zaneveld / karenina

Simulation and modeling tools for studying Anna Karenina effects in animal microbiomes
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Refactor benchmark #53

Closed zaneveld closed 6 years ago

zaneveld commented 6 years ago

Main areas of focus: Closes #51 This is a refactoring pass on fit_timeseries_benchmark, which is now benchmark.py --- Break up large functions into smaller ones that can be tested more readily --- Renamed some variable names to make their meaning more clear. --- Separated out log file lines into a separate function. In future updates the logging module may be a better solution. --- A lot of information was shared between the results and log file entries. The log file entries are now directly generated from the results. https://docs.python.org/3/howto/logging.html#logging-basic-tutorial --- Consolidate graphing code for each parameter into a single function

Closes #52 Fixed an error where the AIC calculation was not getting correct parameters.

-- Closes open plots to prevent unneeded memory usage -- Attempted to update Sphinx documentation (hopefully this worked)