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Example:\n\nwith BngConsole(model) as con:\n    con.action('simulate_ssa', t_end=10, n_steps=100)\n\nThe context manager automatically loads the model into BNG\nand cleans up on exit.","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/85985bc75b4a721bd3e21c8f2e7a3e690a2049db"},{"sha":"af5b9a44c68c6560f2e883df22ef123f15a6781a","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Add pexpect to Travis requirements","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/af5b9a44c68c6560f2e883df22ef123f15a6781a"},{"sha":"4c7f8b539566f05f0efeb5c340c4b1d99a2dd95c","author":{"email":"1d51cd0ae1a1e124301131c6405c31a89c56149d@cornell.edu","name":"Leonard A. Harris"},"message":"Fixed the verbose output in run_ssa. Also changed the action call from\n'simlulate_ssa' to 'simulate({method=>\"ssa\",...})', which is the\npreferred call method. Note that the \"ssa\" argument has to be passed to\nBNG with enclosing quotes. This is true of all string arguments. So\nwe'll have to keep this in mind as we implement more wrappers around BNG\nactions using the console interface. Any args passed in as strings will\nhave to be type checked and enclosed in quotes when building the action\ncall.","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/4c7f8b539566f05f0efeb5c340c4b1d99a2dd95c"},{"sha":"16d5086f23e84793abad4afbbab0d50a39cc9e62","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Python 3 compatibility fix in BngConsole","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/16d5086f23e84793abad4afbbab0d50a39cc9e62"},{"sha":"418f934647445eb4cebba48bc5aad815e250fee0","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"BngConsole auto parameter type detection (quote strings, bool to int)\n\nBioNetGen requires string arguments to be double quoted and booleans\nas 0 or 1. A small class method _bng_param now handles this\nautomatically.\n\nAlso, two quick fixes: BngConsole now extends object, and network\ngeneration in run_ssa() should be done within try block, not\nfinally block (more fault tolerant).","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/418f934647445eb4cebba48bc5aad815e250fee0"},{"sha":"a652ca7b845bbc1b436b160b0af06a2c4b558643","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Add BNGFileInterface, in addition to BNGConsole\n\nBoth BNGFileInterface and BNGConsole have very similar API and usage.\nThe difference is that BNGConsole executes commands instantly and\nwaits for the response using the pexpect library. BNGFileInterface\nbuffers all BNG commands and outputs them to the .bngl file for\nexecution in one go. BNGFileInterface is typically faster (no\nrepeated command/response lag) and cross-platform; BNGConsole is\ngreat for interactive use and development.","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/a652ca7b845bbc1b436b160b0af06a2c4b558643"},{"sha":"851e86351151102d35e67fdcae075890e56ac54c","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Don't try to delete BNG network file twice","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/851e86351151102d35e67fdcae075890e56ac54c"},{"sha":"adbdf93f7d2b888961ec9d09d747607673918523","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Improved BNG cleanup and verbose arguments\n\nCleanup and verbose arguments to run_ssa and generate_network\nare now handled better - verbose is passed to BNG's\ngenerate_network, and cleanup is now passed to the BngFileInterface\nconstructor rather than the BNG simulate call as expected.\n\nThanks to @jamespino for catching the cleanup arg issue.","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/adbdf93f7d2b888961ec9d09d747607673918523"},{"sha":"a1e101e1ef6c0595f3546bc6076a3aaf1554ce53","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Rename BngFileInterface instance from con to bngfile","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/a1e101e1ef6c0595f3546bc6076a3aaf1554ce53"},{"sha":"1ea2d5d41184cf411622028f10d9ce68bf939ddd","author":{"email":"fafc2a4878bcf998dcf2eb8460fb71ad64cbd59d@gmail.com","name":"ortega2247"},"message":"fixed a bug in the creation of bidirectional reactions.","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/1ea2d5d41184cf411622028f10d9ce68bf939ddd"},{"sha":"e0b4d16fb302c850c56a1dfb70f9c1fa9ee4e7b1","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Another reactions_bidirectional fix when initials and rule orders conflict\n\nUnder specific conditions where initial conditions are defined in\na different order to how they appear in rules (see new\ntest_bidrectional_rules_collapse unit test), the\nreaction_cache was not generating hits to combine the reactions\nproperly. This commit fixes this by checking the cache for a\nforward match to (reactants, products) in the cache, as well as\nmatching the reverse key (products, reactants).","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/e0b4d16fb302c850c56a1dfb70f9c1fa9ee4e7b1"},{"sha":"5a16d7bbc4527646bec044158bdf00953d91ed99","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Tidy if/else logic for generating reactions_bidirectional\n\nThanks to @jmuhlich for the suggestion","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/5a16d7bbc4527646bec044158bdf00953d91ed99"},{"sha":"ad779351c7aa17579d57fbe91b9c8d553457f885","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Travis: Install pexpect using anaconda","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/ad779351c7aa17579d57fbe91b9c8d553457f885"},{"sha":"783a06d76dca20cd0caf6edf6c2c91790b338de3","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Decorate BngBaseInterface constructor as abstractmethod","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/783a06d76dca20cd0caf6edf6c2c91790b338de3"},{"sha":"2c82cd5b0038e36fff3aa9898f65b952036200a4","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Allow models with no initial conditions if a synthesis rule is present","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/2c82cd5b0038e36fff3aa9898f65b952036200a4"},{"sha":"dd22d616700d44ea209d321c338b0bcac9224a09","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Fix misuse of action abstractmethod by formatting args in separate classmethod","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/dd22d616700d44ea209d321c338b0bcac9224a09"},{"sha":"0e2262e2e3a9b9712829cdeb670897adef7df3d6","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Generate Python warning when BNG console generates a warning","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/0e2262e2e3a9b9712829cdeb670897adef7df3d6"},{"sha":"c0ae7b7a1a51d2985ee308da6cb02d60189ef71f","author":{"email":"e6fb06210fafc02fd7479ddbed2d042cc3a5155e@alexlubbock.com","name":"Alex Lubbock"},"message":"Improved BNG error handling with new BngInterfaceError class","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/c0ae7b7a1a51d2985ee308da6cb02d60189ef71f"},{"sha":"abaaa1b8dbddbb5baaf4d6113b96cd2907fc37e6","author":{"email":"86596cc1637dc61a0cff2efedb988837076676be@bitflood.org","name":"Jeremy Muhlich"},"message":"Merge pull request #169 from LoLab-VU/bidirectional_fix\n\nfixed a bug in the creation of bidirectional reactions.","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/abaaa1b8dbddbb5baaf4d6113b96cd2907fc37e6"},{"sha":"0c011cf618b4657154543331f7b75d57c2360b7f","author":{"email":"86596cc1637dc61a0cff2efedb988837076676be@bitflood.org","name":"Jeremy Muhlich"},"message":"Merge remote-tracking branch 'LoLab-VU/bngconsole'\n\nManual conflict resolution of #169:\nNew BioNetGen interfaces for console and file based access\n\nConflicts:\n\tpysb/tests/test_bng.py","distinct":false,"url":"https://api.github.com/repos/LoLab-VU/pysb/commits/0c011cf618b4657154543331f7b75d57c2360b7f"}]}