KarrLab/wc_sim

metadata hierarchy

RunResults:
    METADATA_CLASS_TO_NAME = {SimulationMetadata: 'de_sim_metadata',
                              WCSimulationMetadata: 'wc_sim_metadata'}

*** - define semantically_equal
** - include in semantically_equal
* - ignored by semantically_equal
== - define equal
X - done

class WCSimulationMetadata(EnhancedDataClass): ***
    wc_sim_config: WCSimulationConfig **
    wc_simulator_repo: RepositoryMetadata = None **
    wc_model_repo: RepositoryMetadata = None **

class WCSimulationConfig(EnhancedDataClass): *** X
    de_simulation_config SimulationConfig: a simulation configuration for DE-Sim **
    random_seed int: random number generator seed **
    ode_time_step float: ODE submodel timestep (s) **
    dfba_time_step float: dFBA submodel timestep (s) **
    checkpoint_period float: checkpointing timestep (s) **
    submodels_to_skip list of `str: submodels that should not be run, identified by their ids **
    verbose bool: whether to produce verbose output *
    changes list: + not currently used + *
    perturbations list: + not currently used + *

class SimulationMetadata(EnhancedDataClass): # Represents the metadata of a discrete event simulation run *** X
    simulation_config SimulationConfig: information about the simulation's configuration **
    run RunMetadata: information about the simulation's run *
    author AuthorMetadata: information about the person who ran the simulation **
    simulator RepositoryMetadata: metadata about this simulator's git repository **

class SimulationConfig(EnhancedDataClass): *** X
    max_time float: maximum simulation time **
    time_init float: time at which a simulation starts **
    stop_condition function: a simulation terminates if the function returns `True` *
    output_dir str: directory for saving metadata *
    progress bool: *
    profile bool: output a profile of the simulation's performance *
    object_memory_change_interval int: # of simulation events between reporting changes memory use *

class RunMetadata(EnhancedDataClass): # Represent a simulation's run *** X
    ip_address str: ip address of the machine that ran the simulation *
    start_time datetime: simulation clock start time *
    run_time float: simulation run time in seconds *

class AuthorMetadata(EnhancedDataClass): # Represents a simulation's author
    name str: authors' name
    email str: author's email address
    username str: authors' username
    organization str: author's organization

@dataclass
class RepositoryMetadata(object): # Represents metadata about a Git repository
    url: str
    branch: str
    revision: str