v2.8.0

• Update to use latest Python
• Update to use numpy 2
• Fix memory leaks in auto2000 plugin
• Fix calculation of Jacobian for models with differently-sized compartments.

v2.7.0: Merge pull request #1217 from sys-bio/develop

Bugfix release: Save/load state now works across roadrunner instances on mac and linux.

binary files for macOS 12 x86_64 are added as macOS 11 is no longer supported on GitHub Actions

v2.6.0

Updates:

• The seed for both the gillespie integrator and for 'distrib' constructs is now synchronized and settable from r.setSeed(val) and from the global configuration options (Config.setValue(Config.RANDOM_SEED, val)
• The SBML L3v2 'rateOf' function is now implemented.
• That seed value may be extremely large (larger than the previous erroneous 'int' cutoff; limit is now uint64).
• The 'times' input vector for simulation runs has been upgraded:
  • It may now contain numpy ints.
  • It may contain repeated values (after the initial value) (useful when comparing output to collected data with replicates)
• Piecewise functions are now much more robustly handled, with explicit root-finding for the moments when the function switches from one output to another.
• The python 'setValues' command may now take a dictionary as input, instead of separate 'keys' and 'values' arguments.

Bugfixes:

• The gillespie integrator is now initialized with a time-based random seed (in microseconds) instead of the same one every run.
• Gillespie simulations no longer run on models with rate rules, instead of silently ignoring them.
• Gillespie simulations warn for runs with 'time' in event triggers or with event delays.

v2.5.0

Various updates and bugfixes, including:

• Removed ncurses dependency
• Refuse to read models with elements roadrunner cannot interpret (algebraic rules, unknown packages)
• Reset the conservedMoietyAnalysis flag to its previous state after running a steady state analysis.
• Improve named stoichiometry interpretation and setting, and allow setting of arbitrary stoichiometries.
• Fix handling of some reactions in the gillespie integrator (#1135)
• Allow setting init(x) when x has an initial assignment. (#1137)
• getCurrentSBML no longer exports incorrect initial assignments. (#1138)
• getValue('time') now returns the actual current time (#1142)
• The steady state selection vector now doesn't change once set (#1148)
• New 'fluxThreshold' setting for when to zero out flux control coefficients (#1150)

v2.4.0

BEHAVIOR CHANGE: This version of roadrunner now treats the 'absolute tolerance' setting for CVODE simulation differently! We now treat the absolute tolerance the same way that COPASI does.

• If set to a scalar value (the default), that value is now transformed into a vector internally by multiplying the scalar by every value in the state vector. This allows automatic scaling between concentrations and amounts: a small compartment will no longer require an equally-small absolute tolerance value to be set.
  • However, if the value in the state vector is zero, the corresponding value in the absolute tolerance vector is either used as-is, or, if the value is from a species in a non-zero compartment, multiplied by that compartment volume.

The documentation was updated to reflect this, and a few other inaccuracies in the documentation were also fixed.

v2.3.2

Bug fix and potential bugfix release:

• Level 2 events no longer can fire at t0.
• It's possible that we've future-proofed roadrunner against numpy updates.

v2.3.1

Updates mostly for new platforms and dependencies:

• Release for Python 3.11 on all platforms.
• Release for Numpy 1.24.1 on all platforms.

Releases for the Mac ARM/M1 chip require MacOS 13 (Ventura).

v2.2.4

Minor updates with bugfixes:

• Now works with latest version of jinja2
• SED-ML models that reference other models now work.
• Update requirements.

v2.2.2

Maintenance update. Includes:

• Releases for Python 3.10
• Documentation updated
• Fix C API function getStoichiometryMatrix
• Fix C API functions dealing with rates of change.
• Fix calculating elasticities when time explicitly included in reaction rate. (#1020)
• New functions for getting the dependent and independent floating species. Also, make this independent of analysis type.
• Update to use latest libsbml, and switch to using libexpat instead of libxml2.
• When scaling control coefficients, set to zero when scaled reaction rate is itself zero. (#1031)

v2.2.1

This release includes a variety of updates and bugfixes, including:

• Official Python 3.10 releases
• Create universal binaries on MacOS so M1 chip computers are handled.
• Various fixes to get more of the SBML Test Suite to pass.
• Bug fix to handle situation where a species concentration and its compartment's size both change at the same time.
• Handle setting/getting of UCC values better.
• Fix bug in rr-libstruct
• Fix python bug when writing simulation results to file
• Fix MCJit bug when copying model
• Synchronized getting rate values and rate labels.
• Reduce default diffStepSize, and add C interface to allow setting it.