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BEAST2-Dev / bdsky

Birth Death Serial Skyline Model for BEAST2
GNU General Public License v3.0
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BDSKY 1.3.3 release breaks backward compatibility of XML files built with previous BDSKY module versions #17

Closed gattil closed 4 years ago

gattil commented 7 years ago

XML files built with BDSKY version prior 1.3.3 generate the following error during execution.

Error 130 parsing the xml input file

nullThis BEASTInterface (BirthDeathSkySerial.t:clean_H1N1_NA) has no input with name R0. Choose one of these inputs: birthRateChangeTimes,deathRateChangeTimes,samplingRateChangeTimes,removalProbabilityChangeTimes,intervalTimes,birthRateTimesRelative,deathRateTimesRelative,samplingRateTimesRelative,reverseTimeArrays,rhoSamplingTimes,origin,originIsRootEdge,conditionOnRoot,birthRate,deathRate,samplingRate,removalProbability,rho,contemp,reproductiveNumber,becomeUninfectiousRate,samplingProportion,netDiversification,turnOver,forceRateChange,conditionOnSurvival,conditionOnRhoSampling,tree,treeIntervals

Temporary fix: manually search and replace R0 with reproductiveNumber in the XML file

tgvaughan commented 4 years ago

Wow, sorry that nobody got back to you for such a long time, Lorenzo. I don't think we should worry too much about this any more though. Backwards compatibility is important, but I think the current naming is well enough established for us not to start adding compatibility with the older naming now.