NEWS.md

In jpahle/CoRC: COPASI R Connector

CoRC 0.12.0 (2023-03-12)

• Added support for macOS on ARM (aarch64)

• Rebased on COPASI release 4.39 sources.

Included a further fix to prevent a crashing bug in this version of COPASI

• Switched to using manylinux 2014 (up from 2010) for compilation of linux binaries

CoRC 0.11.1 (2023-01-22)

• Fixed errors due to breaking changes in package dependency 'stringr' version 1.5.0.

• Minor changes to keep up with function deprecations in tidyverse packages.

• Minor upgrades.

CoRC 0.11.0 (2021-08-30)

• Rebased on COPASI release 4.34 sources.

• Enabled the COPASI just in time compilation that was added in version 4.30.

• Enabled setting event assignment_target to model properties such as 'Time'.

This can be useful e.g. for stopping timecourses after an event, like the runaway accumulation of a model species, which could trigger an error for stochastic simulation due to 'Internal step limit exceeded'. Such an event can be created like so:

newEvent(name = "abort", trigger_expression = "{Prey.ParticleNumber} > 1e5", assignment_target = "Time", assignment_expression = 1e9).

• Fixed a regression where NaN in experimental data was lost and converted to NA.

It is now correctly exported to the '.txt' experimental data. This matters because COPASI handles NaN differently than NA.

• Minor fixes and code cleanups.

CoRC 0.10.0 (2021-04-29)

• Rebased on COPASI release 4.30 sources.

Disabled JIT compilation for now as it seems to cause crashes.

• Implemented the download of COPASI platform specific libraries during package installation.

This makes getCopasi() obsolete. The function has been deprecated.

Package installation now requires an internet connection by default, which can be circumvented by providing the correct libraries locally with the COPASI_LIB_PATH environment variable. One option to set this variable is with the configure.vars argument of install.packages().

• Added support for working with weights in experimental data of the parameter estimation task.

defineExperiments() has new parameters weights and normalize_weights_per_experiment.

• Fixed a bug in setSpecies() where adjusting species initial concentration in conjunction with species type always defaulted to a initial concentration of 0.

• Various internal adjustments according to R CMD check notes and warnings.

• Minor additions for package stability tests.

CoRC 0.9.0 (2020-11-23)

• Fixed a major issue with addExperiments(), where some experimental data was lost or misassigned.

addExperiments() is also used by runParameterEstimation() and setParameterEstimationSettings().

• Deprecated the name parameter of setParameters().

Renaming parameters on a per reaction basis is not supported by COPASI.

• Improved consistency of fetching of models from URLs.
• Adjusted for new BioModels URL scheme.

Added biomodels_url() helper function to assist with generating URLs where desirable.

• Added support for Combine archives via loadCombineArchive() and saveCombineArchive().
• Minor fixes and code cleanups.

CoRC 0.8.0 (2020-06-25)

• Rebase on COPASI release 4.28 sources.
• Add support for the time course automatic interval option.
• Fix definition of experimental data with columns of type 'ignore'.
• Fix runParameterEstimation() output, in some cases, listing incorrect parameter start values.
• Minor fixes and code cleanups.

CoRC 0.7.1 (2020-05-24)

• Hotfix for windows build having an incorrect COPASI Version annotation.

The COPASI version was incorrectly reported to be 4.12.

CoRC 0.7.0 (2020-05-22)

• Fix system compatility with various linux distros.

CoRC used to crash on various untested linux distros. Compatibility has now been confirmed with Ubuntu (16.04, 18.04, 20.04), CentOS (6, 7, 8), and Fedora (30, 32).

• Use 'readr' package for write out of experimental data, to prevent erroneous conversion of NaN to NA.
• Fix behaviour of autoplot.copasi_ts() function when a timeseries output named 'Time' exists.

'Time' output used to confilict with the invariant time column.

• Rework tidyverse dependencies to be more light weight.
• Minor fixes and code cleanups.

CoRC 0.6.1 (2019-10-24)

• Remove an undocumented dependency on a Visual Studio runtime on windows.

CoRC 0.6.0 (2019-10-06)

• Rebase on COPASI release 4.27 sources.
• Require at least R version 3.2.0.
• Base the linux binaries on the manylinux2010 docker container.
• Add parameter soft_error to runTimeCourse() to allow for readout of incomplete result tables for failed time courses.

CoRC 0.5.0 (2019-04-05)

• Rebase on COPASI release 4.25 sources.
• Add a preserve_concentrations argument to setCompartments() to preserve species concentrations instead of particle numbers on adjustment of compartment sizes.
• Fix a bug where clearing initial expressions in setter functions prevented them from adjusting initial values.
• Enable for getCopasi() to fall back on github as a download mirror.
• Minor fixes and code cleanups.

CoRC 0.4.0 (2018-08-01)

• Rebase on COPASI release 4.24 sources.
• Fix sigma point method for cases other than two dependent variables.
• Use parallel::parLapplyLB() for parallel processing as it was fixed in R version 3.5.
• Minor fixes and code cleanups.

CoRC 0.3.0 (2018-04-19)

• Rebase on COPASI release 4.23 sources.
• Prepare for R version 3.5.
• Add unit system.
• Allow NaN, Inf and -Inf for many values.
• Add getVersion() for retrieving the version of the COPASI backend.

CoRC 0.2.1 (2018-03-01)

• Breaking: Rename first argument of newReaction() from scheme to reaction.
• Rebase on latest COPASI 4.23 sources.
  • Fixes rare crashes.
• Minor fixes.

CoRC 0.2.0 (2018-02-19)

• Rebase on latest COPASI development sources.
• Add functions to handle SBML models as strings (loadSBMLFromString(), saveSBMLToString()).
• Allow for currently running tasks to be terminated interactively (issue #3).
• Fix loadSBML function failing for local files.
• Fix installation on UNIX systems.
• Minor fixes and improvements.

CoRC 0.1.0 (2017-12-04)

• Rebase on latest COPASI development sources.
• Add model event functioniality (event(), event_strict(), getEvents(), setEvents(), newEvent(), deleteEvent()).
• The package now generally uses "" instead of NA to denote unset or empty expressions.
• Allow expressions to be automatically coerced from finite numeric and logical values. E.g. getValue(1) instead of getValue("1").
• Fix crashes on entity deletion. Deletion functions now delete recursively.
• Generally warn if model fails to compile.
• Fix errors with argument type of setCompartments() and setGlobalQuantities().
• Use new Copasi XML parser.

CoRC 0.0.1 (2017-11-15)

• Initial public beta release

jpahle/CoRC documentation built on May 5, 2024, 11:54 p.m.