Consistent inferface for serialization and deserialization

[epatters]

Currently, we use functions like read_graphml both to read from files and to read from a Julia object (XMLDocument), and similarly for write_graphml. This leaves no place for reading from a string.

I like how NetworkX handles this. Use read_ for reading from a file and parse_ for reading from a string or other object, and similarly for write_ and generate_. Adopt this convention across the project.