added branch that merges mystic/trunk and branches/pyina at r87;
reduced dependency footprint for mystic & pyina;
reorganized directories, reduced code duplication, cleaned imports;
pyina now builds around mystic (imported in pyina/__init__.py);
bugfixes/corrections to examples for both pyina (needs testing) & mystic


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/branches/merge-pyina-at-r87/trunk/mystic@88 968178ea-60bd-409e-af13-df8a517b6005
restructured top-level to have trunk for mystic & pyina (also branches)


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@89 968178ea-60bd-409e-af13-df8a517b6005
small final cleanup from movig the "merge" branch into the trunk


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@90 968178ea-60bd-409e-af13-df8a517b6005
fixed typo


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@91 968178ea-60bd-409e-af13-df8a517b6005
fixed small bug in Make.mm files


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@92 968178ea-60bd-409e-af13-df8a517b6005
merged the new 'model refactor' branch back into the trunk;
slightly increased model speed by moving import statements


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@94 968178ea-60bd-409e-af13-df8a517b6005
refactored major filters, strategies into filters.py and strategy.py;
refactored termination conditions into termination.py;
changed IterationRelativeError to IterationRelativeTolerance


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@95 968178ea-60bd-409e-af13-df8a517b6005
whoops... forgot to move these two files in last commit


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@96 968178ea-60bd-409e-af13-df8a517b6005
moved scipy_optimize_fmin to scipy_optimize


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@97 968178ea-60bd-409e-af13-df8a517b6005
replace use of numpy in models where not needed, increase model speed


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@98 968178ea-60bd-409e-af13-df8a517b6005
minor shortcut for speedup


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@99 968178ea-60bd-409e-af13-df8a517b6005
added scipy.optimize notice


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@100 968178ea-60bd-409e-af13-df8a517b6005
updated fmin to scipy 0.6.0


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@101 968178ea-60bd-409e-af13-df8a517b6005
renamed "bounds" methods for more consistency;
added method to ensure initial guess is within bounds;
catch initial Simplex cost in energy_history;
rename termination "IRT" to "CRT";
add termination "NormalizedChangeOverGeneration"


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@102 968178ea-60bd-409e-af13-df8a517b6005
added solver for scipy's fmin_powell (added scipy dependency too = BAD);
corrected output from disp,retall,full_output options to be identical to scipy's


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@103 968178ea-60bd-409e-af13-df8a517b6005
moved fmin_powell to scipy_optimize;
removed scipy dependency;
cleanup of Solver documentation


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@104 968178ea-60bd-409e-af13-df8a517b6005
added AbstractSolver class; added documentation for most methods;
changed method name (_clipGuessWithinRangeBoundary)


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@105 968178ea-60bd-409e-af13-df8a517b6005
removed scipy dependency where solver available in mystic


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@106 968178ea-60bd-409e-af13-df8a517b6005
added CustomSow -- a user-configurable n-variable monitor


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@107 968178ea-60bd-409e-af13-df8a517b6005
fixed typo in several model docs;
built the circle model, a basic standard test case;
updated examples using circle model


git-svn-id: svn+ssh://svn.mystic.cacr.caltech.edu/mystic/mystic@108 968178ea-60bd-409e-af13-df8a517b6005