq_alpha_min=1.0

pqc_eclipse_freq_alpha_max

Type: float Default: 4.0 Meaning: Upper bound for alpha. Example TOML:

pqc_eclipse_freq_alpha_max = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_freq_alpha_max=1.0

pqc_eclipse_freq_alpha_tol

Type: float Default: 0.001 Meaning: Optimization tolerance for alpha. Example TOML:

pqc_eclipse_freq_alpha_tol = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_freq_alpha_tol=1.0

pqc_eclipse_freq_alpha_max_iter

Type: int Default: 64 Meaning: Max iterations for alpha optimizer. Example TOML:

pqc_eclipse_freq_alpha_max_iter = 4

Example CLI:

pleb --config pipeline.toml --set pqc_eclipse_freq_alpha_max_iter=4

pqc_gaussian_bump_enabled

Type: bool Default: False Meaning: Enable Gaussian-bump event detection. Example TOML:

pqc_gaussian_bump_enabled = true

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_enabled=true

pqc_gaussian_bump_min_duration_days

Type: float Default: 60.0 Meaning: Minimum bump duration in days. Example TOML:

pqc_gaussian_bump_min_duration_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_min_duration_days=1.0

pqc_gaussian_bump_max_duration_days

Type: float Default: 1500.0 Meaning: Maximum bump duration in days. Example TOML:

pqc_gaussian_bump_max_duration_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_max_duration_days=1.0

pqc_gaussian_bump_n_durations

Type: int Default: 6 Meaning: Number of duration grid points. Example TOML:

pqc_gaussian_bump_n_durations = 4

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_n_durations=4

pqc_gaussian_bump_min_points

Type: int Default: 20 Meaning: Minimum points for bump detection. Example TOML:

pqc_gaussian_bump_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_min_points=4

pqc_gaussian_bump_delta_chi2_thresh

Type: float Default: 25.0 Meaning: Delta-chi2 threshold for bump detection. Example TOML:

pqc_gaussian_bump_delta_chi2_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_delta_chi2_thresh=1.0

pqc_gaussian_bump_suppress_overlap

Type: bool Default: True Meaning: Suppress overlapping bumps. Example TOML:

pqc_gaussian_bump_suppress_overlap = false

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_suppress_overlap=false

pqc_gaussian_bump_member_eta

Type: float Default: 1.0 Meaning: Per-point membership SNR threshold. Example TOML:

pqc_gaussian_bump_member_eta = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_member_eta=1.0

pqc_gaussian_bump_freq_dependence

Type: bool Default: True Meaning: Fit 1/f^alpha dependence. Example TOML:

pqc_gaussian_bump_freq_dependence = false

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_freq_dependence=false

pqc_gaussian_bump_freq_alpha_min

Type: float Default: 0.0 Meaning: Lower bound for alpha. Example TOML:

pqc_gaussian_bump_freq_alpha_min = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_freq_alpha_min=1.0

pqc_gaussian_bump_freq_alpha_max

Type: float Default: 4.0 Meaning: Upper bound for alpha. Example TOML:

pqc_gaussian_bump_freq_alpha_max = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_freq_alpha_max=1.0

pqc_gaussian_bump_freq_alpha_tol

Type: float Default: 0.001 Meaning: Optimization tolerance for alpha. Example TOML:

pqc_gaussian_bump_freq_alpha_tol = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_freq_alpha_tol=1.0

pqc_gaussian_bump_freq_alpha_max_iter

Type: int Default: 64 Meaning: Max iterations for alpha optimizer. Example TOML:

pqc_gaussian_bump_freq_alpha_max_iter = 4

Example CLI:

pleb --config pipeline.toml --set pqc_gaussian_bump_freq_alpha_max_iter=4

pqc_glitch_enabled

Type: bool Default: False Meaning: Enable glitch event detection. Example TOML:

pqc_glitch_enabled = true

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_enabled=true

pqc_glitch_min_points

Type: int Default: 30 Meaning: Minimum points for glitch detection. Example TOML:

pqc_glitch_min_points = 4

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_min_points=4

pqc_glitch_delta_chi2_thresh

Type: float Default: 25.0 Meaning: Delta-chi2 threshold for glitch detection. Example TOML:

pqc_glitch_delta_chi2_thresh = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_delta_chi2_thresh=1.0

pqc_glitch_suppress_overlap

Type: bool Default: True Meaning: Suppress overlapping glitches. Example TOML:

pqc_glitch_suppress_overlap = false

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_suppress_overlap=false

pqc_glitch_member_eta

Type: float Default: 1.0 Meaning: Per-point membership SNR threshold. Example TOML:

pqc_glitch_member_eta = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_member_eta=1.0

pqc_glitch_peak_tau_days

Type: float Default: 30.0 Meaning: Peak exponential timescale for glitch model. Example TOML:

pqc_glitch_peak_tau_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_peak_tau_days=1.0

pqc_glitch_noise_k

Type: float Default: 1.0 Meaning: Noise-aware threshold multiplier. Example TOML:

pqc_glitch_noise_k = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_noise_k=1.0

pqc_glitch_mean_window_days

Type: float Default: 180.0 Meaning: Rolling-mean window (days) for zero-crossing. Example TOML:

pqc_glitch_mean_window_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_mean_window_days=1.0

pqc_glitch_min_duration_days

Type: float Default: 1000.0 Meaning: Minimum glitch duration (days). Example TOML:

pqc_glitch_min_duration_days = 1.0

Example CLI:

pleb --config pipeline.toml --set pqc_glitch_min_duration_days=1.0

pqc_backend_profiles_path

Type: Optional[str] Default: None Meaning: Optional TOML with per-backend pqc overrides. Example TOML:

pqc_backend_profiles_path = "configs/rules/pqc/backend_profiles.example.toml"

Example CLI:

pleb --config pipeline.toml --set pqc_backend_profiles_path="configs/rules/pqc/backend_profiles.example.toml"

QC report settings

qc_report_backend_col

Type: Optional[str] Default: None Meaning: Backend column name for reports (optional). Example TOML:

qc_report_backend_col = "sys"

Example CLI:

pleb --config pipeline.toml --set qc_report_backend_col="sys"

qc_report_backend

Type: Optional[str] Default: None Meaning: Optional backend key to plot. Example TOML:

qc_report_backend = "NRT.NUPPI.1484"

Example CLI:

pleb --config pipeline.toml --set qc_report_backend="NRT.NUPPI.1484"

qc_report_dir

Type: Optional[Path] Default: None Meaning: Output directory for reports (optional). Example TOML:

qc_report_dir = "results/qc_report"

Example CLI:

pleb --config pipeline.toml --set qc_report_dir="results/qc_report"

qc_report_no_plots

Type: bool Default: False Meaning: Skip transient plots in reports. Example TOML:

qc_report_no_plots = true

Example CLI:

pleb --config pipeline.toml --set qc_report_no_plots=true

qc_report_structure_group_cols

Type: Optional[str] Default: None Meaning: Structure grouping override for reports. Example TOML:

qc_report_structure_group_cols = "value"

Example CLI:

pleb --config pipeline.toml --set qc_report_structure_group_cols="value"

qc_report_no_feature_plots

Type: bool Default: False Meaning: Skip feature plots in reports. Example TOML:

qc_report_no_feature_plots = true

Example CLI:

pleb --config pipeline.toml --set qc_report_no_feature_plots=true

qc_report_compact_pdf

Type: bool Default: False Meaning: Generate compact composite PDF report. Example TOML:

qc_report_compact_pdf = true

Example CLI:

pleb --config pipeline.toml --set qc_report_compact_pdf=true

qc_report_compact_pdf_name

Type: str Default: 'qc_compact_report.pdf' Meaning: Filename for compact PDF report. Example TOML:

qc_report_compact_pdf_name = "qc_compact_report.pdf"

Example CLI:

pleb --config pipeline.toml --set qc_report_compact_pdf_name="qc_compact_report.pdf"

qc_report_compact_outlier_cols

Type: Optional[List[str]] Default: None Meaning: QC report generation setting. Example TOML:

qc_report_compact_outlier_cols = ["bad_point","robust_outlier","robust_global_outlier","bad_mad"]

Example CLI:

pleb --config pipeline.toml --set qc_report_compact_outlier_cols=["bad_point","robust_outlier","robust_global_outlier","bad_mad"]

FixDataset settings

fix_apply

Type: bool Default: False Meaning: Whether FixDataset applies changes and commits. Example TOML:

fix_apply = true

Example CLI:

pleb --config pipeline.toml --set fix_apply=true

fix_branch_name

Type: Optional[str] Default: None Meaning: Name of FixDataset branch. If unset and fix_apply is true, Example TOML:

fix_branch_name = "fix_dataset"

Example CLI:

pleb --config pipeline.toml --set fix_branch_name="fix_dataset"

fix_base_branch

Type: Optional[str] Default: None Meaning: Base branch for FixDataset. Example TOML:

fix_base_branch = "raw_ingest"

Example CLI:

pleb --config pipeline.toml --set fix_base_branch="raw_ingest"

fix_commit_message

Type: Optional[str] Default: None Meaning: Commit message for FixDataset. Example TOML:

fix_commit_message = "FixDataset: normalize flags"

Example CLI:

pleb --config pipeline.toml --set fix_commit_message="FixDataset: normalize flags"

fix_backup

Type: bool Default: True Meaning: Create backup before FixDataset modifications. Example TOML:

fix_backup = false

Example CLI:

pleb --config pipeline.toml --set fix_backup=false

fix_dry_run

Type: bool Default: False Meaning: If True, FixDataset does not write changes. Example TOML:

fix_dry_run = true

Example CLI:

pleb --config pipeline.toml --set fix_dry_run=true

fix_update_alltim_includes

Type: bool Default: True Meaning: Update INCLUDE lines in .tim files. Example TOML:

fix_update_alltim_includes = false

Example CLI:

pleb --config pipeline.toml --set fix_update_alltim_includes=false

fix_min_toas_per_backend_tim

Type: int Default: 10 Meaning: Minimum TOAs per backend .tim. Example TOML:

fix_min_toas_per_backend_tim = 4

Example CLI:

pleb --config pipeline.toml --set fix_min_toas_per_backend_tim=4

fix_required_tim_flags

Type: Dict[str, str] Default: {} Meaning: Required flags for .tim entries. Example TOML:

fix_required_tim_flags = { "-pta" = "EPTA" }

Example CLI:

pleb --config pipeline.toml --set fix_required_tim_flags={ "-pta" = "EPTA" }

fix_system_flag_mapping_path

Type: Optional[str] Default: None Meaning: Editable system-flag mapping JSON (optional). Example TOML:

fix_system_flag_mapping_path = "configs/catalogs/system_flags/system_flag_mapping.example.json"

Example CLI:

pleb --config pipeline.toml --set fix_system_flag_mapping_path="configs/catalogs/system_flags/system_flag_mapping.example.json"

fix_system_flag_table_path

Type: Optional[str] Default: None Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_system_flag_table_path = "system_flag_table.json"

Example CLI:

pleb --config pipeline.toml --set fix_system_flag_table_path="system_flag_table.json"

fix_generate_alltim_variants

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_generate_alltim_variants = true

Example CLI:

pleb --config pipeline.toml --set fix_generate_alltim_variants=true

fix_backend_classifications_path

Type: Optional[str] Default: None Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_backend_classifications_path = "configs/catalogs/variants/backend_classifications_legacy_new.toml"

Example CLI:

pleb --config pipeline.toml --set fix_backend_classifications_path="configs/catalogs/variants/backend_classifications_legacy_new.toml"

fix_alltim_variants_path

Type: Optional[str] Default: None Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_alltim_variants_path = "configs/catalogs/variants/alltim_variants_legacy_new.toml"

Example CLI:

pleb --config pipeline.toml --set fix_alltim_variants_path="configs/catalogs/variants/alltim_variants_legacy_new.toml"

fix_relabel_rules_path

Type: Optional[str] Default: None Meaning: Declarative TOA relabel rules TOML (optional). Example TOML:

fix_relabel_rules_path = "configs/rules/relabel/relabel_rules.example.toml"

Example CLI:

pleb --config pipeline.toml --set fix_relabel_rules_path="configs/rules/relabel/relabel_rules.example.toml"

fix_overlap_rules_path

Type: Optional[str] Default: None Meaning: Declarative overlap rules TOML (optional). Example TOML:

fix_overlap_rules_path = "configs/rules/overlap/overlap_rules.example.toml"

Example CLI:

pleb --config pipeline.toml --set fix_overlap_rules_path="configs/rules/overlap/overlap_rules.example.toml"

fix_overlap_exact_catalog_path

Type: Optional[str] Default: None Meaning: TOML keep->drop map for exact overlap removal. Example TOML:

fix_overlap_exact_catalog_path = "configs/catalogs/system_tables/overlapped_timfiles.toml"

Example CLI:

pleb --config pipeline.toml --set fix_overlap_exact_catalog_path="configs/catalogs/system_tables/overlapped_timfiles.toml"

fix_jump_reference_variants

Type: bool Default: False Meaning: Build per-variant reference-system jump parfiles. Example TOML:

fix_jump_reference_variants = true

Example CLI:

pleb --config pipeline.toml --set fix_jump_reference_variants=true

fix_jump_reference_keep_tmp

Type: bool Default: False Meaning: Keep temporary split tim/par files. Example TOML:

fix_jump_reference_keep_tmp = true

Example CLI:

pleb --config pipeline.toml --set fix_jump_reference_keep_tmp=true

fix_jump_reference_jump_flag

Type: str Default: '-sys' Meaning: Jump flag used in generated variant parfiles. Example TOML:

fix_jump_reference_jump_flag = "-sys"

Example CLI:

pleb --config pipeline.toml --set fix_jump_reference_jump_flag="-sys"

fix_jump_reference_csv_dir

Type: Optional[str] Default: None Meaning: Output directory for jump-reference CSV files. Example TOML:

fix_jump_reference_csv_dir = "results/jump_reference"

Example CLI:

pleb --config pipeline.toml --set fix_jump_reference_csv_dir="results/jump_reference"

fix_infer_system_flags

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_infer_system_flags = true

Example CLI:

pleb --config pipeline.toml --set fix_infer_system_flags=true

fix_system_flag_overwrite_existing

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_system_flag_overwrite_existing = true

Example CLI:

pleb --config pipeline.toml --set fix_system_flag_overwrite_existing=true

fix_wsrt_p2_force_sys_by_freq

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_wsrt_p2_force_sys_by_freq = true

Example CLI:

pleb --config pipeline.toml --set fix_wsrt_p2_force_sys_by_freq=true

fix_wsrt_p2_prefer_dual_channel

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_wsrt_p2_prefer_dual_channel = true

Example CLI:

pleb --config pipeline.toml --set fix_wsrt_p2_prefer_dual_channel=true

fix_wsrt_p2_mjd_tol_sec

Type: float Default: 9.9e-07 Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_wsrt_p2_mjd_tol_sec = 1.0

Example CLI:

pleb --config pipeline.toml --set fix_wsrt_p2_mjd_tol_sec=1.0

fix_wsrt_p2_action

Type: str Default: 'comment' Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_wsrt_p2_action = "comment"

Example CLI:

pleb --config pipeline.toml --set fix_wsrt_p2_action="comment"

fix_wsrt_p2_comment_prefix

Type: str Default: 'C WSRT_P2_PREFER_DUAL' Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_wsrt_p2_comment_prefix = "C WSRT_P2_PREFER_DUAL"

Example CLI:

pleb --config pipeline.toml --set fix_wsrt_p2_comment_prefix="C WSRT_P2_PREFER_DUAL"

fix_backend_overrides

Type: Dict[str, str] Default: {} Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_backend_overrides = { "JBO.DFB.1400.tim" = "DFB" }

Example CLI:

pleb --config pipeline.toml --set fix_backend_overrides={ "JBO.DFB.1400.tim" = "DFB" }

fix_raise_on_backend_missing

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_raise_on_backend_missing = true

Example CLI:

pleb --config pipeline.toml --set fix_raise_on_backend_missing=true

fix_dedupe_toas_within_tim

Type: bool Default: True Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_dedupe_toas_within_tim = false

Example CLI:

pleb --config pipeline.toml --set fix_dedupe_toas_within_tim=false

fix_dedupe_mjd_tol_sec

Type: float Default: 0.0 Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_dedupe_mjd_tol_sec = 1.0

Example CLI:

pleb --config pipeline.toml --set fix_dedupe_mjd_tol_sec=1.0

fix_dedupe_freq_tol_mhz

Type: Optional[float] Default: None Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_dedupe_freq_tol_mhz = 1.0

Example CLI:

pleb --config pipeline.toml --set fix_dedupe_freq_tol_mhz=1.0

fix_dedupe_freq_tol_auto

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_dedupe_freq_tol_auto = true

Example CLI:

pleb --config pipeline.toml --set fix_dedupe_freq_tol_auto=true

fix_check_duplicate_backend_tims

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_check_duplicate_backend_tims = true

Example CLI:

pleb --config pipeline.toml --set fix_check_duplicate_backend_tims=true

fix_remove_overlaps_exact

Type: bool Default: True Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_remove_overlaps_exact = false

Example CLI:

pleb --config pipeline.toml --set fix_remove_overlaps_exact=false

fix_insert_missing_jumps

Type: bool Default: True Meaning: Insert missing JUMP lines. Example TOML:

fix_insert_missing_jumps = false

Example CLI:

pleb --config pipeline.toml --set fix_insert_missing_jumps=false

fix_jump_flag

Type: str Default: '-sys' Meaning: Flag used for inserted jumps. Example TOML:

fix_jump_flag = "-sys"

Example CLI:

pleb --config pipeline.toml --set fix_jump_flag="-sys"

fix_prune_stale_jumps

Type: bool Default: False Meaning: Drop JUMPs not present in timfile flags. Example TOML:

fix_prune_stale_jumps = true

Example CLI:

pleb --config pipeline.toml --set fix_prune_stale_jumps=true

fix_ensure_ephem

Type: Optional[str] Default: None Meaning: Ensure ephemeris parameter exists. Example TOML:

fix_ensure_ephem = "DE440"

Example CLI:

pleb --config pipeline.toml --set fix_ensure_ephem="DE440"

fix_ensure_clk

Type: Optional[str] Default: None Meaning: Ensure clock parameter exists. Example TOML:

fix_ensure_clk = "TT(BIPM2024)"

Example CLI:

pleb --config pipeline.toml --set fix_ensure_clk="TT(BIPM2024)"

fix_ensure_ne_sw

Type: Optional[str] Default: None Meaning: Ensure NE_SW parameter exists. Example TOML:

fix_ensure_ne_sw = "7.9"

Example CLI:

pleb --config pipeline.toml --set fix_ensure_ne_sw="7.9"

fix_force_ne_sw_overwrite

Type: bool Default: False Meaning: Overwrite existing NE_SW values when true. Example TOML:

fix_force_ne_sw_overwrite = true

Example CLI:

pleb --config pipeline.toml --set fix_force_ne_sw_overwrite=true

fix_remove_patterns

Type: List[str] Default: ['NRT.NUPPI.', 'NRT.NUXPI.'] Meaning: Patterns to remove from .par/.tim. Example TOML:

fix_remove_patterns = ["NRT.NUPPI.","NRT.NUXPI."]

Example CLI:

pleb --config pipeline.toml --set fix_remove_patterns=["NRT.NUPPI.","NRT.NUXPI."]

fix_coord_convert

Type: Optional[str] Default: None Meaning: Optional coordinate conversion. Example TOML:

fix_coord_convert = "equatorial_to_ecliptic"

Example CLI:

pleb --config pipeline.toml --set fix_coord_convert="equatorial_to_ecliptic"

fix_prune_missing_includes

Type: bool Default: True Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_prune_missing_includes = false

Example CLI:

pleb --config pipeline.toml --set fix_prune_missing_includes=false

fix_drop_small_backend_includes

Type: bool Default: True Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_drop_small_backend_includes = false

Example CLI:

pleb --config pipeline.toml --set fix_drop_small_backend_includes=false

fix_system_flag_update_table

Type: bool Default: True Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_system_flag_update_table = false

Example CLI:

pleb --config pipeline.toml --set fix_system_flag_update_table=false

fix_default_backend

Type: Optional[str] Default: None Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_default_backend = "NUPPI"

Example CLI:

pleb --config pipeline.toml --set fix_default_backend="NUPPI"

fix_group_flag

Type: str Default: '-group' Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_group_flag = "-group"

Example CLI:

pleb --config pipeline.toml --set fix_group_flag="-group"

fix_pta_flag

Type: str Default: '-pta' Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_pta_flag = "-pta"

Example CLI:

pleb --config pipeline.toml --set fix_pta_flag="-pta"

fix_pta_value

Type: Optional[str] Default: None Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_pta_value = "EPTA"

Example CLI:

pleb --config pipeline.toml --set fix_pta_value="EPTA"

fix_standardize_par_values

Type: bool Default: True Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_standardize_par_values = false

Example CLI:

pleb --config pipeline.toml --set fix_standardize_par_values=false

fix_prune_small_system_toas

Type: bool Default: False Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_prune_small_system_toas = true

Example CLI:

pleb --config pipeline.toml --set fix_prune_small_system_toas=true

fix_prune_small_system_flag

Type: str Default: '-sys' Meaning: FixDataset cleanup/normalization setting. Example TOML:

fix_prune_small_system_flag = "-sys"

Example CLI:

pleb --config pipeline.toml --set fix_prune_small_system_flag="-sys"

fix_qc_remove_outliers

Type: bool Default: False Meaning: Comment/delete TOAs flagged by pqc outputs. Example TOML:

fix_qc_remove_outliers = true

Example CLI:

pleb --config pipeline.toml --set fix_qc_remove_outliers=true

fix_qc_outlier_cols

Type: Optional[List[str]] Default: None Meaning: FixDataset action policy for PQC-derived flags. Example TOML:

fix_qc_outlier_cols = ["bad_point","robust_outlier","robust_global_outlier","bad_mad"]

Example CLI:

pleb --config pipeline.toml --set fix_qc_outlier_cols=["bad_point","robust_outlier","robust_global_outlier","bad_mad"]

fix_qc_action

Type: str Default: 'comment' Meaning: Action for pqc outliers (comment/delete). Example TOML:

fix_qc_action = "comment"

Example CLI:

pleb --config pipeline.toml --set fix_qc_action="comment"

fix_qc_comment_prefix

Type: str Default: 'C QC_OUTLIER' Meaning: Prefix for commented TOA lines. Example TOML:

fix_qc_comment_prefix = "C QC_OUTLIER"

Example CLI:

pleb --config pipeline.toml --set fix_qc_comment_prefix="C QC_OUTLIER"

fix_qc_backend_col

Type: str Default: 'sys' Meaning: Backend column for pqc matching (if needed). Example TOML:

fix_qc_backend_col = "sys"

Example CLI:

pleb --config pipeline.toml --set fix_qc_backend_col="sys"

fix_qc_remove_bad

Type: bool Default: True Meaning: Act on bad/bad_day flags. Example TOML:

fix_qc_remove_bad = false

Example CLI:

pleb --config pipeline.toml --set fix_qc_remove_bad=false

fix_qc_remove_transients

Type: bool Default: False Meaning: Act on transient flags. Example TOML:

fix_qc_remove_transients = true

Example CLI:

pleb --config pipeline.toml --set fix_qc_remove_transients=true

fix_qc_remove_solar

Type: bool Default: False Meaning: Act on solar-elongation flags. Example TOML:

fix_qc_remove_solar = true

Example CLI:

pleb --config pipeline.toml --set fix_qc_remove_solar=true

fix_qc_solar_action

Type: str Default: 'comment' Meaning: Action for solar-flagged TOAs (comment/delete). Example TOML:

fix_qc_solar_action = "comment"

Example CLI:

pleb --config pipeline.toml --set fix_qc_solar_action="comment"

fix_qc_solar_comment_prefix

Type: str Default: '# QC_SOLAR' Meaning: Prefix for solar-flagged TOA comments. Example TOML:

fix_qc_solar_comment_prefix = "# QC_SOLAR"

Example CLI:

pleb --config pipeline.toml --set fix_qc_solar_comment_prefix="# QC_SOLAR"

fix_qc_remove_orbital_phase

Type: bool Default: False Meaning: Act on orbital-phase flags. Example TOML:

fix_qc_remove_orbital_phase = true

Example CLI:

pleb --config pipeline.toml --set fix_qc_remove_orbital_phase=true

fix_qc_orbital_phase_action

Type: str Default: 'comment' Meaning: Action for orbital-phase flagged TOAs (comment/delete). Example TOML:

fix_qc_orbital_phase_action = "comment"

Example CLI:

pleb --config pipeline.toml --set fix_qc_orbital_phase_action="comment"

fix_qc_orbital_phase_comment_prefix

Type: str Default: '# QC_BIANRY_ECLIPSE' Meaning: Prefix for orbital-phase TOA comments. Example TOML:

fix_qc_orbital_phase_comment_prefix = "# QC_BINARY_ECLIPSE"

Example CLI:

pleb --config pipeline.toml --set fix_qc_orbital_phase_comment_prefix="# QC_BINARY_ECLIPSE"

fix_qc_merge_tol_days

Type: float Default: 2.0 / 86400.0 Meaning: MJD tolerance when matching TOAs. Example TOML:

fix_qc_merge_tol_days = 1.0

Example CLI:

pleb --config pipeline.toml --set fix_qc_merge_tol_days=1.0

fix_qc_results_dir

Type: Optional[Path] Default: None Meaning: Directory containing pqc CSV outputs. If unset and Example TOML:

fix_qc_results_dir = "results/EPTA_combination_report_20260319T1200"

Example CLI:

pleb --config pipeline.toml --set fix_qc_results_dir="results/EPTA_combination_report_20260319T1200"

fix_qc_branch

Type: Optional[str] Default: None Meaning: Branch subdir for pqc CSV outputs. If unset and Example TOML:

fix_qc_branch = "main"

Example CLI:

pleb --config pipeline.toml --set fix_qc_branch="main"

Param-scan settings

param_scan_typical

Type: bool Default: False Meaning: Enable typical param-scan profile. Example TOML:

param_scan_typical = true

Example CLI:

pleb --config pipeline.toml --set param_scan_typical=true

param_scan_dm_redchisq_threshold

Type: float Default: 2.0 Meaning: Threshold for DM scan. Example TOML:

param_scan_dm_redchisq_threshold = 1.0

Example CLI:

pleb --config pipeline.toml --set param_scan_dm_redchisq_threshold=1.0

param_scan_dm_max_order

Type: int Default: 4 Meaning: Max DM derivative order. Example TOML:

param_scan_dm_max_order = 4

Example CLI:

pleb --config pipeline.toml --set param_scan_dm_max_order=4

param_scan_btx_max_fb

Type: int Default: 3 Meaning: Max FB derivative order. Example TOML:

param_scan_btx_max_fb = 4

Example CLI:

pleb --config pipeline.toml --set param_scan_btx_max_fb=4

Binary analysis settings

binary_only_models

Type: Optional[List[str]] Default: None Meaning: Limit binary analysis to model names. Example TOML:

binary_only_models = ["ELL1","BTX"]

Example CLI:

pleb --config pipeline.toml --set binary_only_models=["ELL1","BTX"]

Ingest settings

ingest_mapping_file

Type: Optional[Path] Default: None Meaning: JSON mapping file for ingest mode (optional). Example TOML:

ingest_mapping_file = "configs/catalogs/ingest/epta_data.json"

Example CLI:

pleb --config pipeline.toml --set ingest_mapping_file="configs/catalogs/ingest/epta_data.json"

ingest_output_dir

Type: Optional[Path] Default: None Meaning: Output root directory for ingest mode (optional). Example TOML:

ingest_output_dir = "/data/epta-dr3"

Example CLI:

pleb --config pipeline.toml --set ingest_output_dir="/data/epta-dr3"

ingest_commit_branch

Type: bool Default: True Meaning: Create a new branch and commit ingest outputs. Example TOML:

ingest_commit_branch = false

Example CLI:

pleb --config pipeline.toml --set ingest_commit_branch=false

ingest_commit_branch_name

Type: Optional[str] Default: None Meaning: Optional name for the ingest branch. Example TOML:

ingest_commit_branch_name = "raw_ingest"

Example CLI:

pleb --config pipeline.toml --set ingest_commit_branch_name="raw_ingest"

ingest_commit_base_branch

Type: Optional[str] Default: None Meaning: Base branch for the ingest commit. Example TOML:

ingest_commit_base_branch = "main"

Example CLI:

pleb --config pipeline.toml --set ingest_commit_base_branch="main"

ingest_commit_message

Type: Optional[str] Default: None Meaning: Commit message for ingest. Example TOML:

ingest_commit_message = "Ingest: collect tim files"

Example CLI:

pleb --config pipeline.toml --set ingest_commit_message="Ingest: collect tim files"

ingest_verify

Type: bool Default: False Meaning: Ingest setting. Example TOML:

ingest_verify = true

Example CLI:

pleb --config pipeline.toml --set ingest_verify=true

Rendering settings

dpi

Type: int Default: 120 Meaning: Plot resolution. Example TOML:

dpi = 150

Example CLI:

pleb --config pipeline.toml --set dpi=150

max_covmat_params

Type: Optional[int] Default: None Meaning: Max params in covariance heatmaps. Example TOML:

max_covmat_params = 80

Example CLI:

pleb --config pipeline.toml --set max_covmat_params=80