README updated with some newer methods and add_sequences method accepts path to fasta files.

Merge pull request #11 from m-d-grunnill/master

Updated README and add_sequences accepts paths to fasta files.

1.3.1: Merge pull request #9 from m-d-grunnill/master

Hopefully fixed setup.pyand python-publish.yml.

1.3.0

Format/syntax:

• Refactored variables, functions and methods to snake_case. Use of CamalCase is know reserved to classes.
• Changed docstring style to be that used in numpy/scipy.

Modifications:

• BEAST2XML.to_string: returns the xmls tree as a string.
• BEAST2XML.to_xml: writes the xmls to a file.

New features:

• BEAST2XML.change_parameter_state_node: Change the values of the stateNode for a parameter.
• BEAST2XML.change_prior: Change the values of a parameters prior. Only tested for the Uniform distribution.
• BEAST2XML.add_initial_tree adds initial Newick tree to BEAST2 xmls.
• BEAST2XML.add_rate_change_dates: Add specific dates for parameter changes in skyline models.
• BEAST2XML.add_rate_change_times: Add specific times for parameter changes in skyline models.