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Ran 09 Apr 2018 07:24PM UTC

Files 97

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Committed 09 Apr 2018 07:16PM UTC coverage: 75.02% (+0.4%) from 74.574%

Job # 768.1

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

On demand observable trajectory calculation (#337)

* Pattern matcher for PySB components and model test suite

* More documentation on pattern matching functions

* Add some tests for pattern matcher

* Pattern matcher updates from @jmuhlich's feedback

* Pattern matcher functions are now top-level in pysb.pattern
* Add `matches` methods for ComplexPatterns and ReactionPatterns
* `ComplexPattern.is_equivalent_to` now always does exact comparison

* Compartment and ReactionPattern matching tests

* More unit and doctests for pattern matching

* Make Complex._as_graph() private for now

Add underscore prefix to make as_graph() private, as we may change
the internal implementation of pattern graph at a later date.

* Bond wilcard only matches bonds, not Components

* ANY and WILD were switched in _as_graph()

* Dynamic observable calculation

* Update documentation and py3 compatibility

* Remove duplicated function from rebase

* Improve SimulationResult.observable docstring

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