New BioNetGen interfaces for console and file based access #168
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Call any arbitrary BNG command using a context manager
and Python kwargs. Example:
with BngConsole(model) as con:
con.action('simulate_ssa', t_end=10, n_steps=100)
The context manager automatically loads the model into BNG
and cleans up on exit.
'simlulate_ssa' to 'simulate({method=>"ssa",...})', which is the
preferred call method. Note that the "ssa" argument has to be passed to
BNG with enclosing quotes. This is true of all string arguments. So
we'll have to keep this in mind as we implement more wrappers around BNG
actions using the console interface. Any args passed in as strings will
have to be type checked and enclosed in quotes when building the action
call.
BioNetGen requires string arguments to be double quoted and booleans as 0 or 1. A small class method _bng_param now handles this automatically. Also, two quick fixes: BngConsole now extends object, and network generation in run_ssa() should be done within try block, not finally block (more fault tolerant).
Both BNGFileInterface and BNGConsole have very similar API and usage. The difference is that BNGConsole executes commands instantly and waits for the response using the pexpect library. BNGFileInterface buffers all BNG commands and outputs them to the .bngl file for execution in one go. BNGFileInterface is typically faster (no repeated command/response lag) and cross-platform; BNGConsole is great for interactive use and development.
Cleanup and verbose arguments to run_ssa and generate_network are now handled better - verbose is passed to BNG's generate_network, and cleanup is now passed to the BngFileInterface constructor rather than the BNG simulate call as expected. Thanks to @JamesPino for catching the cleanup arg issue.
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Looks good to me. @jmuhlich, do you want to take a look? |
| @@ -12,7 +12,7 @@ before_install: | |||
| - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy matplotlib sympy networkx | |||
| nose h5py | |||
| - pip install -i https://pypi.binstar.org/pypi/simple pygraphviz==1.3rc1 | |||
| - pip install python-coveralls | |||
| - pip install python-coveralls pexpect | |||
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Also pedantic: I think anaconda offers pexpect (see http://docs.continuum.io/anaconda/pkg-docs), so ideally we'd install that with conda rather than pip.
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I think I've addressed all your feedback @jmuhlich - let me know if there's anything I missed. The |
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Hmm, it's good to note that your "allow synthesis instead of initial conditions" fix is rolled up in here too. |
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I've added two new classes,
BngFileInterfaceandBngConsole, for interacting with BioNetGen. Both extend an abstract base classBngBaseInterface. I've adjustedgenerate_networkandrun_ssato useBngFileInterface.Both
BngFileInterfaceandBngConsolehave very similar API and usage. The difference is thatBngConsoleexecutes commands instantly and waits for the response using thepexpectlibrary and the BNG Console interface.BngFileInterfacebuffers all BNG commands and outputs them to the .bngl file for execution in one go.BngFileInterfaceis typically faster (no repeated command/response lag) and cross-platform;BngConsoleis great for interactive use and development, but thepexpectlibrary doesn't support Windows.