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bioDS / beast-phylonco

A BEAST2 package for single-cell cancer evolution
GNU Lesser General Public License v2.1
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Migrate to LPhy 1.3.1 and LPhyBeast 0.4.2 #29

Closed walterxie closed 2 years ago

walterxie commented 2 years ago

LPhy 1.3.0 is a major update: https://github.com/LinguaPhylo/linguaPhylo/releases/tag/1.3.0

LPhyBeast 0.4.1 has less BEAST2 packages to depend on: https://github.com/LinguaPhylo/LPhyBeast/releases

Update to LPhy 1.3.1 and LPhyBeast 0.4.2

walterxie commented 2 years ago

all tests are passed

kche309 commented 2 years ago

Hi @walterxie I'm getting an error when running the LPhy script https://github.com/bioDS/beast-phylonco/blob/lphy1.3/phylonco-lphy/examples/simpleRelaxedError.lphy using gradle task runLPhyStudio from the lphy1.3 branch.

Could you help me check whether this script works from your end? 

lphy.parser.ParserUtils constructGenerator
SEVERE: Parsing generator GT16ErrorModel failed.
lphy.parser.ParserUtils constructGenerator
SEVERE: Parsing generator GT16ErrorModel failed.
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: Cannot invoke "lphy.graphicalModel.Generator.setInput(String, lphy.graphicalModel.Value)" because "generator" is null
    at lphy@1.3.0/lphy.parser.SimulatorListenerImpl$SimulatorASTVisitor.visitDistribution(SimulatorListenerImpl.java:557)
    at lphy@1.3.0/lphy.parser.SimulatorParser$DistributionContext.accept(SimulatorParser.java:1256)
    at org.antlr.antlr4.runtime@4.9.3/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visit(AbstractParseTreeVisitor.java:18)
    at lphy@1.3.0/lphy.parser.SimulatorListenerImpl$SimulatorASTVisitor.visitStoch_relation(SimulatorListenerImpl.java:191)
    at lphy@1.3.0/lphy.parser.SimulatorListenerImpl$SimulatorASTVisitor.visitStoch_relation(SimulatorListenerImpl.java:67)
    at lphy@1.3.0/lphy.parser.SimulatorParser$Stoch_relationContext.accept(SimulatorParser.java:607)
    at org.antlr.antlr4.runtime@4.9.3/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
    at lphy@1.3.0/lphy.parser.SimulatorBaseVisitor.visitRelation(SimulatorBaseVisitor.java:41)
    at lphy@1.3.0/lphy.parser.SimulatorParser$RelationContext.accept(SimulatorParser.java:324)
    at org.antlr.antlr4.runtime@4.9.3/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
    at lphy@1.3.0/lphy.parser.SimulatorBaseVisitor.visitRelation_list(SimulatorBaseVisitor.java:34)
    at lphy@1.3.0/lphy.parser.SimulatorParser$Relation_listContext.accept(SimulatorParser.java:240)
    at org.antlr.antlr4.runtime@4.9.3/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visitChildren(AbstractParseTreeVisitor.java:46)
    at lphy@1.3.0/lphy.parser.SimulatorBaseVisitor.visitInput(SimulatorBaseVisitor.java:20)
    at lphy@1.3.0/lphy.parser.SimulatorParser$InputContext.accept(SimulatorParser.java:131)
    at org.antlr.antlr4.runtime@4.9.3/org.antlr.v4.runtime.tree.AbstractParseTreeVisitor.visit(AbstractParseTreeVisitor.java:18)
    at lphy@1.3.0/lphy.parser.SimulatorListenerImpl.parse(SimulatorListenerImpl.java:928)
    at lphy@1.3.0/lphy.parser.REPL.parse(REPL.java:102)
    at lphy@1.3.0/lphy.core.GraphicalLPhyParser.parse(GraphicalLPhyParser.java:53)
    at lphystudio@1.3.0/lphystudio.app.graphicalmodelpanel.GraphicalModelInterpreter.interpretInput(GraphicalModelInterpreter.java:230)
    at lphystudio@1.3.0/lphystudio.app.graphicalmodelpanel.GraphicalModelPanel.source(GraphicalModelPanel.java:199)
    at lphystudio@1.3.0/lphystudio.app.Utils.readFile(Utils.java:130)
    at lphystudio@1.3.0/lphystudio.app.Utils.readFileFromDir(Utils.java:104)
...
walterxie commented 2 years ago

No problem in my IntelliJ, can you check if your libs were updated? If not, follow https://github.com/LinguaPhylo/LPhyBeast/blob/master/DEV_NOTE.md to update your dependencies' local repo.

Screen Shot 2022-08-08 at 10 14 35 AM
walterxie commented 2 years ago
Screen Shot 2022-08-08 at 10 17 59 AM Screen Shot 2022-08-08 at 10 18 31 AM
kche309 commented 2 years ago

Tested LPhy v1.3.1 compatible version on Intellij. Pull request looks good to merge.