Implementing Logging

[ngraymon]

Logging as described in the python documentation would greatly improve the health of the project.

Goals

• all debug/error/warning statements handled with a logger
• dynamic granularity in output for enhanced debugging
• cleaner and more robust code

Files requiring changes

• condition_class.py
• json_base_class.py
• molecular_species.py
• puzzle_class.py
• reaction_mechanism_class.py
• reagent.py
• solution_class.py
• conc_profiles.py
• experiment_class.py
• handy_functions.py
• input_output.py
• new_driver.py
• plotter.py
• back_end.py
• dialog_boxes.py
• main_window.py
• rxn_widget.py

Example change Replacing print("\n Attempting to plot " + str(number_of_plots) + " concentration profiles") with logger.info('\n Attempting to plot " + str(number_of_plots) + " concentration profiles')

or `print("Another issue has been detected. Reaction "

• str(bad_rxn[0] + 1)
• " is unstable. \n Cannot proceed, crashing.") with logger.error('Another issue has been detected. Reaction "
• str(bad_rxn[0] + 1)
• " is unstable. \n Cannot proceed, crashing')`

Steps to implement

• [x] Design and Implement relevant logger objects for each module in ckwatson that uses I/O
• [x] Document loggers with use cases, to be used as a reference down the road
• [x] Replace all print statements
• [x] Design a root logger module for the web_gui
• [x] Link the loggers to the root logger module so that errors and messages propagate properly
• [ ] Implement loggers in modules that web_gui hasn't touched. This includes the native GUI also.

[ngraymon]

Initial implementation of logging: ckwatson/kernel@1525db050b68d7534a3916d17168e4b357c6d84f ckwatson/web_gui@53a1029620dfd091defee5a0e823e5befc3cdfc1

Current Issues:

• Error Propagation

Logging errors print to output twice. I believe this is a propagation error because the propagation of the logger is turned off.

[tslmy]

Logging errors print to output twice.

This is because the logger object has 2 handlers attached:

• one for printing onto the console (meant for developers)
• one for printing onto the webpage (meat for the user)

I checked this by turning off one of the handlers. When only one handler exists, the -- logging error -- only shows up once.

It is not a propagation error. It merely means that both the handlers are failing.

I think this "double-printing" error is inevitable at this time, unless we make sure no error would happen when trying to log something.

[tslmy]

About the documentation: should we write them in a Wiki? For the time being, I'll just take a quick note down here:

---

For each module, add the following lines to the top:

import logging
logger = logging.getLogger(__name__)

Then we can send messages in various circumstances as described here.