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