Releases: SysBioChalmers/RAVEN
Releases · SysBioChalmers/RAVEN
v2.9.3
- fix:
ravenCobraWrapper
handle empty rxnReferences from COBRA => RAVENreplaceMets
should not contract the whole model, only for the replaced metabolitesgetBlast
can handle paths containing spaces, or makes a custom temp path if required (solves #506)importModel
with empty confidenceScores entriesconstructS
avoid warning about "Colon operands must be real scalars"randomSampling
should output the solutions as full matrix, as sparse matrices occassionally acts weird when using functions likemean
- feature:
getIndexes
supportsecenzymes
,ecrxns
andecgenes
types, to query GECKO3model.ec
fields
- refactor:
- speedup
readYAMLmodel
- speedup
- docs
- update badges and refer to GitHub Discussions instead of Gitter
v2.9.2
v2.9.1
- refactor:
- when running a unit test and a solver is not installed, report the absence of the solver, not the general failing of the test
- fix:
- prevent
glpk
timeout when running selected large FBA calculations - avoid an error when running
solveLP
in parallel and COBRA toolbox is not installed getAllowedBounds
returned inconsistent results when running parallelization⚠️ various changes in relation tosolveLP
swapping the sign of reported objective function (sol.f
), as already announced with RAVEN release 2.7.12, but not actually done at that point- ensure that RAVEN provided libSBML binaries are used, by using unique filenames
removeMets
also considersmetNotes
field if availablesetParam
error message if incorrect paramType is specified
- prevent
- feat:
checkInstallation
reports how RAVEN was installed, as described in the Wiki
- doc:
- minor changes in formatting of function documentation
v2.9.0
- chore:
- update libSBML to version 5.20.2, now including support for Apple Silicon .mexmaca64. The macOS Intel .mexmaci64 is kept at version 5.19.0, as the required compiled mex file is not included in the 5.20.2 release.
- add .mexmaca64 glpk binary for Apple Silicon.
- fix:
simplifyModel
with irreversible backwards-only reactions (solves #529)writeYAMLmodel
do not write lines with empty entries (e.g. reactions without subsystems)getModelFromKEGG
includesmodel.annotation.defaultLB
andmodel.annotation.defaultUB
fieldsgetGenesFromGrRules
can handle genes with '|'getModelFromHomology
remove geneFrom field (solves #533)getMinNrFluxes
reduce default verbositywriteYAMLmodel
allow empty id and name fields, in line with https://github.com/SysBioChalmers/RAVEN/wiki/RAVEN-Model-StructureravenCobraWrapper
prefers to use grRules in COBRA models if present (solves GECKO issue #367)optimizeProb
will throw error when trying to solve MILP with glpk (also if glpk is set via cobra)writeYAMLmodel
will throw an informative error if it cannot write the file to the intended directorymapCompartments
correct horizontal concatenation of cell arraycheckInstallation
during first installation on unix machines,makeBinaryExecutables
threw an error.importModel
correctly parses SBML file that has some missing SBO terms
- feat:
randomSampling
can run in parallel with MATLAB Parallel Computing Toolbox installedsetParam
has an additional option, 'unc' if a reaction's lower and upper bound should be set as unconstrained. If available, this will use the default bounds inmodel.annotation
(otherwise [-1000, 1000]), and considers reversibility (in which case lower bound = 0)- auxiliary
parallelPoolRAVEN
function to check if function should be running in parallel - use alternative ProgressBar, particularly in functions containing
parfor
calls - give execution rights in Terminal for new RAVEN functions
- refactor:
- remove mentions to soplex (which has been replaced by scip).
- avoid cmd windows output by
parallelPoolRaven
. - allow
randomSampling
withnsamples
set to 0, to only getgoodRxns
.
v2.8.7
- fix:
ftINIT
could have removed metabolites that are required for specific tasks.importModel
allows SBML without a specified objective function (this is not valid SBML, but will be tolerated).- Swap
soplex
withscip
as solver. Thesoplex
option introduced in release 2.8.5 should not be used for MILP,scip
is dedicated for these problems. Precompiled binaries for Windows are provided (downloaded upon request), further installation instructions are mentioned in the Wiki. ravenCobraWrapper
properly makescomps
andcompNames
fields when lacking in COBRA model.writeYAMLmodel
can deal with mixture of nested and not-nested cell arrays of subsystems (as COBRA models can have).extractMiriam
should allow cell array of multiple miriamNames as input.checkInstallation
correctly makes binaries executable on Ubuntu (solves #527)
- refactor:
- Reduce the default verbosity and number of messages to the command window for a few functions.
v2.8.6
v2.8.5
- feat:
- Distribute SoPlex binary for Windows with RAVEN, as another open-source alternative, slower than glpk, but suitable for MILP. Installation instructions are updated.
readYAMLmodel
should always make model.c-field, even if no objective function is specified (solves #509).standardizeGrRules
should throw error if no grRules field is found.
- refactor:
addRxnsGenesMets
more detailed error message if reactions cannot be found.getAllowedBounds
use progressbar for reporting status.
v2.8.4
- feat:
metDeltaG
andrxnDeltaG
fields, I/O via YAML. (solves #280)getAllowedBounds
has optional runParallel-flag, true by default.
- fix:
parseScores
andpredictLocalization
handling of data from DeepLoc 2.0. (solves #310)randomSampling
check feasibility after changing bounds to (-)Inf, as suggested in #438.checkModelStruct
no longer checks for duplicate metSmiles with different metabolite names, as it often occurs that these canonical SMILES are non-unique due to e.g. stereochemistry.
v2.8.3
-
fix:
checkFunctionUniqueness
on Mac/Unix with non-RAVEN paths.checkInstallation
findprintOrange
on new RAVEN installations (closes #492).readYAMLmodel
allows for a model that has gene entries that are not present in any grRules: these are unused genes and should be allowed. This also prevents a bug where gene annotations are wrongly assigned.writeYAMLmodel
correct parsing of text to avoid escape characters (e.g. SMILES may contain \C).importModel
assigns -Inf and Inf if no LB and/or UB values are defined.ravenCobraWrapper
makes empty model.c if COBRA model had noc
field (is not necessarily made by readCbModel)
-
feat:
keggPhylDist.mat
includes species names.getMetaCycModelForOrganism
input and output of blastStructure (before cutoffs applied), so that function can repeatedly be run with different cutoffs without having to rerun blast/diamond.
v2.8.2
- fix:
readYAMLmodel
also reads metNotes fieldsgetMetaCycModelForOrganism
handling of large genomes
- feat:
analyzeSampling
no longer requires MATLAB Stats Toolbox- detailed error message if MATLAB Text Analytics Toolbox is installed (see #55)
checkInstallation
has option to only report RAVEN version as outputprogressbar
distributed, will be used to report progress of various functionscheckFunctionUniqueness
can also take alternative set of paths as input, for use by other toolboxes