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  • 5471b672e9bac767dd61afb3da9962efe9ca6800
  • master default protected
  • Lucas_optimizer
  • aggr
  • massive
  • master-eval
  • multi
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Created with Raphaël 2.2.027Nov2330Oct291615823Jul2217161510987626Jun25242322191817161512111085328May272622212019181613121187530Apr2827242120171615141310983130Mar27262513121110653227Feb262524232019171294Sep27Jun167Apr27Mar26251813121128Feb246330Jan29232120Dec17162Jul20Jun429May1530Apr26252423221610922Feb201475128Jan2418171514111087228Dec24211918151312116543130Nov28242218159629Oct2519181412111095228Sep26252421181413121110428Aug2321104327Jul2018121196325Jun22191816May223Apr1312114226Mar231513928Feb22211917161513103231Jan262420119223Dec2120191613762130Nov231817157428Oct26242320181754328Sep2722201930Aug4329Jul27251918118620Jun11130May231816126extend the ProbabilityMatrix to multiple foregroundstreated issues:corrected:Merge branch 'master' of https://gitlab.isb-sib.ch/phylo/fastcodemlremove extra tab in output for LnL0clean.sh to clean after cmakeadd fast_te: extract tree in fastcodeml formatensure that aggregation isn't used with lapackdisable tree reuse (it's not clear how to use it with aggregation)testParameter changed to constLucas_optimizerLucas_optimizerChanged line endingDocumented the distributions extracted from SelectomeRemoved a define in BootstrapRandom and cleaned the classAdded precisions about the Himmelbau termination criterion in the command line/comments in fast.cppReduced range for few variables. Corrected initialization order for OptSQP classMerged latest corrections from LucasRemoved unneeded include files. Added missing initializations in few constructorsMerge branch 'master' of https://gitlab.isb-sib.ch/phylo/fastcodemlExclude .git directory in tarball creation scriptfix fastcodeml output (may break BG/Q)Cleaned the BootstrapRandom file by removing useless/unefficient methods.Added more specific comments in BOXCQPCleaned the BOXCQP class by removing the old solver.Removed useless #defineAdded the argument option --himmelblau-termination, which is an optional stopping criterion based on the function redution AND parameter changes. This is available for SQP and all the nlopt optimizers.Merged Lucas modifications and cleanupRemoved all the unneeded classes (experimental optimizers).Removed unnnecessary #if in OptSQPCleaned the SQP class further, added const where needed, comment where neededLimitted the memory consumption by dealocating the bootstrapper before optimizingCleaned OptSQP by removing the scaling option (useless, has no effects)Changed the name of bootstrap 'evolutionary strategy' to 'genetic algorithm', which is more specificCleaned BOXCQPMerge branch 'SQP_SR1' into LucasCleaned messages OptSQP and BOXCQP. replaced error messages cout by cerr.Added the possibility to use a gradient descent instead of the conjugate gradient (for testing purpose). Still bad convergence. Need to figure out how to restrict the solution to a smaller radius.The negative curvatures create problems.Debugged the SR1 code.Coded the SPG and line search algorithms.