First try at changing the logging facilities

[Hugovdberg]

Ages ago I proposed to migrate to the built in logging facilities to allow for more flexible logging (see #315). Recently I have been using pyemu again and faced the same issue I faced then so here is a PR (work in progress) to add logging instead of writing files directly.
I decided to first tackle the new run_sp method as this was the newest so least likely to break peoples workflows should it be not as stable as I think it is (see #539 / #532).

What I have done is create a little method that returns a logging.Logger object given the boolean flags verbose and logger (which currently is called logfile in other methods). However, logger can also accept a logging.Logger object directly. So if you run something like the following code, all messages are recorded in my_custom.log instead of pyemu.log:

I have added two helpers, one is pyemu.log_utils.get_logger that returns a logging.Logger object that writes to pyemu.log or stdout when requested. The second is pyemu.log_utils.set_logger that either takes a logging.Logger (as a positional only argument) or keyword arguments that are passed directly to logging.basicConfig:

import logging
import pyemu

# option 1: no config, defaults will be used when messages are logged
# Nothing to show here

# option 2: pass basic config arguments to set_logger
pyemu.log_utils.set_logger(filename="my_custom.log", format="{asctime} :: {levelname} :: {message}", style="{")

# option 3: configure your own Logger and pass that to set_logger
logger = logging.Logger()
file_handler = logging.FileHandler("pyemu.log")
file_handler.setFormatter(logging.Formatter("{asctime} :: {name} :: {levelname} :: {message}", style="{"))
logger.addHandler(file_handler)
stdout_handler = logging.StreamHandler(sys.stdout)
stdout_handler.setFormatter(logging.Formatter("{asctime} :: {levelname} :: {message}", style="{"))
logger.addHandler(stdout_handler)
pyemu.log_utils.set_logger(logger)
pyemu.os_utils.run("pestchek case.pst", use_sp=True, logfile=logger)

Of course you can go all out in how complicated you want your logging facilities to be, see https://docs.python.org/3/library/logging.html# for all possibilities.

[p-ortega]

Hey @Hugovdberg, I think you would have to modify or remove this test, utils_test.py::run_sp_capture_output_test, for the CI workflow to work with the new logging capabilities.

Sorry that test was pretty ad-hoc

[Hugovdberg]

Probably a lot of tests will fail once we add this in other places as well :-) testing output is always troublesome..