Does any interface documentation exist, beyond that in the readme?

[rsharris]

This seems relevant to issue 3, which is closed. Please see my comment there.

[jeffdaily]

https://github.com/jeffdaily/parasail-python#quick-example

Gap open and extension penalties are specified as positive integers. When any of the algorithms open a gap, only the gap open penalty alone is applied.

The README is the only documentation, yes.

[rsharris]

Thanks.

There are a lot of good things in the readme. But I think part of what is making the learning curve so steep for me is, for example, that an example aligning two four-character strings doesn't demonstrate much of the interface.

One thing I have been trying to find is definitions for attributes of results. As issue #3 shows, one can examine the returned object to get a list of attribute names. Many of these are not specific to alignment, a few are, and its not necessarily obvious which are which. This is one of the things I was trying to glean from the source code, but as yet I haven't been successful.

I expect/hope I will figure it out, eventually,

Thanks, Bob Harris, (the lastz guy).

[jeffdaily]

I certainly didn't intend to vex. I spent most of my efforts with respect to documentation in the README. I did not add doxygen comments to the C library nor did I add docstrings to the python bindings. I don't have a fully-featured readthedocs page, wiki, or otherwise. In fact, I purposefully created the README as the primary location because I had assumed it would travel everywhere with the code, and show up as a pseduo home page on github.

I can see the value in a walkthrough or hello world type of tutorial. An examples folder perhaps. I'm finding, based on github issues and emails, that the python bindings are used most frequently so perhaps I should start here. I will not make any promises, and certainly not any timely ones, because I do not want to disappoint. But I have heard you for sure.

[rsharris]

Thanks for listening!