Add support to use mapping file categories

User can now specify a category in a mapping file to create the
semivariograms and color them by that field.
Merge branch 'master' of git://github.com/qiime/qiime into semivariogram_updates
Add functionality to create a color-legend
Add get_qiime_hex_string_color

Retrieves a hexadecimal string for use with matplotlib, etc.
Add usage examples and sample test data

Change some strings to make them fit 80 columns.
Merge pull request #986 from ElDeveloper/semivariogram_updates

plot_semivariogram.py updates
Fixes #996
Merge pull request #997 from jrrideout/issue-996

Fixes #996
added check for qcli
updated to import command line processing functionality from qcli
added qcli to dependency list
updated changelog to mention qcli dependency
removed as we're now using code from qcli
removed make_qiime_rst_file.py in favor of qcli_make_rst
updated changelog
Update add_alpha_to_mapping_file.rst
ported run_script_usage_tests to qcli
ported qiime_system_call to qcli
updated to reflect new parameter names since prot to qcli
ported timeout functionality to qcli