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coverage: 71.366%. First build
533.2

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jmuhlich 
Initial concentration sensitivity analysis tool (#246)

* Creating sensitivity analysis branch.
Adding initial concentrations sensitivity in pysb.tools. Adding test using tyson.

* updating sensitivity to reflect notation from 2016 bioinformatics paper

* Added a few tests to make sure the operations are working correctly.

Trying to change flags when exporting to svg. For some reason inkscape can't open some of the svgs without having to manually edit the files. Not required but would be nice to use the svgs with inkscape.

* Added 'yexpr' to the Solver class

* Added a '_supports' dict to base.py with 'multi_initials' and
'multi_param_values' keys that indicates whether the specific Simulator
class supports multiple initials and param_values (i.e., multiple
simulation runs). In base.py, both are set to False and must be
explicitly overridden in derived classes that support multiple
simulation runs (e.g., CupSodaSimulator). Also had to update some tests
to work with the new code.

* Restored test_simulationresult.test_simres_dataframe() since
ScipyOdeSimulator now supports multiple simulation runs.

* Removed 'tout' as a member variable of Simulator and modified the
SimulationResult constructor to take 'tout' as an argument (instead of
extracting it from the Simulator object). Updated ScipyOdeSimulator and
test_simulationresult.py accordingly.

* Removing lines that are causing unit tests to fail

Removing matplotlib specific lines. They were only added to make the svg outputs readable by inkscape. They actually didn't help like I thought they would.

* Updating file according to @alubbock comments. Made pep8 style formatting changes, switched doc strings to numpy, and cleaned up tests.

* Changing default "view_plots" to False. Failing with travis as there are no displays.

* Adding example for sensitivity analysis class.

Updated sensitivity analysis class to take a solver as an argument.

Improved coverage to 95% for sensitivity analysis class. Began docstring example.

* Finished example for docstring

* Only show scipy integration timesteps at log level EXTENDED_DEBUG

* Minor fixes, PEP8 and docstring improvements

* Use temporary directory for unit tests

* Fixes and tidying for Tyson sensitivity analysis example

* Set matplotlib backend to generate plots on Travis CI

* Tidy up call signatures and docstrings

* Revert some stupids

* Improvements to documentation and final code tweaks

* Change "proteins" to "species" in sensitivity analysis code

* Sensitivity analysis requires simulator object in the constructor, not run()

* Sensitivity analysis now uses logging system

* Clean up _create_index_of_species function

* Sensitivity analysis plot fns now return figure objects

* Refine naming of private methods in sensitivity analysis

4556 of 6384 relevant lines covered (71.37%)

0.71 hits per line

Source Files on job 533.2