LinguaPhylo/LPhyBeast issues and pull requests

#110 - Release 1.0.1

Issue - State: open - Opened by walterxie over 1 year ago

#109 - Update all operators to BEAST 2.7.x

Issue - State: open - Opened by walterxie almost 2 years ago
Labels: enhancement

#108 - LPhyBEAST release dependency description incorrect

Issue - State: closed - Opened by kche309 almost 2 years ago
Labels: documentation

#107 - Command line arguments cannot take names containing spaces

Issue - State: open - Opened by walterxie almost 2 years ago
Labels: bug

#106 - BEAST new loader not working in GitHub

Issue - State: open - Opened by walterxie almost 2 years ago
Labels: bug

#105 - Log all intermediate alignments

Issue - State: closed - Opened by walterxie almost 2 years ago
Labels: enhancement

#104 - Command line args do not behaviour properly when using relative paths

Issue - State: open - Opened by walterxie almost 2 years ago - 1 comment
Labels: bug

#103 - Alignment editor

Issue - State: open - Opened by walterxie almost 2 years ago
Labels: enhancement

#102 - Release 1.0.0

Issue - State: closed - Opened by walterxie almost 2 years ago

#101 - NoClassDefFoundError: groovy.lang.Closure

Issue - State: closed - Opened by walterxie about 2 years ago - 2 comments
Labels: bug

#100 - B2.7

Pull Request - State: closed - Opened by walterxie about 2 years ago

#99 - B2.7

Pull Request - State: closed - Opened by walterxie about 2 years ago

#98 - Migrate to beast 2.7

Issue - State: closed - Opened by walterxie about 2 years ago - 1 comment
Labels: enhancement

#97 - Use LPhyBeastConfig to contain all settings

Issue - State: closed - Opened by walterxie about 2 years ago
Labels: enhancement

#96 - simulate alignment from the 2nd lphy script

Issue - State: closed - Opened by walterxie about 2 years ago - 3 comments
Labels: enhancement

#95 - Create LPhyBeastConfig to contain all settings

Issue - State: closed - Opened by walterxie about 2 years ago - 1 comment
Labels: duplicate, enhancement

#94 - Add lphy script to the top of XML

Issue - State: open - Opened by walterxie about 2 years ago
Labels: enhancement

#93 - specify the right size for SubtreeSlide

Issue - State: open - Opened by walterxie over 2 years ago - 2 comments
Labels: enhancement

#92 - LPhyBEAST wraps the execution of BEAST

Issue - State: open - Opened by walterxie over 2 years ago
Labels: enhancement

#91 - phyloCTMC.getQ() => phyloCTMC.getQValue()

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: enhancement

#90 - Should use getAsRealParameter()

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: bug

#89 - Compress constants sites from the original alignment

Issue - State: open - Opened by walterxie over 2 years ago - 1 comment
Labels: enhancement

#88 - general approach to convert a unicode string to an ascii string for variable names

Issue - State: open - Opened by walterxie over 2 years ago - 1 comment
Labels: enhancement

#87 - release 0.4.2

Issue - State: closed - Opened by walterxie over 2 years ago

#86 - script lphybeast finds the lphy lib

Issue - State: open - Opened by walterxie over 2 years ago
Labels: enhancement

#85 - auto set pre-burnin is skipped

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: bug

#84 - DPG TreeWithTraitLogger

Issue - State: closed - Opened by walterxie over 2 years ago - 1 comment
Labels: bug

#83 - LPhyBEASTLoader somehow adds LPhyBEASTExtImpl twice

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: bug

#82 - D_trait.treeLikelihood is missing in the parameters logger

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: bug

#81 - Missing SA operators

Issue - State: closed - Opened by walterxie over 2 years ago - 1 comment
Labels: enhancement

#80 - Convert 1-line lphy script into correct XML

Issue - State: open - Opened by walterxie over 2 years ago
Labels: enhancement

#79 - new tests

Pull Request - State: closed - Opened by walterxie over 2 years ago - 1 comment

#78 - Add tests for lphy example scripts to convert into BEAST 2 XMLs

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: enhancement

#77 - Extension mechanism for operators and loggers

Pull Request - State: closed - Opened by walterxie over 2 years ago - 1 comment

#76 - Extension mechanism for IIDToBEAST

Issue - State: open - Opened by walterxie over 2 years ago
Labels: enhancement

#75 - Extension mechanism for loggers

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: enhancement

#74 - Extension mechanism for operators

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: enhancement

#73 - Add tests for all tutorials to check if XMLs are generated

Issue - State: closed - Opened by walterxie over 2 years ago - 1 comment
Labels: enhancement

#72 - siteRates sampled from DiscretizeGamma cannot create XML

Issue - State: closed - Opened by walterxie over 2 years ago - 2 comments
Labels: bug

#71 - morphological data type not working

Issue - State: closed - Opened by walterxie over 2 years ago - 1 comment
Labels: bug

#70 - lack of information when the LPhy code cannot be converted into BEAST 2 xml

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: enhancement

#69 - bdtree not released as a BEAST2 package

Issue - State: closed - Opened by walterxie over 2 years ago - 1 comment
Labels: enhancement, wontfix

#68 - Add credits to command line launcher

Issue - State: open - Opened by walterxie over 2 years ago
Labels: enhancement

#67 - Lphy1.3

Pull Request - State: closed - Opened by walterxie over 2 years ago - 1 comment

#66 - LPhyBEASTLoader should be cached to reduce time

Issue - State: closed - Opened by walterxie over 2 years ago
Labels: enhancement

#65 - Lphy1.3

Pull Request - State: closed - Opened by walterxie over 2 years ago - 1 comment

#64 - Warnings from LPhyBEASTLoader while registering data types

Issue - State: open - Opened by walterxie almost 3 years ago - 1 comment
Labels: enhancement

#63 - GUI to launcher LPhyBEAST

Issue - State: open - Opened by walterxie almost 3 years ago - 2 comments
Labels: enhancement

#62 - Compatible to LPhy 1.3.0 and BEAST 2.6.7

Issue - State: closed - Opened by walterxie almost 3 years ago - 1 comment

#61 - lphybeast Zip creates a subfolder when PackageManager installs it

Issue - State: closed - Opened by walterxie about 3 years ago - 1 comment
Labels: bug

#60 - merge 3 places defining the version into 1

Issue - State: open - Opened by walterxie about 3 years ago
Labels: enhancement

#59 - migrate to Gradle project

Issue - State: closed - Opened by walterxie about 3 years ago
Labels: enhancement

#58 - Relaxed clock operators missing IDs

Issue - State: closed - Opened by kche309 over 3 years ago - 3 comments

#57 - Relaxed clock in development Exception

Issue - State: closed - Opened by kche309 over 3 years ago - 1 comment

#56 - Node count function produces Exception

Issue - State: closed - Opened by kche309 over 3 years ago

#55 - Fixed relaxed clock operators

Pull Request - State: closed - Opened by kche309 over 3 years ago

#54 - build broken after beast2 change the master branch to module

Issue - State: closed - Opened by walterxie over 3 years ago
Labels: bug

#53 - Turn auto optimization off for Dirichlet operators

Pull Request - State: closed - Opened by kche309 over 3 years ago - 4 comments

#52 - Convergence issue in gt16 default operator schedule

Issue - State: closed - Opened by kche309 over 3 years ago - 1 comment
Labels: wontfix

#51 - Fix exclusions list in BEASTContext

Pull Request - State: closed - Opened by kche309 over 3 years ago - 1 comment

#50 - Exclusions list for plugins not working

Issue - State: closed - Opened by kche309 over 3 years ago
Labels: bug

#49 - add WeightedDirichlet prior

Issue - State: closed - Opened by walterxie over 3 years ago - 2 comments
Labels: enhancement

#48 - Switch to use beast.core.util.Slice

Issue - State: closed - Opened by walterxie over 3 years ago
Labels: bug, enhancement

#47 - make true log and tress at the same format with BEAST for multiple simulations

Issue - State: closed - Opened by walterxie over 3 years ago - 3 comments

#46 - log tree length

Issue - State: closed - Opened by walterxie over 3 years ago
Labels: enhancement

#45 - remove outercore from the dependencies

Issue - State: closed - Opened by walterxie over 3 years ago
Labels: enhancement

#44 - split LPhyBeast to core and ext

Issue - State: closed - Opened by walterxie over 3 years ago - 10 comments
Labels: enhancement

#43 - Class.newInstance() is deprecated

Issue - State: closed - Opened by walterxie over 3 years ago - 1 comment
Labels: enhancement

#42 - move createKeyParameter together with create***Parameter

Issue - State: closed - Opened by walterxie over 3 years ago - 1 comment
Labels: enhancement

#41 - Bayesian Skyline SkylineToBSP is broken

Issue - State: closed - Opened by walterxie over 3 years ago - 1 comment
Labels: bug

#40 - extension mechanism for LPhyBEAST to adapt with LPhy

Issue - State: closed - Opened by walterxie over 3 years ago - 6 comments
Labels: enhancement

#39 - Example of GT16 with Err model

Issue - State: closed - Opened by walterxie over 3 years ago
Labels: enhancement

#38 - Example for *BEAST2

Issue - State: open - Opened by walterxie almost 4 years ago
Labels: enhancement

#37 - Example for bModelTest

Issue - State: open - Opened by walterxie almost 4 years ago
Labels: enhancement

#36 - handle absolute path to lphy script.

Issue - State: closed - Opened by bredelings almost 4 years ago - 6 comments
Labels: bug

#35 - add working dir to command line args

Issue - State: closed - Opened by walterxie almost 4 years ago - 2 comments
Labels: enhancement

#34 - create BEASTFactory

Issue - State: closed - Opened by walterxie almost 4 years ago
Labels: enhancement

#33 - Skyline pop size index has to be same as group size

Issue - State: closed - Opened by walterxie almost 4 years ago - 2 comments
Labels: bug

#32 - beast.math.distributions.Gamma has no input with name 'shape'

Issue - State: closed - Opened by walterxie about 4 years ago
Labels: bug

#31 - Initialisation issue in DPG XML because of trait rate indicators

Issue - State: closed - Opened by walterxie about 4 years ago
Labels: bug

#30 - VectorizedFunctionToBEAST IllegalArgumentException

Issue - State: closed - Opened by walterxie about 4 years ago
Labels: bug

#29 - Implement discrete phylogeography

Issue - State: closed - Opened by walterxie about 4 years ago - 7 comments
Labels: enhancement

#28 - Add ExpMultiToBEAST

Issue - State: closed - Opened by walterxie about 4 years ago
Labels: enhancement

#27 - Trait "age" bug in BEAST core

Issue - State: closed - Opened by walterxie about 4 years ago
Labels: bug

#26 - Mascot logs beast.mascot.dynamics.Constant

Issue - State: closed - Opened by walterxie about 4 years ago - 2 comments
Labels: bug

#25 - StructuredCoalescent: metadata name is number

Issue - State: closed - Opened by walterxie about 4 years ago - 7 comments
Labels: bug

#24 - add StructuredTreeLogger for MASCOT

Issue - State: closed - Opened by walterxie about 4 years ago
Labels: enhancement

#23 - make LPhyBEAST as a BEAST 2 package

Issue - State: closed - Opened by walterxie about 4 years ago - 3 comments
Labels: enhancement

#22 - mode="tree" is missing in Tree logger

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: bug

#21 - NumberArrayValueToBEAST suppresses IntegerArrayValueToBEAST

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: bug

#20 - log TreeHeight and TreeLikelihood

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: bug

#19 - TreeWithMetaDataLogger is required to log meta data with trees

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: bug

#18 - Skyline plots to BEAST is broken

Issue - State: closed - Opened by walterxie over 4 years ago - 4 comments
Labels: bug

#17 - Wilson Balding operator is missing

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: bug

#16 - Add preBurnin

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: enhancement

#15 - improve parameters logged in XML

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: enhancement

#14 - extract the fileNameStem from outfile

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: enhancement

#8 - Slice not working in the parameter in LPhyBEAST

Issue - State: closed - Opened by walterxie over 4 years ago
Labels: bug

#7 - It would be good to output the true/initial values to a Tracer compatible log file alongside the XML

Issue - State: closed - Opened by alexeid over 4 years ago - 1 comment
Labels: enhancement

#6 - LPhyBEAST not stop after Exception

Issue - State: closed - Opened by walterxie over 4 years ago - 2 comments
Labels: enhancement

GitHub / LinguaPhylo/LPhyBeast issues and pull requests