How does cogent3 relate to PyCogent?

cogent3 is a significantly changed library from the original PyCogent. The renaming has been done to emphasise these differences and to make the project name and import statement consistent (cogent was always the import name, originating in the pyevolve project from 2004).

Most of the changes from PyCogent involved elimination of modules, rationalisation of interfaces and the addition of new features. The rewrite was a massive amount of work and unfortunately the changes to the API are only indirectly documented by virtue of having the documentation match the library state. Thus, the best way to get older scripts working is to check the Library documentation related to your code. More explicitly, you can also search in the repository history.