Python implementation

This section describes how the computer software described in the Software design (independent of programming language) is currently implemented in the Python programming language. For a detailed reference of the resulting Python package pycopancore, see API reference.

Because it allows a comfortable mix of object-oriented and imperative programming, is well-established in many scientific communities and provides powerful tools for statistical analysis and data management and exchange, we chose to implement the software in the standard Python programming language, using the current grammar version 3, with the option to port it later to other Python variants like Cython or to other object-oriented languages such as C++ or Java.

Typographic conventions

In this documentation, <text in this kind of brackets> is always a placeholder, e.g., <variable name> is a placeholder for a variable name.

Main package structure

pycopancore

   data_model
      master_data_model
         cell.py
         culture.py
         environment.py
         individual.py
         social_metabolism.py
         social_system.py
         world.py
         ...
      dimensions.py
      dimensional_quantity.py
      reference_variable.py
      set_variable.py
      unit.py
      variable.py
      ...

   model_components
      <component name>
         implementation
            cell.py
            culture.py
            ...
         interface.py
         model.py
         ...
      <other component name>
         ...
      ...

   models
      <model_name>.py
      ...

   private
      _abstract_entity_mixin.py
      _abstract_process.py
      _abstract_runner.py
      _expressions.py
      ...

   process_types
      explicit.py
      event.py
      implicit.py
      ODE.py
      step.py
      ...

   runners
      scipy_odeint_runner.py
      ...

   util
      functions.py
      ...

Local workspace

Users work in a local workspace folder of a slighty similar but simpler structure:

pycopancore-workspace

   model_components
      _component_template
         ...
      <component name>
         ...

   models
      _model_template.py
      <model_name>.py
      ...

   studies
      _study_template.py
      <some_simulation_script>.py
      ...

• Model component subpackages