Clean up logger and reduce the amount of debug messages printed

doc/index.rst

@@ -141,9 +141,15 @@ The following flags exist:
    * - ``disable_stiffness_check``
      - :python:`False`
      - Set to True to disable stiffness check.
+   * - ``disable_analytic_solver``
+     - :python:`False`
+     - Set to True to return numerical solver recommendations, and no propagators, even for ODEs that are analytically tractable.
    * - ``disable_singularity_detection``
      - :python:`False`
-     - Set to True to disable detection of conditions under which numerical singularities (division by zero) could occur.
+     - Set to True to disable detection of conditions under which numerical singularities (division by zero) could occur in the generated analytic solver. This can be useful for analytic solvers containing a large amount of conditions, which could take a long time to compute. If True, no warning messages or mitigations will be returned in case of potential singularities.
+   * - ``disable_singularity_mitigation``
+     - :python:`False`
+     - (Only useful if ``disable_singularity_detection`` is False.) Set to True to disable mitigation of conditions under which numerical singularities (division by zero) could occur in the generated analytic solver. This can be useful for analytic solvers containing a large amount of conditions, which could take a long time to compute. If True, at most one analytic solver will be returned, in which numerical singularities could occur.
    * - ``use_alternative_expM``
      - :python:`False`
      - If :python:`False`, use the sympy function ``sympy.exp`` to compute the matrix exponential. If :python:`True`, use an alternative function (see :py:func:`odetoolbox.sympy_helpers.expMt` for details). This can be useful as calls to ``sympy.exp`` can sometimes take a very large amount of time.
@@ -154,6 +160,7 @@ The following flags exist:
      - :python:`logging.WARN`
      - Sets the logging threshold. Logging messages which are less severe than ``log_level`` will be ignored. Log levels can be provided as an integer or string, for example "INFO" (more messages) or "WARN" (fewer messages). For a list of valid logging levels, see https://docs.python.org/3/library/logging.html#logging-levels
 
+
 Input
 -----
 
@@ -372,6 +379,10 @@ The following global options are defined. Note that all are typically formatted
      - :python:`["oo", "zoo", "nan", "NaN", "__h"]`
      - list of strings
      - For each forbidden name: emit an error if a variable or parameter by this name occurs in the input.
+   * - ``use_alternative_expM``
+     - :python:`False`
+     - boolean
+     - If :python:`False`, use the sympy function ``sympy.exp`` to compute the matrix exponential. If :python:`True`, use an alternative function (see :py:func:`odetoolbox.sympy_helpers.expMt` for details). This can be useful as calls to ``sympy.exp`` can sometimes take a very large amount of time.
 
 
 Output

ode_analyzer.py

@@ -51,32 +51,33 @@
         parsed_args.preserve_expressions = True
 
     _init_logging(log_level=parsed_args.log_level)
-    logging.info("Reading input file...")
+    logging.getLogger(__name__).info("Reading input file...")
 
     if not os.path.isfile(parsed_args.infile):
-        logging.error("The file '%s' does not exist." % parsed_args.infile)
+        logging.getLogger(__name__).error("The file '%s' does not exist." % parsed_args.infile)
         sys.exit(1)
 
     with open(parsed_args.infile) as infile:
         try:
             indict = json.load(infile)
         except Exception as e:
-            logging.error("The input JSON file could not be parsed; error: " + e.msg)
+            logging.getLogger(__name__).error("The input JSON file could not be parsed; error: " + e.msg)
             sys.exit(1)
 
     try:
         result = odetoolbox.analysis(indict,
                                      disable_stiffness_check=parsed_args.disable_stiffness_check,
                                      disable_analytic_solver=parsed_args.disable_analytic_solver,
                                      disable_singularity_detection=parsed_args.disable_singularity_detection,
+                                     disable_singularity_mitigation=parsed_args.disable_singularity_mitigation,
                                      preserve_expressions=parsed_args.preserve_expressions,
                                      log_level=parsed_args.log_level)
     except MalformedInputException as e:
-        logging.error("The input JSON file could not be parsed; error: " + e.message)
+        logging.getLogger(__name__).error("The input JSON file could not be parsed; error: " + e.message)
         sys.exit(1)
 
     basename = os.path.basename(parsed_args.infile.rsplit(".", 1)[0])
     outfname = "%s_result.json" % basename
-    logging.info("Writing output to file %s..." % outfname)
+    logging.getLogger(__name__).info("Writing output to file %s..." % outfname)
     with open(outfname, 'w') as outfile:
         outfile.write(json.dumps(result, indent=2))