7.1.2.1.1.1.2. intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing package

7.1.2.1.1.1.2.1. Submodules

7.1.2.1.1.1.2.2. intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.__main__ module

Example command line program

Author

Jonathan Karr <jonrkarr@gmail.com>

Date

2017-05-12

Copyright

2017, Karr Lab

License

MIT

class intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.__main__.App(label=None, **kw)[source]

Bases: cement.core.foundation.App

class Meta[source]

Bases: object

base_controller = 'base'[source]
handlers = [<class 'intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.__main__.BaseController'>][source]
label = 'intro_to_wc_modeling'[source]
class intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.__main__.BaseController(*args, **kw)[source]

Bases: cement.ext.ext_argparse.ArgparseController

class Meta[source]

Bases: object

arguments = [(['arg'], {'type': <class 'str'>, 'help': 'Example argument'})][source]
description = 'Example command line interface'[source]
label = 'base'[source]
intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.__main__.main()[source]

7.1.2.1.1.1.2.3. intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.core module

Example python code

Author

Jonathan Karr <jonrkarr@gmail.com>

Date

2017-05-12

Copyright

2017, Karr Lab

License

MIT

class intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.core.Simulation(k_syn=1.0, k_deg=1.0, verbose=False)[source]

Bases: object

Simulates the synthesis and degradation of a species

k_syn[source]

zeroth-order synthesis rate

Type

float

k_keg[source]

first-order degradation rate

Type

float

verbose[source]

if True, print status information to stdout

Type

bool

run(value_init=5, time_max=10)[source]

Runs a simulation for time_max seconds starting with value_init molecules

Parameters

  • value_init (float, optional) – initial number of species

  • time_max (int, optional) – simulation length in s

Returns

simulated trajectory

Return type

Trajectory

Raises

ValueError – if time_max is negative

class intro_to_wc_modeling.concepts_skills.software_engineering.unit_testing.core.Trajectory(time_max)[source]

Bases: object

Represents a simulated trajectory

times[source]

array of times of predicted values in s

Type

numpy.ndarray

values[source]

array of predicted values

Type

numpy.ndarray of float

7.1.2.1.1.1.2.4. Module contents