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LPhy v1.5.0
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@walterxie walterxie released this 31 Jan 20:55
· 398 commits to master since this release
1.5.0
334cb56

New command line for SLPhy to replace values in a lphy script using Macro language:

YOUR_PATH/slphy -D 'n=5;L=50' MacroLanguage.lphy

Significant changes:

  • Refactor the core and split function and distribution to base #294
  • Improve parser grammar and the implementation of LPhyMetaParser #372
  • Untangle cyclic dependencies #384
  • Refactoring and merge SPI and Loaders #400
  • Introduce macro language to lphy script #420
  • new interface for writing values to a file #437

New features and bug fixes:

  • Data clamping needs more work #284
  • ReadDelim function #409
  • removeTaxa function #412
  • LPhy doc not show parameters are optional #413
  • ElementWise2ArgsTest.test1DPlus2D test should not look for lphy.base.spi.LPhyBaseImpl #414
  • Creating taxa and set dates from TableValue returned by readDelim #415
  • SpeciesTaxa has wrong view in studio #418
  • codeString bug for taxa(names=1:n) #421
  • SLPhy script not working #422
  • The position of replicates is incorrectly changed after the script is rendered #423
  • Register the missing functions in the core #424
  • GeneratorInfo annotation is not found #425
  • Exception when loading example jcCoal.lphy #427
  • The module not loading properly in the Gradle tests after splitting core and base #428
  • Improve the simulator code #429
  • move CanonicalCodeBuilder to the core #430
  • LPhyValueFormatter SPI not working in LPhyBEAST #431
  • OutputSystem bug FileNotFoundException #432
  • Recover unit test after significant change in SPI #435
  • Add SLPhy command argument to specify which random var(s) not logged #438
  • IID RuntimeException for Expected VectorizedRandomVariable after data clamping #441
  • OutputSystem bug to handle the output dir #442
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