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NEWS.txt
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NEWS.txt
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-- Version 1.3.2
* Fix conserved moieties bug (wcopeland)
-- Version 1.3.1
* Fix #91 for negative spec amts in Gillespie
* Fix #92 for internal bug in Python wrapper
-- Version 1.3
* New Python ND array type which inherits from the numpy ndarray, contains row/column name info, and
prints the row/col names in nicely formatted output.
* Added row/column fields to DoubleMatrix, these are populated by a majority of RoadRunner methods.
* plotting compatibility between roadrunner and tellurium
* DoubleMatrix correctly writes csv format to stream
* Update to libSBML 5.11
* Add extra time steps in variable step mode to add timesteps at the exact point of event triggers,
results in crisp vertical lines on plots.
* C++ and Python documentation updates.
* new C++11 proxy classes to compile on OSX 10.9
* Introduce new LLVM symbol caching optimiztion and scoped cache blocks for read combining
-- results in SIGNIFICANT imporovments in both compile time and run time performance.
* memory leak fixes in numpy binding.
* code cleanup and new reset option to apply init assignment rules to global params
* added SBML version converter to optionaly version convert resulting sbml string
from getSBML and getCurrentSBML
* many RoadRunner objects are now properly a Dictionary and methods now accept a
Dictionary interface.
* SteadyState solvers properly created by factory.
-- Version 1.2.7
* made the NLEQ steadystate single threaded -- it will block all other threads
and only let one thread at a time be in the steadyState function.
The FORTRAN77 code that it was written in uses globals for everything, there was
no possible way that it was ever thread safe.
* NLEQ steadystate function now uses a static var to hold a pointer to the model object
* Added getKMatrix() method to RoadRunner object, updated python and C++ docs to reflect this.
* Added new 'eigenr' and 'eigenc' selections to get real and complex values of eigenvalues,
note, the existing 'eigen' is the same as 'eigenr' -- will get real part of eigenvalue.
* new rrtest testing file format.
* Removed RoadRunner::getEigenvalues and replaced with getFullEigenValues and
getReducedEigenValues which return the eigenvalues for the respective Jacobians.
* support for 'distrib' SBML package for random distributions.
-- Version 1.2.6
* Python dynamic properties are now on the RoadRunner instead of the RoadRunner.model object
* Fixed bug in dynamic properties where they were not cleared when a new model is loaded.
* Added boundary species to python dynamics properties
* Redesign dynamic property generations - new code is much cleaner.
* testing files in roadrunner.testing are automatically enumerated and run from
roadrunner.testing.test_files
* Fix for ordering variables correctly when creating an SimulateOptions from a libSBML test suite
txt file.
* If model has comp extension, automatically flatten.
- Note, libSBML comp extension has numerous memory issues, comp extension models *might* cause
instability.
* Upgrade to libSBML 5.10.2
* All logging output is re-directed to the IPython socket when running in the QT IPython
console. This allows allows logging messages to show up in the IPython console.
* Support mixed mode arithmetic.
* workarounds for buggy MSVC stdlib functions.
* Significantly improve error messages for mal-formed SBML models.
-- Version 1.2.5
* New parallel ensemble function and 'roadrunner.stochastic' python module.
* Added new example files to python package.
* New function in C API to create RRDataPtr directly from RoadRunner object,
completly bypassing RoadRunnerData C++ object.
* Conserved moiety species amounts and concentrations are directly mutable.
* RoadRunner.reset is now very flexible, can reset a variety of values based on args.
-- Version 1.2.4
* Extended information such as git branch and last commit available via
getVersionStr()
* Test case for reduced / full Jacobian in both amount and concentration mode.
* Reduced Jacobian now works in either amount or concentration mode.
* Added getFloatingSpeciesConcentrationRates() function to get rates of change
of floating species concentrations.
* Made model reset smarter when resetting model with conserved moieties. If users
changes CMs, they will only be reset if users also changes init species cond.
* Correctly display CM ids.
* Major cleanup in handling temp dir path, added config value for specifiying
tmp dir and log file path.
* Added model checks to getCurrentSBML, fixes with CM is enabled.
* Merged Alex's documentation updates to C API.
* Fixed bug with CM being displayed twice in items.
* Fix bug when getting stoich matrix when CM is enabled.
* New Runge-Kutta integrator, available via simulate using integrator="rk4".
* Full Jacobian works in either concentration or amount mode.
* Update make_docs.sh shell script to work with spaces in directory names.
* More user proofing and robustness.
-- Version 1.2.3
* Improvments to error and display messeges.
* Integrator state is NOT reset when changing integrators, i.e. if one does a
r.simulate(integrator="gillepsie")
r.simulate(integrator="cvode")
r.simulate(integrator="gillepsie")
the state of the integrators (including the random number stream) continues from
the previous state.
* The 'seed' keyword argument to simulate resets the RNG to the given seed. All subsequent
calls to simulate pick up the RNG in its current state. The RNG is ONLY reset when the
'seed' keyword argument is given.
* Integrators now implement the dictionary protocol. For example, when using the Gilespie
integrator, it supports the following keys:
r.getIntegrator().keys()
['seed', 'rand']
* The 'rand' value grabs the next random number from the stream, and the 'seed' resets the RNG
to the given seed.
* User specifiable RNG seed. The seed can be specified either via an optional 'seed' argument to
simulate, i.e.
r.simulate(0, 10, seed=23)
Or, can be specified via the SimulateOptions object, either with a new one, or the existing one:
o = SimulateOptions()
o.start = 0
o.end = 10
o.integrator = SimulateOptions.GILLESPIE
o['seed'] = 23 # SimulatOptions behaves as a dictionary, any new integrator specific values
# can be added here.
r.simulate(o)
Or, the existing one can be modified:
r.simulateOptions['seed'] = 23
To get back to the default behavior of using the system time, just delete this value from the
existing object:
del r.simulatOptions['seed']
* Fixed an issue with conserved moieties not being calculated correctly with multi-compartment
models.
* Added getFullStoichiometryMatrix() and getReducedStochiometryMatrix() methods to RoadRunner
object.
* Cleanup in steady state solver, introduced new configuration parameters for steady state solver:
STEADYSTATE_RELATIVE,
STEADYSTATE_MAXIMUM_NUM_STEPS,
STEADYSTATE_MINIMUM_DAMPING
* Initial value assignment rules now access the present value of parameters rather than their
initial value.
* Never-ending memory leak fixes in libSBML.
* Added support for global parameter rates via selections if the global parameter has a rate rule.
* Fixed atanh but on Windows.
* Fixed bug with incorrect model resetting when changing integrators.
* Fixed row/column major bug with Python API.
* python RoadRunner simulate returns (optionally) a copy of the simulation result.
-- Version 1.2.2
* Fixed bug in Python simulate method not accepting 4'th position argument in certain cases.
* Added LLVM info to version info
* Added methods to Compiler interface to get info about current JIT processor and system.
* Added support for compiling with LLVM 3.5, we now support LLVM version 3.1 - 3.5
-- Version 1.2.1
* Added models and data files from the Discrete Stochastic Models Test Suite,
https://code.google.com/p/dsmts/
to the roadrunner.testing package.
* New function in the roadrunner.testing package to enumerate testing data files.
* Clean up of SBML warning messages (thanks Lucian)
* Fixed major bug with how absolute and relative tolerances are handled (major thanks to Matthias
Koenig)
* Added support for reading values of reaction rates inside the model (identified by Matthias)
* Event status is not available as a selection, i.e. r.model["my_event_id"] will return 1 or -1
depending on whether or not the event is triggered.
* The plot method no longer tries to parse labels from SBML ids as LaTeX.
* made structuredResult behavior backward compatible (some users like the structured result).
* major revamp of the Python simulate method, it now accepts a variety of positional and named
arguments.
* fix bug when compiling with clang3.4 in c++ 11 mode (identified by Andrew Millspaugh)
* Gillespie integrator now supports fixed and variable time step mode.
* Variable time step mode fixes with deterministic solver.
-- Version 1.2.0
* Enabled mutable initial conditions when conserved moities are used, implemented Jacobian
calculation when conserved moieties are used.
* Fixed memory leaks related to how CVODE is used. With the mem leaks fixed, we leak a total of 16
bytes ONCE, in a 3rd party library in the beginning for running the entire test suite.
* Fixed bugs with stiff solver not being selected
* New getValue / setValue methods on SimulationOptions to set arbitrary settings, will be used by
future integrators.
* Prototype Gillespie stochastic integrator
* Added missing init amount method to python API
* Clean up IL code generation
* Structured result disabled by default
* New parameters in simulate and plot methods (Herbert has these, waiting on feedback),
simulate now accepts all SimulateOptions field names as keywords and has plot option,
i.e. simulate(plot=True)
* Raise exception on invalid selection strings
* Removed pointless bool return value on exception raising methods.
* All instance variables in public classes moved to private internal struct -- result is that we
can now add and remove instance variables and never break binary compatibility. Relevant to C++
users.
* Future versions may accept more complex types for configuration settings, API is set up so we
never break binary compatibility as we add new features like this.
* Continuous documentation updates and enhancements.
-- Version 1.1.0
* Config system. RoadRunner can now read and write most default configuration parameters
from / to a config file
* fixed memory leak in moiety conservation converter
* new colored logging
* Can read SBML files through HTTP on all platforms. The RoadRunner constructor
or load methods are smart in that accept a string which can be either:
a: the contents of a SBML document
b: a local file path, i.e. /home/andy/feedback.xml
c: a full URI identifier that can be either a local file or a remote file,
this can even be a BioModels identifier, i.e.
r=roadrunner.RoadRunner("http://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000275")
* upgraded to standard Poco 1.5 distribution. RoadRunner's Poco is now linked
directly to the official Poco git repository.
* lots of integrator tuning parameters are now accessible via the SimulateOptions object.
* Can run the integrator in new MULTI_STEP mode where the integrator determines
time step size.
* New SBML events -- users can register listeners for any SBML event. Whenever a
SBML event is triggered or assigned, the user can be notified.
* New integrator events -- users can register listeners for integrator events
such as when a time step completes or an event was detected.
* Significantly improved integrator error handling. Whenever CVODE encounters any
error such as numeric instability, the error is written directly to the Roadrunner
logging system with exact details about the error. Descriptive exceptions are
now raised detailing the exact source of the error.
* cleanup of integrator code.
* new distutils based python installation system. We now provide binaries for
32/64 bit Linux (Intel), 64 bit Mac OSX and 32 bit Windows.
-- Version 1.0.1
* Fixed bug where nested SBML functions were not handled properly. Now
it correctly reports when SBML functions are called with invalid
number of args.
* Fixed bug where where a log trace message incorrectly created.
* Display version info correctly in the command line rr program.
* Cache selection types and indices in model.getValue / setValue,
significant improvement in SBML symbol access times.
* Fixed memory leaks in Python API, performance improvements in
selections.
* New RoadRunner constructor which takes a URI and load options.
* Plugins moved to Tellurium project.
* Added getStateVectorRate and getStateVectorIds to ExecutableModel interface,
readily allows roadrunner to be used with external integrators.
* SBML variable access performance improvements.
-- Version 1.0.0
* Initial release