** THIS CODE IS PRE-ALPHA ** We'll be releasing the alpha version as soon as we can!
As a part of eons, we follow all eons conventions.
Style
Namespaces
Biology is broken into the following namespaces:
- common (base) - the corollary to real-life mathematics; used everywhere.
- physical (nodes) - adds relativity, base classes, & real-life type simulacra.
- log (logging) - logs
- chemical (edges) - expands on physical base classes, adding bonds, reactions, and structure.
- molecular (values) - adds symmetry and context to chemical base classes.
- genetic (modules) - adds the ability to combine molecules & proteins into discrete packages.
- cellular (library interface) - combines all lower namespaces and provides common points for library extension.
- organism (binary interface) - provides a means of running Biology code.
Extension
In order to facilitate cross-namespace type extension, some special rules should be followed in order to create consistency between domains.
When defining extendable types, primarily through the use of physical::Perspectives, it is customary to define the type with a capital (i.e. Type) in the main bio namespace, ignoring any other namespaces the type would otherwise belong to. The definitions of type-returning functions or raw types should then be placed in a lowercase namespace; again, this namespace should be directly under the main bio namespace and not in whatever sub-namespace the type would otherwise belong to. For example, States are defined in the physical folder but not in the physical namespace. They are then defined in the bio::state namespace. This snippet is from "bio/chemical/States.h"
So, you can say
To recap, extendable types should follow these rules:
- Type is defined in bio namespace.
- Type is UpperCamelCase.
- Corresponding namespace is defined in bio namespace.
- Corresponding namespace is lower_snake_case.
Templates
Templates are handled in a WYSIWYG manner where T (or the appropriate typename) is never modified. This means if you call Add < T > you will get a T returned, not a T* or anything else.
Inheritance & Naming
All Biology classes, with few exceptions, are virtual and may be extended as far as you would like. To accommodate this, objects are almost always passed by pointer; meaning, you can pass references to your derived classes and functions will treat them as the base class. Your code is then executed through virtual method calls.
AbstractClasses cannot be instantiated but can be used to pass implementations by pointer.
Classes may be templated if they necessarily require a template. Otherwise, they contain the minimal functionality they represent and may be extended.
ClassOf<> will be used if Class is functional on its own, and we also want a templated derivation. The template (i.e. ClassOf<>) will share the same name as the base Class with the addition of "of" in order to avoid file name conflicts. It will NEVER be the case that a Class derives from a templated base class of the same name (i.e. Class : ClassOf<> is invalid as are Class<> : Class and Class : Class<>). Use of ClassOf<> is discouraged; a more descriptive name is preferred (i.e. what does the template override provide?).
Thus, in terms of possible templates, we get either Class<> on its own, Class<> : AbstractClass, or ClassOf<> : Class, depending on whether the base class is functional (of course, we also have Class : OtherClass<> but that's just general inheritance).
Building
Code
This project depends on the eons Basic Build System, which can be installed with pip install ebbs.
With that said, this is just c++ code. Build it however you want.
Build using ebbs:
installation instructions coming soon (need package manager / repository semantics for module delivery)
Docs
Documentation is available on the Develop Biology website
Branding
Colors
- Dark Blue: #5ca3ff rgb(92, 163, 255)
- Cyan: #13f4ef rgb(19, 244, 239)
- Green: #68ff00 rgb(104, 255, 0)
- Yellow: #faff00 rgb(250, 255, 0)
- Orange: #ffbf00 rgb(255, 191, 0)
- Magenta: #ff5794 rgb(255, 87, 148)
