Index

A

alltim_variants_path (pleb.FixDatasetConfig attribute), [1]

apply (pleb.FixDatasetConfig attribute), [1]

B

backend (pleb.QCReportConfig attribute) backend_classifications_path (pleb.FixDatasetConfig attribute), [1] backend_col (pleb.QCReportConfig attribute) backend_overrides (pleb.FixDatasetConfig attribute), [1]

backup (pleb.FixDatasetConfig attribute), [1] binary_only_models (pleb.PipelineConfig attribute), [1] BinaryAnalysisConfig (class in pleb) branches (pleb.PipelineConfig attribute), [1]

C

check_duplicate_backend_tims (pleb.FixDatasetConfig attribute), [1] cleanup_output_tree (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute) cleanup_work_dir (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute)

compact_pdf (pleb.QCReportConfig attribute) compact_pdf_name (pleb.QCReportConfig attribute) coord_convert (pleb.FixDatasetConfig attribute), [1]

D

dataset_name (pleb.IngestConfig attribute) (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] dedupe_freq_tol_auto (pleb.FixDatasetConfig attribute)

dedupe_freq_tol_mhz (pleb.FixDatasetConfig attribute) dedupe_mjd_tol_sec (pleb.FixDatasetConfig attribute) dedupe_toas_within_tim (pleb.FixDatasetConfig attribute), [1] dpi (pleb.PipelineConfig attribute), [1] dry_run (pleb.FixDatasetConfig attribute), [1]

E

ensure_clk (pleb.FixDatasetConfig attribute), [1] ensure_ephem (pleb.FixDatasetConfig attribute), [1]

ensure_ne_sw (pleb.FixDatasetConfig attribute), [1] epoch (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1]

F

fix_alltim_variants_path (pleb.PipelineConfig attribute) fix_apply (pleb.PipelineConfig attribute), [1] fix_backend_classifications_path (pleb.PipelineConfig attribute) fix_backend_overrides (pleb.PipelineConfig attribute) fix_backup (pleb.PipelineConfig attribute), [1] fix_base_branch (pleb.PipelineConfig attribute), [1] fix_branch_name (pleb.PipelineConfig attribute), [1] fix_check_duplicate_backend_tims (pleb.PipelineConfig attribute) fix_commit_message (pleb.PipelineConfig attribute), [1] fix_coord_convert (pleb.PipelineConfig attribute), [1] fix_dedupe_freq_tol_auto (pleb.PipelineConfig attribute) fix_dedupe_freq_tol_mhz (pleb.PipelineConfig attribute) fix_dedupe_mjd_tol_sec (pleb.PipelineConfig attribute) fix_dedupe_toas_within_tim (pleb.PipelineConfig attribute) fix_default_backend (pleb.PipelineConfig attribute) fix_drop_small_backend_includes (pleb.PipelineConfig attribute) fix_dry_run (pleb.PipelineConfig attribute), [1] fix_ensure_clk (pleb.PipelineConfig attribute), [1] fix_ensure_ephem (pleb.PipelineConfig attribute), [1] fix_ensure_ne_sw (pleb.PipelineConfig attribute), [1] fix_flag_sys_freq_rules_enabled (pleb.PipelineConfig attribute) fix_flag_sys_freq_rules_path (pleb.PipelineConfig attribute) fix_force_ne_sw_overwrite (pleb.PipelineConfig attribute), [1] fix_generate_alltim_variants (pleb.PipelineConfig attribute) fix_group_flag (pleb.PipelineConfig attribute) fix_infer_system_flags (pleb.PipelineConfig attribute) fix_insert_missing_jumps (pleb.PipelineConfig attribute), [1] fix_jump_flag (pleb.PipelineConfig attribute), [1] fix_jump_reference_csv_dir (pleb.PipelineConfig attribute), [1] fix_jump_reference_jump_flag (pleb.PipelineConfig attribute), [1] fix_jump_reference_keep_tmp (pleb.PipelineConfig attribute), [1] fix_jump_reference_variants (pleb.PipelineConfig attribute), [1] fix_min_toas_per_backend_tim (pleb.PipelineConfig attribute), [1] fix_overlap_exact_catalog_path (pleb.PipelineConfig attribute), [1] fix_overlap_rules_path (pleb.PipelineConfig attribute), [1] fix_prune_missing_includes (pleb.PipelineConfig attribute) fix_prune_small_system_flag (pleb.PipelineConfig attribute) fix_prune_small_system_toas (pleb.PipelineConfig attribute) fix_prune_stale_jumps (pleb.PipelineConfig attribute), [1] fix_pta_flag (pleb.PipelineConfig attribute) fix_pta_value (pleb.PipelineConfig attribute) fix_pulsar_dataset() (in module pleb)

fix_qc_action (pleb.PipelineConfig attribute), [1] fix_qc_backend_col (pleb.PipelineConfig attribute), [1] fix_qc_branch (pleb.PipelineConfig attribute), [1] fix_qc_comment_prefix (pleb.PipelineConfig attribute), [1] fix_qc_merge_tol_days (pleb.PipelineConfig attribute), [1] fix_qc_orbital_phase_action (pleb.PipelineConfig attribute), [1] fix_qc_orbital_phase_comment_prefix (pleb.PipelineConfig attribute), [1] fix_qc_outlier_cols (pleb.PipelineConfig attribute) fix_qc_remove_bad (pleb.PipelineConfig attribute), [1] fix_qc_remove_orbital_phase (pleb.PipelineConfig attribute), [1] fix_qc_remove_outliers (pleb.PipelineConfig attribute), [1] fix_qc_remove_solar (pleb.PipelineConfig attribute), [1] fix_qc_remove_transients (pleb.PipelineConfig attribute), [1] fix_qc_results_dir (pleb.PipelineConfig attribute), [1] fix_qc_solar_action (pleb.PipelineConfig attribute), [1] fix_qc_solar_comment_prefix (pleb.PipelineConfig attribute), [1] fix_raise_on_backend_missing (pleb.PipelineConfig attribute) fix_relabel_rules_path (pleb.PipelineConfig attribute), [1] fix_remove_overlaps_exact (pleb.PipelineConfig attribute) fix_remove_patterns (pleb.PipelineConfig attribute), [1] fix_required_tim_flags (pleb.PipelineConfig attribute), [1] fix_standardize_par_values (pleb.PipelineConfig attribute) fix_system_flag_mapping_path (pleb.PipelineConfig attribute), [1], [2] fix_system_flag_overwrite_existing (pleb.PipelineConfig attribute) fix_system_flag_table_path (pleb.PipelineConfig attribute) fix_system_flag_update_table (pleb.PipelineConfig attribute) fix_update_alltim_includes (pleb.PipelineConfig attribute), [1] fix_wsrt_p2_action (pleb.PipelineConfig attribute) fix_wsrt_p2_comment_prefix (pleb.PipelineConfig attribute) fix_wsrt_p2_force_sys_by_freq (pleb.PipelineConfig attribute) fix_wsrt_p2_mjd_tol_sec (pleb.PipelineConfig attribute) fix_wsrt_p2_prefer_dual_channel (pleb.PipelineConfig attribute) FixDatasetConfig (class in pleb) flag_sys_freq_rules_enabled (pleb.FixDatasetConfig attribute), [1] flag_sys_freq_rules_path (pleb.FixDatasetConfig attribute), [1] force_ne_sw_overwrite (pleb.FixDatasetConfig attribute), [1] force_rerun (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] from_dict() (pleb.IngestConfig static method) (pleb.ParamScanConfig static method) (pleb.PipelineConfig static method) (pleb.QCReportConfig static method) (pleb.WorkflowRunConfig static method)

G

generate_alltim_variants (pleb.FixDatasetConfig attribute), [1]

H

home_dir (pleb.IngestConfig attribute) (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1]

I

infer_system_flags (pleb.FixDatasetConfig attribute), [1] ingest_commit_base_branch (pleb.IngestConfig attribute) (pleb.PipelineConfig attribute), [1] ingest_commit_branch (pleb.PipelineConfig attribute), [1] ingest_commit_branch_name (pleb.IngestConfig attribute) (pleb.PipelineConfig attribute), [1] ingest_commit_message (pleb.IngestConfig attribute) (pleb.PipelineConfig attribute), [1]

ingest_mapping_file (pleb.IngestConfig attribute) (pleb.PipelineConfig attribute), [1] ingest_output_dir (pleb.IngestConfig attribute) (pleb.PipelineConfig attribute), [1] ingest_verify (pleb.IngestConfig attribute) (pleb.PipelineConfig attribute) IngestConfig (class in pleb) insert_missing_jumps (pleb.FixDatasetConfig attribute), [1]

J

jobs (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] jump_flag (pleb.FixDatasetConfig attribute), [1]

jump_reference_csv_dir (pleb.FixDatasetConfig attribute) jump_reference_jump_flag (pleb.FixDatasetConfig attribute) jump_reference_keep_tmp (pleb.FixDatasetConfig attribute) jump_reference_variants (pleb.FixDatasetConfig attribute), [1]

L

load() (pleb.IngestConfig static method) (pleb.ParamScanConfig static method) (pleb.PipelineConfig static method) (pleb.QCReportConfig static method) (pleb.WorkflowRunConfig static method)

M

make_binary_analysis (pleb.PipelineConfig attribute), [1] make_change_reports (pleb.PipelineConfig attribute), [1] make_covariance_heatmaps (pleb.PipelineConfig attribute), [1] make_covmat (pleb.PipelineConfig attribute), [1] make_outlier_reports (pleb.PipelineConfig attribute), [1] make_plots (pleb.PipelineConfig attribute), [1]

make_reports (pleb.PipelineConfig attribute), [1] make_residual_plots (pleb.PipelineConfig attribute), [1] make_toa_coverage_plots (pleb.PipelineConfig attribute), [1] max_covmat_params (pleb.PipelineConfig attribute), [1] min_toas_per_backend_tim (pleb.FixDatasetConfig attribute), [1] module pleb

N

no_feature_plots (pleb.QCReportConfig attribute)

no_plots (pleb.QCReportConfig attribute)

O

only_models (pleb.BinaryAnalysisConfig attribute) outdir_name (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1]

overlap_exact_catalog_path (pleb.FixDatasetConfig attribute), [1] overlap_rules_path (pleb.FixDatasetConfig attribute), [1]

P

param_scan_btx_max_fb (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] param_scan_dm_max_order (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] param_scan_dm_redchisq_threshold (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] param_scan_typical (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] ParamScanConfig (class in pleb) PipelineConfig (class in pleb) pleb module pqc_add_airmass (pleb.PipelineConfig attribute), [1] pqc_add_elevation (pleb.PipelineConfig attribute), [1] pqc_add_freq_bin (pleb.PipelineConfig attribute), [1] pqc_add_orbital_phase (pleb.PipelineConfig attribute), [1] pqc_add_parallactic_angle (pleb.PipelineConfig attribute), [1] pqc_add_solar_elongation (pleb.PipelineConfig attribute), [1] pqc_backend_col (pleb.PipelineConfig attribute), [1] pqc_backend_profiles_path (pleb.PipelineConfig attribute), [1] pqc_delta_chi2_thresh (pleb.PipelineConfig attribute), [1] pqc_dm_step_delta_chi2_thresh (pleb.PipelineConfig attribute) pqc_dm_step_enabled (pleb.PipelineConfig attribute) pqc_dm_step_min_points (pleb.PipelineConfig attribute) pqc_dm_step_scope (pleb.PipelineConfig attribute) pqc_drop_unmatched (pleb.PipelineConfig attribute), [1] pqc_eclipse_center_phase (pleb.PipelineConfig attribute), [1] pqc_eclipse_events_enabled (pleb.PipelineConfig attribute), [1] pqc_eclipse_freq_alpha_max (pleb.PipelineConfig attribute), [1] pqc_eclipse_freq_alpha_max_iter (pleb.PipelineConfig attribute), [1] pqc_eclipse_freq_alpha_min (pleb.PipelineConfig attribute), [1] pqc_eclipse_freq_alpha_tol (pleb.PipelineConfig attribute), [1] pqc_eclipse_freq_dependence (pleb.PipelineConfig attribute), [1] pqc_eclipse_member_eta (pleb.PipelineConfig attribute), [1] pqc_eclipse_min_points (pleb.PipelineConfig attribute), [1] pqc_eclipse_width_max (pleb.PipelineConfig attribute), [1] pqc_eclipse_width_min (pleb.PipelineConfig attribute), [1] pqc_event_instrument (pleb.PipelineConfig attribute), [1] pqc_exp_dip_min_duration_days (pleb.PipelineConfig attribute), [1] pqc_fdr_q (pleb.PipelineConfig attribute), [1] pqc_freq_bins (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_delta_chi2_thresh (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_enabled (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_freq_alpha_max (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_freq_alpha_max_iter (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_freq_alpha_min (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_freq_alpha_tol (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_freq_dependence (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_max_duration_days (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_member_eta (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_min_duration_days (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_min_points (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_n_durations (pleb.PipelineConfig attribute), [1] pqc_gaussian_bump_suppress_overlap (pleb.PipelineConfig attribute), [1] pqc_glitch_delta_chi2_thresh (pleb.PipelineConfig attribute), [1]

pqc_glitch_enabled (pleb.PipelineConfig attribute), [1] pqc_glitch_mean_window_days (pleb.PipelineConfig attribute), [1] pqc_glitch_member_eta (pleb.PipelineConfig attribute), [1] pqc_glitch_min_duration_days (pleb.PipelineConfig attribute), [1] pqc_glitch_min_points (pleb.PipelineConfig attribute), [1] pqc_glitch_noise_k (pleb.PipelineConfig attribute), [1] pqc_glitch_peak_tau_days (pleb.PipelineConfig attribute), [1] pqc_glitch_suppress_overlap (pleb.PipelineConfig attribute), [1] pqc_mark_only_worst_per_day (pleb.PipelineConfig attribute), [1] pqc_merge_tol_seconds (pleb.PipelineConfig attribute), [1] pqc_min_points (pleb.PipelineConfig attribute), [1] pqc_observatory_path (pleb.PipelineConfig attribute), [1] pqc_orbital_phase_cut (pleb.PipelineConfig attribute), [1] pqc_orbital_phase_cut_center (pleb.PipelineConfig attribute), [1] pqc_orbital_phase_cut_enabled (pleb.PipelineConfig attribute), [1] pqc_orbital_phase_cut_min_points (pleb.PipelineConfig attribute), [1] pqc_orbital_phase_cut_nbins (pleb.PipelineConfig attribute), [1] pqc_orbital_phase_cut_sigma (pleb.PipelineConfig attribute), [1] pqc_outlier_gate_enabled (pleb.PipelineConfig attribute), [1] pqc_outlier_gate_resid_col (pleb.PipelineConfig attribute), [1] pqc_outlier_gate_sigma (pleb.PipelineConfig attribute), [1] pqc_outlier_gate_sigma_col (pleb.PipelineConfig attribute), [1] pqc_robust_enabled (pleb.PipelineConfig attribute) pqc_robust_scope (pleb.PipelineConfig attribute) pqc_robust_z_thresh (pleb.PipelineConfig attribute) pqc_solar_approach_max_deg (pleb.PipelineConfig attribute), [1] pqc_solar_events_enabled (pleb.PipelineConfig attribute), [1] pqc_solar_freq_alpha_max (pleb.PipelineConfig attribute), [1] pqc_solar_freq_alpha_max_iter (pleb.PipelineConfig attribute), [1] pqc_solar_freq_alpha_min (pleb.PipelineConfig attribute), [1] pqc_solar_freq_alpha_tol (pleb.PipelineConfig attribute), [1] pqc_solar_freq_dependence (pleb.PipelineConfig attribute), [1] pqc_solar_member_eta (pleb.PipelineConfig attribute), [1] pqc_solar_min_points_global (pleb.PipelineConfig attribute), [1] pqc_solar_min_points_near_zero (pleb.PipelineConfig attribute), [1] pqc_solar_min_points_year (pleb.PipelineConfig attribute), [1] pqc_solar_tau_max_deg (pleb.PipelineConfig attribute), [1] pqc_solar_tau_min_deg (pleb.PipelineConfig attribute), [1] pqc_step_delta_chi2_thresh (pleb.PipelineConfig attribute) pqc_step_enabled (pleb.PipelineConfig attribute) pqc_step_min_points (pleb.PipelineConfig attribute) pqc_step_scope (pleb.PipelineConfig attribute) pqc_structure_circular_features (pleb.PipelineConfig attribute), [1] pqc_structure_detrend_features (pleb.PipelineConfig attribute), [1] pqc_structure_group_cols (pleb.PipelineConfig attribute), [1] pqc_structure_min_per_bin (pleb.PipelineConfig attribute), [1] pqc_structure_mode (pleb.PipelineConfig attribute), [1] pqc_structure_nbins (pleb.PipelineConfig attribute), [1] pqc_structure_p_thresh (pleb.PipelineConfig attribute), [1] pqc_structure_test_features (pleb.PipelineConfig attribute), [1] pqc_tau_corr_minutes (pleb.PipelineConfig attribute), [1] pqc_tau_rec_days (pleb.PipelineConfig attribute), [1] pqc_window_mult (pleb.PipelineConfig attribute), [1] prune_stale_jumps (pleb.FixDatasetConfig attribute), [1] pulsars (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1]

Q

qc_action (pleb.FixDatasetConfig attribute), [1] qc_backend_col (pleb.FixDatasetConfig attribute), [1] qc_branch (pleb.FixDatasetConfig attribute), [1] qc_comment_prefix (pleb.FixDatasetConfig attribute), [1] qc_cross_pulsar_dir (pleb.PipelineConfig attribute) qc_cross_pulsar_enabled (pleb.PipelineConfig attribute) qc_cross_pulsar_event_cols (pleb.PipelineConfig attribute) qc_cross_pulsar_include_events (pleb.PipelineConfig attribute) qc_cross_pulsar_include_outliers (pleb.PipelineConfig attribute) qc_cross_pulsar_min_pulsars (pleb.PipelineConfig attribute) qc_cross_pulsar_outlier_cols (pleb.PipelineConfig attribute) qc_cross_pulsar_time_col (pleb.PipelineConfig attribute) qc_cross_pulsar_window_days (pleb.PipelineConfig attribute) qc_merge_tol_days (pleb.FixDatasetConfig attribute), [1] qc_orbital_phase_action (pleb.FixDatasetConfig attribute), [1] qc_orbital_phase_comment_prefix (pleb.FixDatasetConfig attribute), [1] qc_outlier_cols (pleb.FixDatasetConfig attribute) qc_remove_bad (pleb.FixDatasetConfig attribute), [1]

qc_remove_orbital_phase (pleb.FixDatasetConfig attribute), [1] qc_remove_outliers (pleb.FixDatasetConfig attribute), [1] qc_remove_solar (pleb.FixDatasetConfig attribute), [1] qc_remove_transients (pleb.FixDatasetConfig attribute), [1] qc_report (pleb.PipelineConfig attribute), [1] qc_report_backend (pleb.PipelineConfig attribute), [1] qc_report_backend_col (pleb.PipelineConfig attribute), [1] qc_report_compact_outlier_cols (pleb.PipelineConfig attribute) qc_report_compact_pdf (pleb.PipelineConfig attribute), [1] qc_report_compact_pdf_name (pleb.PipelineConfig attribute), [1] qc_report_dir (pleb.PipelineConfig attribute), [1] qc_report_no_feature_plots (pleb.PipelineConfig attribute), [1] qc_report_no_plots (pleb.PipelineConfig attribute), [1] qc_report_structure_group_cols (pleb.PipelineConfig attribute), [1] qc_results_dir (pleb.FixDatasetConfig attribute), [1] qc_solar_action (pleb.FixDatasetConfig attribute), [1] qc_solar_comment_prefix (pleb.FixDatasetConfig attribute), [1] QCReportConfig (class in pleb)

R

raise_on_backend_missing (pleb.FixDatasetConfig attribute), [1] reference_branch (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] relabel_rules_path (pleb.FixDatasetConfig attribute), [1] remove_overlaps_exact (pleb.FixDatasetConfig attribute), [1] remove_patterns (pleb.FixDatasetConfig attribute), [1] report_dir (pleb.QCReportConfig attribute) required_tim_flags (pleb.FixDatasetConfig attribute), [1] resolved() (pleb.PipelineConfig method)

resolved_output_root() (pleb.IngestConfig method) results_dir (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1] run_dir (pleb.QCReportConfig attribute) run_fix_dataset (pleb.PipelineConfig attribute), [1] run_param_scan() (in module pleb) run_pipeline() (in module pleb) run_pqc (pleb.PipelineConfig attribute), [1] run_tempo2 (pleb.PipelineConfig attribute), [1]

S

save_json() (pleb.PipelineConfig method) singularity_image (pleb.ParamScanConfig attribute) (pleb.PipelineConfig attribute), [1]

structure_group_cols (pleb.QCReportConfig attribute) system_flag_mapping_path (pleb.FixDatasetConfig attribute), [1] system_flag_overwrite_existing (pleb.FixDatasetConfig attribute), [1] system_flag_table_path (pleb.FixDatasetConfig attribute), [1]

T

tempo2_dataset_name (pleb.FixDatasetConfig attribute) tempo2_home_dir (pleb.FixDatasetConfig attribute) tempo2_singularity_image (pleb.FixDatasetConfig attribute) testing_mode (pleb.PipelineConfig attribute), [1]

to_dict() (pleb.IngestConfig method) (pleb.ParamScanConfig method) (pleb.PipelineConfig method) to_pipeline_config() (pleb.ParamScanConfig method)

U

update_alltim_includes (pleb.FixDatasetConfig attribute), [1]

W

workflow_file (pleb.WorkflowRunConfig attribute) WorkflowRunConfig (class in pleb) write_binary_analysis() (in module pleb) write_fix_report() (in module pleb)

wsrt_p2_action (pleb.FixDatasetConfig attribute) wsrt_p2_comment_prefix (pleb.FixDatasetConfig attribute) wsrt_p2_force_sys_by_freq (pleb.FixDatasetConfig attribute) wsrt_p2_mjd_tol_sec (pleb.FixDatasetConfig attribute) wsrt_p2_prefer_dual_channel (pleb.FixDatasetConfig attribute)