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LPhy v1.6.0
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@walterxie walterxie released this 19 Sep 02:27
· 75 commits to master since this release
1.6.0
dadb379

The project has been transitioned to use Maven, which can automatically set up the IntelliJ project.

The command line to start the studio: YOUR_PATH/bin/lphystudio

Significant changes:

  • Re-run model block code if data block updated. #66
  • Console cannot recognise existing variables #183
  • Extract vectorMatch from ParserUtils #364
  • Make Viewer extendable #453
  • Make sure sample() method is only called by 3 scenarios: #473
  • Change to setup IntelliJ as Maven project #498
  • An option to choose resampling to go through parser #503
  • DiscretizeGamma needs to renormalise category rates #514

New features and bug fixes:

  • Improve studio GUI layout #273
  • Use ParameterNames to collect some frequently used parameter names #281
  • suppress unnamed argument in graphic model #370
  • Cannot find the sequence type in SequenceTypeLoader in the integration test #397
  • readTree function #419
  • GUI is stuck with large alignment #434
  • simulate method should not log #443
  • ReadFasta needs to guess sequence types #445
  • Parser bug to handle the vector containing variables #447
  • The static method to import an alignment in a fasta format from reader #448
  • Generic the Table column #449
  • ValueCreator cannot handle List #452
  • It should have a default ValueFormatter instead of throwing Exception #455
  • Unit test getOldestNode() #460
  • Implement LocalClock for FLC #461
  • LPhy argument matching does not handle the array of objects #464
  • Sample method called twice #468
  • Trees from 'readTrees' Cannot Apply in PhyloCTMC #469
  • Add a New Object TimeTreeBranch #470
  • Change Exponential growth function name #471
  • Implement SampleBranch Distribution #472
  • Implement SubstituteClade Function #475
  • Improve GuessType in ReadDelim #476
  • Lphy script throw "Row names 0 must be same to the sample count 1 !" error after pressing Sample button #477
  • some GenerativeDistribution missing setParam #478
  • Improve ValueEditor in studio #479
  • Some leaf nodes are not considered as leaf nodes in getInternalNodes() #481
  • implement setUnion function #482
  • merge popFunc viewer #483
  • IllegalArgumentException in sampler #485
  • implement SubsampledTree function #489
  • implement MRCA function #490
  • let PhyloCTMC use branch rates from tree if not given #491
  • Resample birthDeathOnRootAgeAndTaxa.lphy and birthDeathRhoSampling.lphy fail randomly #492
  • setParam should throw Exception #493
  • implement labelClade function #494
  • save metaData for internal nodes when writing Newick tree #495
  • Unit tests throw NoClassDefFoundError while running #500
  • Add constant popSize #501
  • ReadFasta can accept not aligned sequences fasta file and throw out of index error #507
  • Method call for Table #508
  • After loading a script, the data and model panel does not show the code #510
  • correct implementation of Sequence #511
  • move setState to TaxaCharacterMatrix #512
  • make TaxaCharacterMatrix loggable #517
  • Log internal node sequences #518
  • Save files to directory #519
  • Broken links in README.md file. #520
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