Bionetgen

Behavior change, now most calls to `BNG2.pl` won't result in verbose output, the default has changed to suppress output. The only call that retains the output is a command line call to the subcommand `run`. Bugfix where the library run function didn't respect suppress option if timeout keyword was used. Bugfix to atomizer where atomization failed if the model only had syn/desyn rules.

Bugfixes to various parts of cpy simulator code. cpy simulator now tries to identify independent parameters to pass to the c simulator and also returns the time points used for integration.

Defaults for regulatory visualization are changed. `setup_simulator` now uses `mkdtemp` to avoid issues with Windows temporary file system.

BNGResult representation didn't have spaces between model names.

Fixed a bug where calling simulators with just the model string was failing.

Added a set of custom exceptions and replaced most errors raised with custom exceptions for more descriptive errors. Added proper logging. Added a pattern reader and experimental canonicalization of pattern objects using PyNauty. This feature is not fully functional yet.