Standardize logging - final places (gwastro#4665)

* start standardizing logging in bin/plotting

* add a default_level option to init_logging

* more work

* named loggers in modules

* CC

* missed comma, typo, etc.

* thinko

* minor typo/thinko

* missed import

* final few places

* copy/paste error

* thinko

* missed again

* I made that mistake a lot

* import order

* Add a file to tell pylint that 'logger' is an allowed variable namex

* comment pylint file, allow 1/2 character variable names

* be more explicit re the single-character variables

* opts != args

* thinko

* pycbc not imported implicitly

* removed line which should have been kept

* remove double import

* grammar

* AT comments

* grammar

* missed some stuff during rebasing

* No idea how that line got deleted

* default level in pycbc_page_snrchi

* default level in bin/plotting/pycbc_page_vetotable

* improve import readability

* default level in  bin/plotting/pycbc_plot_qscan

* remove unused import in bin/pygrb/pycbc_pygrb_minifollowups

* unused import in bin/pygrb/pycbc_pygrb_page_tables

* formatting error in pycbc/transforms.py

* use logger in pycbc/scheme

.pylintrc

@@ -0,0 +1,3 @@
+[BASIC]
+# Allow certain names for variables
+good-names=logger,Run,i,j,k,v,_

bin/all_sky_search/pycbc_bin_templates

@@ -12,8 +12,8 @@ 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('--verbose', action="count")
 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_fit_sngls_binned

@@ -126,11 +126,7 @@ if args.output_file is not None and len(args.stat_threshold) > 1:
     raise RuntimeError("Cannot plot more than one threshold in a single "
                        "output file!")
 
-if args.verbose:
-    log_level = logging.DEBUG
-else:
-    log_level = logging.WARN
-logging.basicConfig(format='%(asctime)s : %(message)s', level=log_level)
+pycbc.init_logging(args.verbose)
 
 statname = "reweighted SNR" if args.sngl_ranking == "new_snr" else \
            args.sngl_ranking.replace("_", " ").replace("snr", "SNR")

bin/all_sky_search/pycbc_get_loudest_params

@@ -13,8 +13,6 @@ from pycbc import init_logging
 import pycbc.events
 from pycbc.pnutils import mass1_mass2_to_mchirp_eta
 
-logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
-
 parser = argparse.ArgumentParser(description=__doc__)
 pycbc.add_common_pycbc_options(parser)
 parser.add_argument('--single-ifo-trigs', type=str, required=True,

bin/all_sky_search/pycbc_make_bayestar_skymap

@@ -33,10 +33,9 @@ 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('--verbose', action='count',
-                    help="Make the logging increasingly more verbose")
 parser.add_argument('--bayestar-executable',
                     help="The bayestar-localize-coinc executable to be run. "
                          "If not given, will use whatever is available in "
@@ -52,9 +51,9 @@ parser.add_argument('--output-file', required=True,
 wavebank.add_approximant_arg(parser)
 args, unknown = parser.parse_known_args()
 
-# Default logging is set higher than normal for this job
-logging_level = args.verbose + 1 if args.verbose else None
-init_logging(logging_level)
+# Default logging level is info: --verbose adds to this
+pycbc.init_logging(args.verbose, default_level=1)
+
 logging.info("Starting")
 
 bayestar_exe = args.bayestar_executable or 'bayestar-localize-coincs'

bin/all_sky_search/pycbc_prepare_xml_for_gracedb

@@ -28,12 +28,13 @@ import h5py
 import matplotlib
 matplotlib.use('agg')
 
-import pycbc
 import lal
 import lal.series
 from ligo.lw import lsctables
 from ligo.lw import utils as ligolw_utils
 from ligo.segments import segment, segmentlist
+
+import pycbc
 from pycbc.io.ligolw import (
     LIGOLWContentHandler,
     snr_series_to_xml,
@@ -44,8 +45,7 @@ from pycbc.types import MultiDetOptionAction
 from pycbc.results import generate_asd_plot, generate_snr_plot
 
 parser = argparse.ArgumentParser(description=__doc__)
-parser.add_argument("--verbose", action='count',
-                    help="Increase logging level, default=info")
+pycbc.add_common_pycbc_options(parser)
 parser.add_argument("--psd-files", nargs='+', required=True,
                     help='HDF file(s) containing the PSDs to upload')
 parser.add_argument("--snr-timeseries", nargs='+', required=True,
@@ -72,11 +72,8 @@ parser.add_argument('--delta-f', type=float, default=0.25,
 
 args = parser.parse_args()
 
-if args.verbose:
-    args.verbose += 1
-else:
-    args.verbose = 1
-pycbc.init_logging(args.verbose)
+# Default logging level is info: --verbose adds to this
+pycbc.init_logging(args.verbose, default_level=1)
 
 xmldoc = ligolw_utils.load_filename(args.input_file,
                              contenthandler=LIGOLWContentHandler)

bin/all_sky_search/pycbc_upload_single_event_to_gracedb

@@ -32,6 +32,7 @@ import lal
 from pycbc.io.gracedb import gracedb_tag_with_version
 
 parser = argparse.ArgumentParser(description=__doc__)
+pycbc.add_common_pycbc_options(parser)
 parser.add_argument('--xml-file-for-upload', required=True, type=str,
                     help='LIGOLW XML file containing the event.')
 parser.add_argument('--log-message', type=str, metavar='MESSAGE',
@@ -62,7 +63,8 @@ parser.add_argument('--labels', nargs='+',
 
 args = parser.parse_args()
 
-pycbc.init_logging(logging.INFO)
+# Default logging level is info: --verbose adds to this
+pycbc.init_logging(args.verbose, default_level=1)
 # Make the scitokens logger a little quieter
 # (it is called through GraceDB)
 logging.getLogger('scitokens').setLevel(logging.root.level + 10)

bin/hwinj/pycbc_generate_hwinj_from_xml

@@ -60,9 +60,8 @@ parser.add_argument('--ifos', nargs='+', default=['H1', 'L1'], required=True,
 # parse command line
 opts = parser.parse_args()
 
-# setup logging - default level is DEBUG (2)
-logging_level = 2 if opts.verbose is None else opts.verbose + 2
-init_logging(logging_level)
+# Default logging level is debug: --verbose adds to this
+init_logging(args.verbose, default_level=2)
 
 # read in injection LIGOLW XML file
 logging.info('Reading injection file')

bin/hwinj/pycbc_insert_frame_hwinj

@@ -57,9 +57,8 @@ _strain.insert_strain_option_group(parser)
 # parse command line
 opts = parser.parse_args()
 
-# setup log: default is DEBUG (2)
-logging_level = 2 if opts.verbose is None else opts.verbose + 2
-init_logging(logging_level)
+# Default logging level is debug: --verbose adds to this
+init_logging(opts.verbose, default_level=2)
 
 # get strain
 strain = _strain.from_cli(opts, precision=opts.precision)

bin/inference/pycbc_inference_create_fits

@@ -35,9 +35,11 @@ import numpy
 import argparse
 import subprocess
 
+from pycbc import add_common_pycbc_options, init_logging
 from pycbc.inference import io
 
 parser = argparse.ArgumentParser(description=__doc__)
+add_common_pycbc_options(parser)
 parser.add_argument('--input-file', required=True,
                     help='The inference or posterior hdf file to load.')
 parser.add_argument('--output-file', required=True,
@@ -68,6 +70,8 @@ parser.add_argument('--tc', default='tc',
                          '"tc".')
 opts = parser.parse_args()
 
+init_logging(opts.verbose)
+
 fp = io.loadfile(opts.input_file, 'r')
 samples = fp.read_samples([opts.ra, opts.dec, opts.distance, opts.tc])
 fp.close()

bin/inference/pycbc_inference_plot_gelman_rubin

@@ -19,19 +19,20 @@
 
 import argparse
 import logging
-import matplotlib as mpl; mpl.use("Agg")
+import matplotlib
+matplotlib.use("Agg")
 import matplotlib.pyplot as plt
 import sys
-from pycbc import results
-from pycbc import __version__ 
+
+from pycbc import (
+    __version__, results, init_logging, add_common_pycbc_options
+)
 from pycbc.inference import (gelman_rubin, io, option_utils)
 
 # add options to command line
 parser = io.ResultsArgumentParser(skip_args=['walkers'])
 
-# verbose option
-parser.add_argument("--verbose", action="store_true", default=False,
-                    help="Print logging info.")
+add_common_pycbc_options(parser)
 parser.add_argument('--version', action='version', version=__version__,
                     help='show version number and exit')
 
@@ -55,11 +56,7 @@ parser.add_argument("--segment-step", type=int, required=True,
 opts = parser.parse_args()
 
 # setup log
-if opts.verbose:
-    log_level = logging.DEBUG
-else:
-    log_level = logging.WARN
-logging.basicConfig(format="%(asctime)s : %(message)s", level=log_level)
+init_logging(opts.verbose)
 
 # enfore that this is not a single iteration
 if opts.iteration is not None:

bin/inference/pycbc_inference_plot_mcmc_history

@@ -31,6 +31,7 @@ from pycbc.inference import io
 from pycbc.results import metadata
 
 parser = argparse.ArgumentParser(description=__doc__)
+pycbc.add_common_pycbc_options(parser)
 parser.add_argument('--input-file', type=str, required=True,
                     help='Path to the input HDF file.')
 parser.add_argument('--output-file', type=str, required=True,
@@ -48,7 +49,8 @@ parser.add_argument('-b', '--plot-nchains-burned-in', action='store_true',
                          'ensemble samplers, this will be all or nothing.')
 opts = parser.parse_args()
 
-pycbc.init_logging(True)
+# Default logging level is info: --verbose adds to this
+pycbc.init_logging(opts.verbose, default_level=1)
 
 nplots = sum([opts.plot_act, opts.plot_effective_nsamples,
               opts.plot_nchains_burned_in, opts.plot_checkpoint_dt])

bin/inference/pycbc_inference_plot_skymap

@@ -31,8 +31,10 @@ import sys
 import subprocess
 from PIL import Image, PngImagePlugin
 
+from pycbc import add_common_pycbc_options, init_logging
 
 parser = argparse.ArgumentParser(description=__doc__)
+add_common_pycbc_options(parser)
 parser.add_argument('--input-file', required=True,
                     help='Input fits file"')
 parser.add_argument('--output-file', required=True,
@@ -42,6 +44,8 @@ parser.add_argument('--colormap',
 
 opts = parser.parse_args()
 
+init_logging(opts.verbose)
+
 cmd = 'ligo-skymap-plot {} -o {} --annotate --contour 50 90'.format(
     opts.input_file, opts.output_file)
 if opts.colormap is not None:

bin/inference/pycbc_inference_plot_thermodynamic_integrand

@@ -31,10 +31,13 @@ matplotlib.use("agg")
 from matplotlib import rc
 import matplotlib.pyplot as plt
 import numpy
+
+from pycbc import add_common_pycbc_options, init_logging
 from pycbc.inference import io
 import pycbc.version
 
 parser = argparse.ArgumentParser()
+add_common_pycbc_options(parser)
 parser.add_argument("--inference-file", type=str,
                     help="The PyCBC multi-temper inference file.")
 parser.add_argument("--thin-start", type=int, default=None,
@@ -52,6 +55,8 @@ parser.add_argument("--integrand-logarithmic", action="store_true",
 parser.add_argument("--output-file", type=str)
 args = parser.parse_args()
 
+init_logging(args.verbose)
+
 # Read in the necessary data
 fp = io.loadfile(args.inference_file, "r")
 logl = fp.read_samples("loglikelihood", thin_start=args.thin_start,

bin/inference/pycbc_inference_start_from_samples

@@ -6,10 +6,13 @@ import argparse
 import numpy
 import h5py
 from numpy.random import choice
+
+from pycbc import add_common_pycbc_options, init_logging
 from pycbc.inference.io import loadfile
 from pycbc.inference.sampler import samplers
 
 parser = argparse.ArgumentParser()
+add_common_pycbc_options(parser)
 parser.add_argument('--input-file')
 parser.add_argument('--output-file')
 parser.add_argument('--sampler', default='emcee_pt',
@@ -18,6 +21,8 @@ parser.add_argument('--ntemps', type=int)
 parser.add_argument('--nwalkers', type=int)
 args = parser.parse_args()
 
+init_logging(opts.verbose)
+
 # populate an emcee start file with
 # values chosen from a dynesty file
 # each temperature and walker will get a random

bin/inference/pycbc_validate_test_posterior

@@ -5,15 +5,21 @@ test posterior model.
 import sys
 import numpy
 import argparse
-from matplotlib import use; use('Agg')
+from matplotlib import use
+use('Agg')
 import pylab
+
+from scipy.stats import gaussian_kde, ks_2samp
+
 from pycbc.distributions.utils import prior_from_config
 from pycbc.inference import models, io
-from scipy.stats import gaussian_kde, ks_2samp
 from pycbc.io import FieldArray
+from pycbc import add_common_pycbc_options, init_logging
+
 numpy.random.seed(0)
 
 parser = argparse.ArgumentParser()
+add_common_pycbc_options(parser)
 parser.add_argument('--input-file', help='inference posterior file')
 parser.add_argument('--output-file', help='diagnostic plot')
 parser.add_argument('--p-value-threshold', help='minimum ks test p-value',
@@ -22,6 +28,8 @@ parser.add_argument('--ind-samples', help='use only this number of samples',
                     default=1000, type=int)
 args = parser.parse_args()
 
+init_logging(args.verbose)
+
 size = int(1e6)
 d1 = io.loadfile(args.input_file, 'r')
 

bin/minifollowups/pycbc_foreground_minifollowup

@@ -69,8 +69,7 @@ wf.add_workflow_settings_cli(parser, include_subdax_opts=True)
 args = parser.parse_args()
 
 # Default logging level is info: --verbose adds to this
-log_level = 1 if args.verbose is None else args.verbose + 1
-init_logging(log_level)
+init_logging(args.verbose, default_level=1)
 
 workflow = wf.Workflow(args)
 

bin/minifollowups/pycbc_injection_minifollowup

@@ -163,8 +163,7 @@ args = parser.parse_args()
 
 
 # Default logging level is info: --verbose adds to this
-log_level = 1 if args.verbose is None else args.verbose + 1
-init_logging(log_level)
+init_logging(args.verbose, default_level=1)
 
 workflow = wf.Workflow(args)
 

bin/minifollowups/pycbc_sngl_minifollowup

@@ -97,8 +97,7 @@ stat.insert_statistic_option_group(parser,
 args = parser.parse_args()
 
 # Default logging level is info: --verbose adds to this
-log_level = 1 if args.verbose is None else args.verbose + 1
-init_logging(log_level)
+init_logging(args.verbose, default_level=1)
 
 workflow = wf.Workflow(args)
 workflow.ifos = [args.instrument]

bin/minifollowups/pycbc_upload_prep_minifollowup

@@ -66,8 +66,7 @@ wf.add_workflow_settings_cli(parser, include_subdax_opts=True)
 args = parser.parse_args()
 
 # Default logging level is info: --verbose adds to this
-log_level = 1 if args.verbose is None else args.verbose + 1
-init_logging(log_level)
+init_logging(args.verbose, default_level=1)
 
 workflow = wf.Workflow(args)