biocore/scikit-bio — pull request #644 by jairideout (2014-08-26 17:23:39+00:00)
Title: Port DissimilarityMatrix/DistanceMatrix delimited text format to skbio.io

**Not ready for merge.** There are still a few things @ebolyen and I are going to discuss today, mainly related to documentation strategy for supported formats in `skbio.io`. Opening this PR now to let the tests run.

Ported delimited text format for `DissimilarityMatrix`/`DistanceMatrix` to `skbio.io.dm`. Added a sniffer for the file format. Refactored parser and test code to be shorter and cleaner.

TODO:

- [ ] properly deprecate `DissimilarityMatrix.from_file`/`to_file` with warnings (they're currently deleted)
- [ ] add changelog mention
- [ ] fill out `DissimilarityMatrix.read`/`write` and `skbio.io.dm` docstrings (they're pretty sparse)
- [ ] fill in any missing tests for public API (only the underlying readers, writers, and sniffer are tested)

Fixes #626.