Add a standard --version option to common pycbc options (gwastro#4811)

* Start moving to a common --version argument

* Fix version importing

* Continue moving to a common --version argument

* Continue moving to a common --version argument

* Moving minifollowups to a common --version argument

* Moving plotting to a common --version argument

* Move workflows to use standard versioning

* Moving pygrb to a common --version argument

* Moving executables in /bin to a common --version argument

* allow ---version to provide a level of information set by the user

* Move help into the class definition

* minor wording clarification

* Fix# to the pygrb_initialize_plot_parser

* fix missed imports

* CC

* fix missed imports

* Fix some places where --version fails

* Allow pycbc_pygrb_exclusion_dist_table to use standard logging and version

* Add --version testing to the CI, add version modifer test

* Re-add failing codes

* Do the exclusion of certain codes properly

* Remove unused variable, move test_results into its own function in pycbc_test_suite.sh

* Remove some code information that is no longer needed

* Tabs-->spaces, allow log file not to be set in test_results

bin/all_sky_search/pycbc_add_statmap

@@ -26,8 +26,6 @@ def get_ifo_string(fi):
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-files', nargs='+',
     help="List of coinc files to be combined")
 parser.add_argument('--background-files', nargs='+', default=None,

bin/all_sky_search/pycbc_apply_rerank

@@ -10,8 +10,6 @@ from shutil import copyfile
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--stat-files', nargs='+',
     help="Statistic files produced by candidate followup codes")
 parser.add_argument('--followup-file',

bin/all_sky_search/pycbc_average_psd

@@ -26,13 +26,11 @@ import argparse
 import numpy as np
 import pycbc
 from pycbc.io import HFile
-from pycbc.version import git_verbose_msg as version
 from pycbc.types import MultiDetOptionAction, FrequencySeries
 
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument('--input-files', nargs='+', required=True, metavar='PATH',
                     help='HDF5 files from pycbc_calculate_psd (one per '
                          'detector) containing the input PSDs to average.')

bin/all_sky_search/pycbc_bin_templates

@@ -8,12 +8,10 @@ import numpy as np
 
 import pycbc
 import pycbc.pnutils
-from pycbc.version import git_verbose_msg as version
 from pycbc.events import background_bin_from_string
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument("--ifo", type=str, required=True)
 parser.add_argument("--f-lower", type=float, default=15.,
                     help='Enforce a uniform low frequency cutoff to '

bin/all_sky_search/pycbc_bin_trigger_rates_dq

@@ -16,11 +16,9 @@ from pycbc.events.veto import (select_segments_by_definer,
                                segments_to_start_end)
 from pycbc.types.optparse import MultiDetOptionAction
 from pycbc.io.hdf import SingleDetTriggers
-from pycbc.version import git_verbose_msg as version
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument("--template-bins-file", required=True)
 parser.add_argument("--trig-file", required=True)
 parser.add_argument("--flag-file", required=True)

bin/all_sky_search/pycbc_calculate_psd

@@ -5,15 +5,13 @@ import logging, argparse, numpy, multiprocessing, time, copy
 from six.moves import zip_longest
 import pycbc, pycbc.psd, pycbc.strain, pycbc.events
 from pycbc.io import HFile
-from pycbc.version import git_verbose_msg as version
 from pycbc.fft.fftw import set_measure_level
 from pycbc.workflow import resolve_td_option
 from ligo.segments import segmentlist, segment
 set_measure_level(0)
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument("--low-frequency-cutoff", type=float, required=True,
                     help="The low frequency cutoff to use for filtering (Hz)")
 parser.add_argument("--analysis-segment-file",  required=True,

bin/all_sky_search/pycbc_coinc_findtrigs

@@ -2,8 +2,8 @@
 import copy, argparse, logging, numpy, numpy.random
 import shutil, uuid, os.path, atexit
 from ligo.segments import infinity
+import pycbc
 from pycbc.events import veto, coinc, stat, ranking, cuts
-import pycbc.version
 from pycbc.io import HFile
 from pycbc import pool, init_logging
 from numpy.random import seed, shuffle
@@ -12,7 +12,6 @@ from pycbc.types.optparse import MultiDetOptionAction
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version", version=pycbc.version.git_verbose_msg)
 parser.add_argument("--veto-files", nargs='*', action='append', default=[],
                     help="Optional veto file. Triggers within veto segments "
                          "contained in the file are ignored")

bin/all_sky_search/pycbc_coinc_hdfinjfind

@@ -6,12 +6,12 @@ files.
 import argparse, logging, types, numpy, os.path
 from ligo.lw import lsctables, utils as ligolw_utils
 from ligo import segments
+import pycbc
 from pycbc import events, init_logging
 from pycbc.events import indices_within_segments
 from pycbc.types import MultiDetOptionAction
 from pycbc.inject import CBCHDFInjectionSet
 from pycbc.io import HFile
-import pycbc.version
 from pycbc.io.ligolw import LIGOLWContentHandler
 
 
@@ -57,8 +57,6 @@ def xml_to_hdf(table, hdf_file, hdf_key, columns):
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--trigger-files', nargs='+', required=True)
 parser.add_argument('--injection-files', nargs='+', required=True)
 parser.add_argument('--veto-file')

bin/all_sky_search/pycbc_coinc_mergetrigs

@@ -4,9 +4,8 @@
 """
 
 import numpy, argparse, h5py, logging
-import pycbc.version
 from pycbc.io import HFile
-from pycbc import init_logging
+from pycbc import add_common_pycbc_options, init_logging
 
 def changes(arr):
     l = numpy.where(arr[:-1] != arr[1:])[0]
@@ -31,9 +30,7 @@ def region(f, key, boundaries, ids):
                      dtype=h5py.special_dtype(ref=h5py.RegionReference))
 
 parser = argparse.ArgumentParser()
-pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
+add_common_pycbc_options(parser)
 parser.add_argument('--trigger-files', nargs='+')
 parser.add_argument('--output-file', required=True)
 parser.add_argument('--bank-file', required=True)

bin/all_sky_search/pycbc_coinc_statmap

@@ -10,7 +10,7 @@ the FANs of any other gravitational waves in the dataset.
 import argparse, itertools
 import lal, logging, numpy
 from pycbc.events import veto, coinc, significance
-import pycbc.version, pycbc.pnutils, pycbc.io
+import pycbc.pnutils, pycbc.io
 import sys
 import pycbc.conversions as conv
 
@@ -35,8 +35,6 @@ class fw(object):
 parser = argparse.ArgumentParser()
 # General required options
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--coinc-files', nargs='+',
                     help='List of coincidence files used to calculate the '
                          'FAP, FAR, etc.')

bin/all_sky_search/pycbc_coinc_statmap_inj

@@ -6,15 +6,12 @@ with producing the combined foreground and background triggers
 """
 import argparse, logging, itertools, copy, pycbc.io, numpy, lal
 from pycbc.events import veto, coinc, significance
-import pycbc.version
 import pycbc.conversions as conv
 from pycbc import init_logging
 
 parser = argparse.ArgumentParser()
 # General required options
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--cluster-window', type=float, default=10,
                     help='Length of time window in seconds to cluster coinc '
                          'events [default=10s]')

bin/all_sky_search/pycbc_combine_coincident_events

@@ -9,7 +9,6 @@ import logging
 
 import pycbc
 from pycbc.io import HFile
-import pycbc.version
 
 def com(f, files, group):
     """ Combine the same column from multiple files into another file f"""
@@ -56,7 +55,6 @@ def com_with_detector_key(f, files, group):
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version", version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-files', nargs='+',
                     help="List of coinc files to be redistributed")
 parser.add_argument('--output-file', help="name of output file")

bin/all_sky_search/pycbc_combine_statmap

@@ -5,12 +5,10 @@ significant foreground, but leaves the background triggers alone.
 """
 
 import numpy, argparse, logging, pycbc, pycbc.events, pycbc.io, lal
-import pycbc.version
 from ligo import segments
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version", version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-files', nargs='+',
                     help="List of coinc files to be redistributed")
 parser.add_argument('--cluster-window', type=float)

bin/all_sky_search/pycbc_cut_merge_triggers_to_tmpltbank

@@ -26,13 +26,10 @@ import argparse
 import numpy
 import h5py
 import pycbc
-import pycbc.version
 from pycbc.io import HFile
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument("--input-file", required=True,
                     help="Input merge triggers HDF file.")
 parser.add_argument("--output-file", required=True,

bin/all_sky_search/pycbc_distribute_background_bins

@@ -1,9 +1,7 @@
 #!/bin/env python
 import argparse, numpy, pycbc.events, logging, pycbc.events, pycbc.io
-import pycbc.version
 
 parser = argparse.ArgumentParser()
-parser.add_argument("--version", action=pycbc.version.Version)
 pycbc.add_common_pycbc_options(parser)
 parser.add_argument('--coinc-files', nargs='+',
                     help="List of coinc files to be redistributed")

bin/all_sky_search/pycbc_exclude_zerolag

@@ -5,14 +5,11 @@ coincidences from *any* coincidence type with ifar above a certain threshold
 """
 
 import numpy as np, argparse, logging, pycbc, pycbc.io
-import pycbc.version
 from pycbc.events import veto, coinc, significance
 import pycbc.conversions as conv
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-file', type=str,
     help="Coinc statmap file to be recalculated based on foreground removal")
 parser.add_argument('--other-statmap-files', nargs='+',

bin/all_sky_search/pycbc_fit_sngls_binned

@@ -22,20 +22,19 @@ from matplotlib import pyplot as plt
 
 import copy, numpy as np
 
+import pycbc
 from pycbc import events, bin_utils, results
 from pycbc.events import triggers
 from pycbc.events import trigger_fits as trstats
 from pycbc.events import stat as pystat
 from pycbc.io import HFile
-import pycbc.version
 
 #### MAIN ####
 
 parser = argparse.ArgumentParser(usage="",
     description="Perform maximum-likelihood fits of single inspiral trigger"
                 " distributions to various functions")
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action=pycbc.version.Version)
 parser.add_argument("--trigger-file",
                     help="Input hdf5 file containing single triggers. "
                     "Required")

bin/all_sky_search/pycbc_fit_sngls_by_template

@@ -18,11 +18,11 @@ import argparse, logging
 
 import copy, numpy as np
 
+import pycbc
 from pycbc import events, init_logging
 from pycbc.events import triggers, trigger_fits as trstats
 from pycbc.events import stat as statsmod
 from pycbc.types.optparse import MultiDetOptionAction
-import pycbc.version
 from pycbc.io import HFile
 
 #### DEFINITIONS AND FUNCTIONS ####
@@ -61,7 +61,6 @@ parser = argparse.ArgumentParser(usage="",
     description="Perform maximum-likelihood fits of single inspiral trigger"
                 " distributions to various functions")
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action=pycbc.version.Version)
 parser.add_argument("--trigger-file",
                     help="Input hdf5 file containing single triggers. "
                     "Required")

bin/all_sky_search/pycbc_fit_sngls_over_multiparam

@@ -13,8 +13,10 @@
 # Public License for more details.
 
 
-import sys, argparse, logging, pycbc.version, numpy
+import sys, argparse, logging, numpy
 from scipy.stats import norm
+
+import pycbc
 from pycbc.events import triggers
 from pycbc.io import HFile
 from pycbc import init_logging
@@ -177,7 +179,6 @@ parser = argparse.ArgumentParser(usage="",
                 "background model.")
 
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action=pycbc.version.Version)
 parser.add_argument("--template-fit-file", required=True, nargs='+',
                     help="hdf5 file(s) containing fit coefficients for each "
                          "individual template. Can smooth over multiple "

bin/all_sky_search/pycbc_fit_sngls_over_param

@@ -18,10 +18,10 @@ import argparse, logging
 
 import numpy as np
 
+import pycbc
 from pycbc import init_logging
 from pycbc.io import HFile
 from pycbc.events import triggers
-import pycbc.version
 
 parser = argparse.ArgumentParser(usage="",
     description="Smooth (regress) the dependence of coefficients describing "
@@ -30,7 +30,6 @@ parser = argparse.ArgumentParser(usage="",
                 "background model.")
 
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action=pycbc.version.Version)
 parser.add_argument("--template-fit-file",
                     help="Input hdf5 file containing fit coefficients for each"
                          " individual template. Required")

bin/all_sky_search/pycbc_followup_file

@@ -7,8 +7,6 @@ from pycbc.io import HFile
 
 parser = argparse.ArgumentParser()
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version',
-    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--statmap-file',
     help="Statmap file containing the candidates/background to follow up")
 parser.add_argument('--bank-file',

bin/all_sky_search/pycbc_foreground_censor

@@ -1,15 +1,14 @@
 #!/usr/bin/env python
 """Make segment file to blind the results from foreground related triggers """
 
-import os, argparse, logging, pycbc.version
+import os, argparse, logging
 from urllib.parse import urlunparse
 import pycbc.events
 from pycbc.workflow import SegFile
 from pycbc.io import HFile
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=pycbc.version.git_verbose_msg)
 parser.add_argument('--foreground-triggers',
                     help="HDF file containing the zerolag foreground triggers "
                          "from the analysis")

bin/all_sky_search/pycbc_make_bayestar_skymap

@@ -26,16 +26,14 @@ import tempfile
 
 from ligo.lw import lsctables, utils as ligolw_utils
 
-import pycbc.version
+import pycbc
 from pycbc import init_logging
 from pycbc.waveform import bank as wavebank
 from pycbc.io import WaveformArray
 from pycbc.io.ligolw import LIGOLWContentHandler
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument('--bayestar-executable',
                     help="The bayestar-localize-coinc executable to be run. "
                          "If not given, will use whatever is available in "

bin/all_sky_search/pycbc_merge_psds

@@ -18,12 +18,10 @@
 """ Merge hdf psd files
 """
 import logging, argparse, numpy, pycbc.types
-from pycbc.version import git_verbose_msg as version
 from pycbc.io import HFile
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument('--version', action='version', version=version)
 parser.add_argument('--psd-files', nargs='+')
 parser.add_argument("--output-file", required=True)
 

bin/all_sky_search/pycbc_reduce_template_bank

@@ -26,13 +26,10 @@ import logging
 import imp
 import argparse
 import pycbc
-import pycbc.version
 from pycbc.io import HFile
 
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
-parser.add_argument("--version", action="version",
-                    version=pycbc.version.git_verbose_msg)
 parser.add_argument("--input-bank", required=True,
                     help="Input template bank HDF file.")
 parser.add_argument("--output-bank", required=True,