LPhy v1.5.0

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

LPhy v1.4.5

Patch release for a bug fix:

• CharSet parsing is incorrect #411

Download and move the lphy-1.4.5.jar into your lphy lib folder, such as /Applications/lphystudio-1.4.4/lib in Mac, and delete the old jar file (lphy-1.4.4.jar) and keep the rest unchanged.

LPhy v1.4.4

Bug fixes:

• cannot have a method call to itself when data clamping #405
• Linux: lphystudio script cannot resolve the working dir #408

LPhy v1.4.3

Bug fixes:

• Narrative says Pr(null|....) #385
• Correct vector index in Narrative #390
• Null Id in CompoundVectorValue when sampling #394

For Linux, we recommend unzipping the "lphy-studio-*.zip" file to the /usr/local. directory. By doing so, the launch script for LPhyBEAST will automatically detect the library path $LPHY_LIB. Alternatively, you have the option to manually assign the environment variable $LPHY_LIB to the location where LPhy Studio is installed if you choose to install it in a different directory.

LPhy v1.4.2

Documentation: https://linguaphylo.github.io/linguaPhylo/
Setup instructions: https://linguaphylo.github.io/setup/

Significant changes:

• replicates should >= 0 #350
• Merge data and model in ANTRL #357

New features and bug fixes:

• Problem for the Greek characters rendered incorrectly in Windows due to new installer #145
• Allow home directory variable to path #288
• RSV2 narrative metadataalignment #316
• Fix jekyll heading rendering in LPhy 1.4.1 reference docs #331
• RuntimeException: Expected VectorizedRandomVariable #302
• Edit value does fresh panel #307
• Windows version of slphy #323
• Update reference manual markdown files #325
• Command line slphy scripts produce ClassNotFoundException #327
• No viewer for 2d Integer array #338
• Add hyperprior example #344
• Cannot use build-in function in model #345
• Improve IID err message #346
• Document ANTLR grammar #347
• Add hyper prior model #348
• Add option in preferences for hiding toolbar #351
• Update images in manuscript figure to hide toolbar and OS specific images #352
• LPhy Studio console should default to model panel #354
• add ifelse function #358
• add product(array[]) function #360
• Array2DValue toString Exception #361
• change logical operation from BinaryOperator to BiFunction #362
• Refactor ElementWise2Args #363
• rename lphy.core.LPhyParser #368
• Add BooleanArray2DEditor #369

LPhy v1.4.1

Documentation: https://github.com/LinguaPhylo/linguaPhylo/blob/1.4.1-docs/lphy/doc/index.md
Setup instructions: https://linguaphylo.github.io/setup/

New features:

• User friendly installer #274
• Add sort function #280
• Implement Map viewer #290
• Add output to simulate function to log true values #291
• Generation of a single sequence as root sequence #296
• Add save alignment dropdown to File menu #297
• Command line simulator #301
• History buffer in console #304
• Colorblind friendly palette #305
• Create scripts for command line #308

Bug fixes and improvements:

• Improve the example scripts #218
• Improve LPhy studio menu #252
• Improve error message in constructGenerator #268
• Set working dir in unit test not working in jcCoal.lphy #269
• Gradle run not set user.dir #270
• Sampling a fraction of sites and then duplicating alignments #275
• Exception when 'round' function returned Double #276
• NullPointerException: String.startsWith(String) #277
• FileSystemNotFoundException #282
• Simulate function sample twice #283
• Sample bug to break graphical model #285
• Issues at simulate function #287
• The alignment clamped should show the clamped data, not simulated data #289
• Vertical JSplitPane's bar hangs when the studio is empty #293
• Alignment tab in LPhyStudio should not be editable #298
• Tutorial in menu is confusing #303
• Confusing narratives for PhyloCTMC #311
• Repeated the in narrative of datatypes #314
• Add license for Oracle toolbar icons #315
• Update readme with new colors #317
• Split the lphy.graphicalModel.Utils into 2 classes #324

LPhy v1.4.0

This release is supporting the lphybeast's migration to use BEAST 2.7.x.

Require Java 17. Download and unzip the Zip file, and use the following command line to launch LPhy Studio in the directory.

java -p lib -m lphystudio

Critical changes:

• Require LPhy to upgrade ANTLR to 4.11.1 #261

Bug fixes and new features:

• Upgrade JUnit version from 5.8.2 to 5.9.0 #246
• upgrade publisher of unit test results to version 2 #247
• Add Lineage-through-time plot to tree viewer #248
• [] can be removed in the label of constants #249
• Add TimeTree test #251
• LPhy studio keeps previous view in the Current tab after reloading new script #253
• Export Alignment #254
• Support counting constant sites #255
• Create lphy.graphicalModel.logger package #256
• disable build folder at root project #257
• Logging intermediate alignments #259
• Allow data clamping the alignment simulated by 2nd lphy script #260
• Move Newick parser to lphy.parser #264

LPhy v1.3.2

New LPhy doc: 1) add built-in functions, 2) categorise generative distributions and functions into few categories, 3) add links to types in the MD doc, 4) enable the extension doc to create links to lphy core types, 5) implement annotation to add descriptions for types.

https://github.com/LinguaPhylo/linguaPhylo/blob/1.3.2/lphy/doc/index.md

Completely reorganise examples, and make them easy to find by categories named as subfolders.

Critical change:

• Rename DiscreteUniform #229

Bug fixes and new features:

• Add Negative Binomial distribution #211
• BirthDeathSampling(lambda=λ, mu=0.0, rho=0.6349, rootAge=65.092); not working #224
• Remove java class for math functions e.g. abs, floor, ceil, round #226
• Improve LPhy Doc #227
• Rename PriorDistributionGenerator to ParametricDistribution #230
• Add offset to LogNormal #231
• Parser did not catch the err of having no ; #234
• probit function should be numerical implementation of the inverse error function #237
• module lphy does not export enough packages #238
• extract getGeneratorMarkdown out from Generator #239
• Add a description to the markdown of data types #240
• Allow 1-level sub-folder to organise LPhy scripts in the examples #241
• assert if any Exception in the test to run lphy examples #242
• fix the URL in the extension doc #243
• LPhy data types should be init when register extensions #244

See also https://search.maven.org/search?q=g:io.github.linguaphylo

LPhy v1.3.1

Require Java 17. The project has been migrated to a Gradle project.

Download and unzip the Zip file, and use the following command line to launch LPhy Studio in the directory.

java -p lib -m lphystudio

where -p declares your module path which includes the jar file of LPhy Studio and the lib folder under the jar file to contain all required libraries. You can replace your lib folder to a different path. -m declares the module name and it should be always "lphystudio".
If you are using any extensions, copy it into the lib folder and then launch LPhy Studio.

Alternatively launch Model Guide from the command line:

java -p lib -m lphystudio/lphystudio.app.ModelGuideApp

The available functions and models: https://github.com/LinguaPhylo/linguaPhylo/blob/1.3.1/lphy/doc/index.md

Critical change:

• H5N1 tutorial should use D_trait.canonicalStateCount() #221

Bug fixes and new features:

• Upgrade to JUnit 5 #219
• Upgrade Gradle to 7.5 #220
• add Viewer of Value<List<?>> #222

LPhy v1.3.0

Require Java 17. The project has been migrated to a Gradle project.

Download and unzip the Zip file, and use the following command line to launch LPhy Studio in the directory.

java -p lib -m lphystudio

where -p declares your module path which includes the jar file of LPhy Studio and the lib folder under the jar file to contain all required libraries. You can replace your lib folder to a different path. -m declares the module name and it should be always "lphystudio".
If you are using any extensions, copy it into the lib folder and then launch LPhy Studio.

Add two new applications in Tools menu: 1) Model Guide #184, 2) Extension Manager #159.
Alternatively launch from the command line:

java -p lib -m lphystudio/lphystudio.app.ModelGuideApp

The available functions and models: https://github.com/LinguaPhylo/linguaPhylo/blob/1.3.0/lphy/doc/index.md

Some critical changes:

• Distributions, tree priors, and samplers should share a single random generator #152
• Make LPhy command line consisting with OS default #168
• refactor package lphystudio.app #171
• IOUtils is bad name #186
• refactor package lphy.core.functions and lphy.evolution #197
• export lphystudio packages #199
• GenerativeDistribution parameters should be Number rather than Double #204
• Abstract class for prior distributions #207

Other bug fixes and new features:

• Standard data type matters #114
• wag is broken #128
• Auto-generate Jekyll markdown from LPhy scripts #130
• Better way to handle data types #136
• Special characters not showing in the embedded html in markdown #138
• the Greek characters rendered incorrectly in Windows #145
• NarrativeCreator creates null0 for taxa name #147
• should java.awt.Color be in the core? #149
• PhyloMultivariateBrownianTest failed randomly #162
• studio ClassCastException for showArgumentLabels = true #169
• Disable build caching #170
• Add about menu to show credits #173
• Always getting parser from GraphicalModelComponent #174
• Class cast exception when editing the value of SquareButton #176
• StringIndexOutOfBoundsException sanitizeDOI(String doi) #179
• Cannot add link to books #181
• reuse the exporting code to Utils #187
• Coalescent not used, but SerialCoalescent has TODO in logDensity #188
• Gradle build issue on Windows #189
• MultispeciesCoalescent is missing return type #190
• readFasta incorrect description #191
• getMenuShortcutKeyMask is deprecated #193
• The current viewer cannot show VectorizedFunction properly #196
• ErrorPanel allows no INFO before messages #200
• density() is not implemented in lphy.core.distributions.Exp #203
• Multivariate Normal distribution does not recontruct after setParam #205
• Weibull has wrong logDensity #206
• Cauchy distribution has some errors #208
• Add Geometric and Weibull distribution #209
• Apache math version conflict to BEAST 2 #215