Expand capabilities of execution status logging

[jonrkarr]

BioSimulators utils

• [x] Execute each SED document, task, and output
  • [x] Catch exceptions so that the execution doesn't stop on the first failure
  • [x] Collect all exceptions and raise them at the end of the execution of the entire archive
  • [x] When there's at least one exception, terminate with non-zero exit code
  • [x] Generate as much of each output as possible
• [x] For each archive, task, and output capture:
  • [x] Exception
    • [x] Type
    • [x] Message
  • [x] Reason for skip
  • [x] Stdout/err
    • [x] Stdout/err merged together
    • [x] ANSI formatting codes
  • [x] Walltime (duration)
• [x] For each task capture
  • [x] The KiSAO id for the algorithm that was executed
  • [x] Additional simulator-specific details of the execution such as the method and its arguments
• [x] Make CLI print errors in red
• [x] Print warnings in yellow

tellurium

• [x] Apply changes to exec_sed_doc in biosimulators_tellurium

[jonrkarr]

Code to highlight unhandled exceptions

def set_highlighted_excepthook():
    import sys, traceback
    from pygments import highlight
    from pygments.lexers import get_lexer_by_name
    from pygments.formatters import TerminalFormatter

    lexer = get_lexer_by_name("pytb" if sys.version_info.major < 3 else "py3tb")
    formatter = TerminalFormatter()

    def myexcepthook(type, value, tb):
        tbtext = ''.join(traceback.format_exception(type, value, tb))
        sys.stderr.write(highlight(tbtext, lexer, formatter))

    sys.excepthook = myexcepthook

set_highlighted_excepthook()

[jonrkarr]

Done. The changes to the simulators just need to be pushed.

[jonrkarr]

Simulators are pushed with the expanded logging capabilities.