Standardize logging - final places

[GarethCabournDavies]

Final places where we need to standardise including the logging

This looks like more places than it is because I've added two things in order to simplify logging setup:

• a default_level kwarg to init_logging, which means we can easily state that logging should happen, but --verbose make it a higher level
• a to_file kwarg, which sets up logging to a file instead of to the stderr

[GarethCabournDavies]

To check that all executables have the standardized logging, when we check the repo for files which don't have init_logging, I get no output, i.e. (grep -Le means list of files which don't contain the string):

$ grep -Le init_logging bin/**/pycbc_*

returns nothing

The common pycbc options added to the parser is slightly more complicated, as some of the pygrb codes use a common parser setup, so we see:

$ grep -Le common_pycbc bin/**/pycbc_*
bin/pygrb/pycbc_pygrb_efficiency
bin/pygrb/pycbc_pygrb_page_tables
bin/pygrb/pycbc_pygrb_plot_chisq_veto
bin/pygrb/pycbc_pygrb_plot_coh_ifosnr
bin/pygrb/pycbc_pygrb_plot_injs_results
bin/pygrb/pycbc_pygrb_plot_null_stats
bin/pygrb/pycbc_pygrb_plot_skygrid
bin/pygrb/pycbc_pygrb_plot_snr_timeseries
bin/pygrb/pycbc_pygrb_plot_stats_distribution

but the common options are called within pygrb_initialize_plot_parser, so we can see the same group of files which have that option (grep -le means list of files which do contain the string):

$ grep -le pygrb_initialize_plot_parser bin/**/pycbc_*
bin/pygrb/pycbc_pygrb_efficiency
bin/pygrb/pycbc_pygrb_page_tables
bin/pygrb/pycbc_pygrb_plot_chisq_veto
bin/pygrb/pycbc_pygrb_plot_coh_ifosnr
bin/pygrb/pycbc_pygrb_plot_injs_results
bin/pygrb/pycbc_pygrb_plot_null_stats
bin/pygrb/pycbc_pygrb_plot_skygrid
bin/pygrb/pycbc_pygrb_plot_snr_timeseries
bin/pygrb/pycbc_pygrb_plot_stats_distribution

[GarethCabournDavies]

Codeclimate failures are unrelated to these changes

[GarethCabournDavies]

Note i realised i skipped a couple of places for the init_logging check, and saw

grep -Le init_logging bin/pycbc_*
bin/pycbc_copy_output_map
bin/pycbc_live_nagios_monitor
bin/pycbc_splitbank
bin/pycbc_split_inspinj
bin/pycbc_stageout_failed_workflow
bin/pycbc_submit_dax

of these, pycbc_copy_output_map, pycbc_stageout_failed_workflow and pycbc_submit_dax are bash scripts, the others do not have any logging

[GarethCabournDavies]

This silences the codeclimate "logger is not a valid name" complaints

[GarethCabournDavies]

The other variables are the pyint defaults

[GarethCabournDavies]

This is probably the best place to start the review - the more significant change is here:

• We add a default_level kwarg so that the code can define the default level of logging to be higher, but --verbose still adds incremental logging levels
• We add a to_file kwarg, so that we can define logging to a file through the init_logging interface. If wanting logging to more than one file, or to both stderr and the file, we can call init_logging twice with different to_file values

[GarethCabournDavies]

Outwith this change, all the changes in pycbc directory are:

• adding the named logger to the module
• updating logging --> logger to use the named logger
• some reordering/reformatting of imports

[ArthurTolley]

I'm sure that 99% of my changes (the most I've ever done by far) are related to simple changes or wanting to understand a bit more the 'standardised' part of things. I imagine I'm just misinformed on a few pythonic things, such as my import pycbc comment so if you answer it once then feel free to ignore the rest.

[ArthurTolley]

lfg