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SNaQ 2.0 #215

Closed
wants to merge 52 commits into from
Closed

SNaQ 2.0 #215

wants to merge 52 commits into from

Commits on Mar 7, 2021

  1. multithreading logPsuedoLik calculation

    @tkchafin
    tkchafin committed Mar 7, 2021
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Commits on Mar 8, 2021

  1. multithreading all quartet operations

    @tkchafin
    tkchafin committed Mar 8, 2021
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  2. testing lock in logPseudoLik

    @tkchafin
    tkchafin committed Mar 8, 2021
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  3. removed race condition in logPseudoLik thread version

    @tkchafin
    tkchafin committed Mar 8, 2021
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  4. thread call for quartet operations

    @tkchafin
    tkchafin committed Mar 8, 2021
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  5. trying again with threads macro...

    @tkchafin
    tkchafin committed Mar 8, 2021
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  6. removing profiling package

    @tkchafin
    tkchafin committed Mar 8, 2021
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Commits on Apr 14, 2021

  1. added getIndexEdge from Vector{Edge}

    @tkchafin
    tkchafin committed Apr 14, 2021
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Commits on Apr 15, 2021

  1. added deltaCF calculation

    @tkchafin
    tkchafin committed Apr 15, 2021
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  2. added deltaCF attribute to Quartet

    @tkchafin
    tkchafin committed Apr 15, 2021
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  3. added sampleEdgeQuartetWeighted

    @tkchafin
    tkchafin committed Apr 15, 2021
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  4. added probQR

    @tkchafin
    tkchafin committed Apr 15, 2021
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  5. overload functions needed for modified chooseEdgesGamma call

    @tkchafin
    tkchafin committed Apr 15, 2021
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Commits on Apr 16, 2021

  1. removed net argument for sampleEdgeQuartetWeighted

    @tkchafin
    tkchafin committed Apr 16, 2021
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  2. added weighted choose functions for NNI, mv target/source

    @tkchafin
    tkchafin committed Apr 16, 2021
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  3. added temp print of loglik

    @tkchafin
    tkchafin committed Apr 16, 2021
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Commits on Apr 20, 2021

  1. removed temp prints

    @tkchafin
    tkchafin committed Apr 20, 2021
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Commits on May 1, 2021

  1. added 'sampled' variable to Quartet

    @tkchafin
    tkchafin committed May 1, 2021
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  2. added qinf and propQuartets arguments to snaq

    @tkchafin
    tkchafin committed May 1, 2021
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  3. added function to find uninformative quartets

    @tkchafin
    tkchafin committed May 1, 2021
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  4. skip update/ pseudolik for unsampled quartets

    @tkchafin
    tkchafin committed May 1, 2021
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  5. update uninformative quartets in snaq() function

    @tkchafin
    tkchafin committed May 1, 2021
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  6. Merge pull request #1 from crsl4/master 

    Merge changes from crsl4/PhyloNetworks.jl
    Tyler Chafin authored May 1, 2021
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Commits on May 2, 2021

  1. got qinfTest working

    @tkchafin
    tkchafin committed May 2, 2021
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  2. function to reset Quartet.sampled in DataCF.quartet

    @tkchafin
    tkchafin committed May 2, 2021
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Commits on May 3, 2021

  1. added functions to sample quartets and update Quartet.sampled

    @tkchafin
    tkchafin committed May 3, 2021
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  2. added Quartet.uninformative boolean

    @tkchafin
    tkchafin committed May 3, 2021
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  3. finished quartet subsetting

    @tkchafin
    tkchafin committed May 3, 2021
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Commits on May 4, 2021

  1. iupac() function to convert codes to alleles

    @tkchafin
    tkchafin committed May 4, 2021
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Commits on May 18, 2021

  1. beta version of ReadPhylip2CF

    @tkchafin
    tkchafin committed May 18, 2021
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Commits on May 19, 2021

  1. added index for tracking progress

    @tkchafin
    tkchafin committed May 19, 2021
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  2. added index for tracking progress

    @tkchafin
    tkchafin committed May 19, 2021
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  3. added table write to readPhylip2CF

    @tkchafin
    tkchafin committed May 19, 2021
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  4. added table write to readPhylip2CF

    @tkchafin
    tkchafin committed May 19, 2021
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  5. fix bug in readPhylip2CF

    @tkchafin
    tkchafin committed May 19, 2021
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Commits on Sep 26, 2021

  1. Merge branch 'crsl4:master' into master

    @tkchafin
    tkchafin authored Sep 26, 2021
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Commits on Apr 20, 2024

  1. fix bug in weighted/probQR NNI moves

    @tkchafin
    tkchafin committed Apr 20, 2024
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Commits on Apr 21, 2024

  1. merge

    @tkchafin
    tkchafin committed Apr 21, 2024
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Commits on Sep 10, 2024

  1. merging with main repo

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  2. updated test to include probQR argument

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  3. removed unused argument from chooseEdgeOriginTarget!

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  4. updated function call to match version on master

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  5. new functions lead to different RNG outcomes, so loglik bounds need t… 

    …o be changed
    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  6. fixed test regex

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  7. added probQR and propQuartets to bootstrap function calls

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  8. these methods don't show log messages anymore and the format causes a… 

    …n error, so we can remove the @test_logs calls
    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  9. if tests failed when stdout was redirected, stdout was ruined for all… 

    … remaining tests
    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  10. updated proposedTop! overrides to include blank DataCF() for parsimon… 

    …y optimizations
    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  11. added 0.0 for probQR

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  12. fixed d=d --> d

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  13. changed tests to account for different RNG generation on different ma… 

    …chines
    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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  14. updated version number

    @NathanKolbow
    NathanKolbow committed Sep 10, 2024
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