Releases: LinguaPhylo/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:
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
LPhy v1.2.0
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.
The available functions and models: https://github.com/LinguaPhylo/linguaPhylo/blob/1.2.0/lphy/doc/index.md
LPhy v1.1.0
Require Java 16. 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.
The available functions and models: https://github.com/LinguaPhylo/linguaPhylo/blob/1.1.0/lphy/doc/index.md
- GenerateDocs not working from IntelliJ after migrating to Gradle #166
- Gradle auto-generated script not working after setting main module #165
- fix errors to generate Javadoc #163
- Get version from a gradle build to be included in runtime Swing application #161
- Node count function produces Exception duplicate #160
- GenerateDocs for lphy extensions documentation #158
- remove unused lib "batik" dependencies #157
LPhy v1.0.0
Require Java 16. Enable the extension mechanism for LPhy #146 using the latest technology known as the Java Platform Module System (JPMS) :
Use the following command line to launch LPhy Studio.
java -p lib:lphy-studio-1.0.0.jar -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.
The available functions and models: https://github.com/LinguaPhylo/linguaPhylo/blob/1.0.0/LPhy/doc/index.md
LPhy v0.0.5
Setup https://linguaphylo.github.io/setup/ and About LPhy https://linguaphylo.github.io/about/
The available functions and models can be https://github.com/LinguaPhylo/linguaPhylo/blob/0.0.5/doc/index.md
Fixed bugs:
LPhy v0.0.4
The available functions and models can be https://github.com/LinguaPhylo/linguaPhylo/blob/0.0.4/doc/index.md
Make the data type as the compulsory input of PhyloCTMC, if not given, then use the nucleotide data type (default).
CMD using the absolute path:
java -jar LPhy.v0.0.4.jar ~/WorkSpace/linguaPhylo/tutorials/RSV2.lphy
CMD using the relative path:
cd ~/WorkSpace/linguaPhylo/tutorials/
java -jar $JAR_PATH/LPhy.v0.0.4.jar RSV2.lphy
The data is in ~/WorkSpace/linguaPhylo/tutorials/data/RSV2.nex.
LPhy v0.0.3
The available functions and models can be https://github.com/LinguaPhylo/linguaPhylo/blob/0.0.3/doc/index.md
Important change to handle the relative path:
Every time after loading a script file, LPhy Studio will set user.dir to the folder containing this file. This folder will be used as the reference when the data path inside the scrips is a relative path. So, for a LPhy script, the relative path is always referring to the folder where it is. Then the data can be easily organized with the scripts together. Please see https://github.com/LinguaPhylo/linguaPhylo/blob/0.0.3/tutorials/RSV2.lphy and https://github.com/LinguaPhylo/linguaPhylo/blob/0.0.3/examples/fullDataExample.lphy, etc.
CMD using the absolute path:
java -jar LPhy.v0.0.3.jar ~/WorkSpace/linguaPhylo/tutorials/RSV2.lphy
CMD using the relative path:
cd ~/WorkSpace/linguaPhylo/tutorials/
java -jar $JAR_PATH/LPhy.v0.0.3.jar RSV2.lphy
The data is in ~/WorkSpace/linguaPhylo/tutorials/data/RSV2.nex.
LPhy v0.0.2
The available functions and models can be https://github.com/LinguaPhylo/linguaPhylo/blob/0.0.2/doc/index.md
Add an optional argument for a LPhy script file name to LinguaPhylo Studio java -jar LPhy.v0.0.2.jar tutorials/RSV2.lphy
This version includes scripts for 4 LPhy BEAST tutorials:
- Time-stamped data tutorial
- Skyline plots
- Structured coalescent
- Discrete phylogeography
LPhy v0.0.1
Use command line to run LinguaPhylo Studio java -jar LPhy.v?.?.?.jar