bella-companion 0.0.27__py3-none-any.whl → 0.0.28__py3-none-any.whl

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@@ -1,7 +1,7 @@
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  <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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- <beast
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+ <beast
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  namespace="
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- beast.base.inference
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+ :beast.base.inference
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  :beast.base.inference.parameter
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  :beast.base.evolution.branchratemodel
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  :beast.base.evolution.substitutionmodel
@@ -27,171 +27,324 @@
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  :feast.parameter
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  :feast.fileio
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  :feast.function
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- :feast.expressions"
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+ :feast.expressions
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+ :glmprior.util"
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  required="BEAST.base v2.7.7:BDMM-Prime v2.2.2"
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  version="2.7"
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  >
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- <map name="Uniform">beast.base.inference.distribution.Uniform</map>
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- <map name="Exponential">beast.base.inference.distribution.Exponential</map>
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- <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
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- <map name="Normal">beast.base.inference.distribution.Normal</map>
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- <map name="prior">beast.base.inference.distribution.Prior</map>
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-
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- <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
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- <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
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- <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
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-
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- <alignment id="alignment" spec="AlignmentFromFasta" fileName="$(msa_file)"/>
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- <TaxonSet id="TaxonSet" spec="TaxonSet" alignment="@alignment"/>
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- <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@TaxonSet"/>
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- <TraitSetFromTaxonSet id="dateTraitSet" traitname="date" dateFormat="yyyy-M-dd" delimiter= "|" everythingAfterLast="true" taxa="@TaxonSet"/>
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- <typeSet id="typeSet" spec="TypeSet" typeTraitSet="@typeTraitSet"/>
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-
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- <parameter id="processLength" spec="RealParameter" value="1.0"/>
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-
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- <Re id="ReSP" spec="SkylineVectorParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
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- <skylineValues id="Re" spec="RealParameter" dimension="$(ReDimension)" value="1.0"/>
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- <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
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+ <map name="Uniform" >beast.base.inference.distribution.Uniform</map>
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+ <map name="Exponential" >beast.base.inference.distribution.Exponential</map>
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+ <map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
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+ <map name="Normal" >beast.base.inference.distribution.Normal</map>
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+ <map name="Poisson" >beast.base.inference.distribution.Poisson</map>
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+ <map name="prior" >beast.base.inference.distribution.Prior</map>
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+
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+ <alignment id="alignment" spec= "AlignmentFromFasta" fileName = "$(aligned_fasta)"/>
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+
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+ <typeSet id="typeSetBDMMPrime" spec="TypeSet">
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+ <typeTraitSet id="typeTraitSet" spec="TraitSetFromTaxonSet" traitname="type" delimiter="|" takeGroup="1">
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+ <taxa spec="TaxonSet" alignment="@alignment"/>
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+ </typeTraitSet>
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+ </typeSet>
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+
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+ <trait id="dateTrait" spec="TraitSetFromTaxonSet" traitname="date" dateFormat="yyyy-M-dd" delimiter= "|" everythingAfterLast="true">
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+ <taxa spec="TaxonSet" alignment="@alignment"/>
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+ </trait>
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+
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+ <processLength id="originBDMMPrime" spec="RealParameter">10.0</processLength>
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+
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+ <Re id="ReSV" spec="SkylineVectorParameter" timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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+ <skylineValues id="ReValues" spec="RealParameter">1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4</skylineValues>
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+ <changeTimes id="ReRateChangeTimes" spec="RealParameter">0.123</changeTimes>
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  </Re>
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- <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet" changeTimes="0.123 0.205">
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- <skylineValues id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
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+ <samplingProportion id="samplingProportionSV" spec="SkylineVectorParameter"
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+ timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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+ <skylineValues id="samplingProportionValues" spec="RealParameter" dimension="15" lower="0.0" upper="1.0">1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0</skylineValues>
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+ <changeTimes id="samplingProportionChangeTimes" spec="RealParameter">0.123 0.205</changeTimes>
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  </samplingProportion>
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+
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+ <becomeUninfectiousRate id="becomeUninfectiousRateSV" spec="SkylineVectorParameter"
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+ typeSet="@typeSetBDMMPrime">
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+ <skylineValues id="becomeUninfectiousValues" spec="RealParameter">36.5</skylineValues>
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+ </becomeUninfectiousRate>
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- <becomeUninfectiousRate id="becomeUninfectiousRateSP" spec="SkylineVectorParameter" typeSet="@typeSet" skylineValues="36.5"/>
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+ <migrationRate id="migrationRateSM" spec="SkylineMatrixParameter"
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+ timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
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- <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
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- <skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
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- <plate var="predictorFile" range="$(predictorFiles)">
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- <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
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+ <skylineValues id="migrationRateValues" spec="bella.BayesMLP" nodes="$(nodes)">
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+ <plate var="predictor" range="$(GLMpredictor_files)">
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+ <predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
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  </plate>
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+
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  <plate var="n" range="$(layersRange)">
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  <weights idref="migrationW$(n)"/>
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  </plate>
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+
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  </skylineValues>
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- <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
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- </migrationRate>
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75
- <removalProb id="removalProbSP" spec="SkylineVectorParameter" skylineValues="1.0" processLength="@processLength" typeSet="@typeSet"/>
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+ <changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV"
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+ fileName="$(GLMpredictor_changetimes)"/>
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+ </migrationRate>
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77
- <startTypePriorProbs id="typeFrequencies" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
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79
- <siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4" proportionInvariant="0.0">
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+
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+ <removalProb id="removalProbSV" spec="SkylineVectorParameter" skylineValues="1.0"
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+ processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime"/>
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+
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+ <startTypePriorProbs id="typeFrequencies" spec="RealParameter"
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+ estimate="false" lower="0.0" upper="1.0">1.0 0.0 0.0 0.0 0.0</startTypePriorProbs>
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+
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+
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+ <!-- Site Model -->
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+ <siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4">
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101
  <parameter id="gammaShape" name="shape" value="1.0"/>
102
+ <parameter name="mutationRate" estimate="false" value="1.0"/>
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+ <parameter name="proportionInvariant" estimate="false" value="0.0"/>
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+
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105
  <substModel spec="HKY">
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106
  <kappa id="kappa" spec="RealParameter" value="2.0"/>
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  <frequencies id="empiricalFreqs" spec="Frequencies" data="@alignment"/>
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  </substModel>
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  </siteModel>
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87
- <branchRateModel id="branchRateModel" spec="StrictClockModel" clock.rate="8.0E-4"/>
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111
 
89
- <popFunc id="popFunc" spec="ConstantPopulation" popSize="0.1"/>
112
+ <!-- Branch rate Model -->
113
+ <branchRateModel id="branchRateModel" spec="StrictClockModel">
114
+ <parameter id="clockRate" name="clock.rate" estimate="false">8.0E-4</parameter>
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+ </branchRateModel>
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+
117
+
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+ <!-- Population Model for Tree initialiser -->
119
+ <popFunc id="popFunc" spec="ConstantPopulation">
120
+ <popSize spec="RealParameter" value="0.1"/>
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+ </popFunc>
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+
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91
- <run spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
124
+ <!-- MCMC -->
125
+ <run id="mcmc" spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
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126
 
93
- <state spec="State" storeEvery="5000">
94
- <stateNode id="treeBDMMPrime" spec="RandomTree" taxa="@alignment" populationModel="@popFunc" trait="@dateTraitSet"/>
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- <stateNode idref="processLength"/>
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- <stateNode idref="Re"/>
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- <stateNode idref="samplingProportion"/>
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+ <!-- State -->
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+ <state id="state" spec="State">
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+
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+ <stateNode id="treeBDMMPrime" spec="RandomTree"
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+ taxa="@alignment"
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+ populationModel="@popFunc"
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+ trait="@dateTrait">
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+ </stateNode>
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+
136
+ <stateNode idref="originBDMMPrime"/>
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+ <stateNode idref="ReValues"/>
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+ <stateNode idref="samplingProportionValues"/>
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139
  <plate var="n" range="$(layersRange)">
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140
  <stateNode spec="RealParameter" id="migrationW$(n)" value="0"/>
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141
  </plate>
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+
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143
  <stateNode idref="kappa"/>
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144
  <stateNode idref="gammaShape"/>
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+
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  </state>
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147
 
148
+
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+ <!-- Posterior Distribution -->
105
150
  <distribution id="posterior" spec="CompoundDistribution">
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+
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+ <!-- Tree Likelihood -->
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153
  <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
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- <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@treeBDMMPrime" siteModel="@siteModel" branchRateModel="@branchRateModel"/>
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+
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+ <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood"
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+ data="@alignment"
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+ tree="@treeBDMMPrime"
158
+ siteModel="@siteModel"
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+ branchRateModel="@branchRateModel"/>
160
+
108
161
  </distribution>
109
162
 
163
+ <!-- Prior distribution -->
110
164
  <distribution id="prior" spec="CompoundDistribution">
111
- <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@treeBDMMPrime" conditionOnSurvival="true" finalSampleOffset="0.0" typeTraitSet="@typeTraitSet" startTypePriorProbs="@typeFrequencies">
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- <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" Re="@ReSP" samplingProportion="@samplingProportionSP" becomeUninfectiousRate="@becomeUninfectiousRateSP" migrationRate="@migrationRateSP" removalProb="@removalProbSP" typeSet="@typeSet"/>
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+
166
+ <!-- BDMM-Prime tree prior distribution -->
167
+ <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution"
168
+ tree="@treeBDMMPrime"
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+ conditionOnSurvival="true"
170
+ finalSampleOffset="0.0"
171
+ typeTraitSet="@typeTraitSet"
172
+ startTypePriorProbs="@typeFrequencies">
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+
174
+ <!-- Parameterization BDMM-Prime -->
175
+ <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization"
176
+ processLength="@originBDMMPrime"
177
+ Re="@ReSV"
178
+ samplingProportion="@samplingProportionSV"
179
+ becomeUninfectiousRate="@becomeUninfectiousRateSV"
180
+ migrationRate="@migrationRateSM"
181
+ removalProb="@removalProbSV"
182
+ typeSet="@typeSetBDMMPrime"/>
183
+
113
184
  </distribution>
114
185
 
115
- <prior name="distribution" x="@processLength">
186
+
187
+ <!-- Priors on parameters -->
188
+ <!-- BDMMPrime parameters priors -->
189
+
190
+ <prior id="originBDMMPrimePrior" name="distribution" x="@originBDMMPrime">
116
191
  <LogNormal name="distr" M="-1.0" S="0.2"/>
117
192
  </prior>
118
- <distribution spec="SmartZeroExcludingPrior" x="@Re">
193
+
194
+ <!-- Reproductive number Prior -->
195
+ <distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
119
196
  <LogNormal name="distr" M="0.8" S="0.5"/>
120
197
  </distribution>
121
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
198
+
199
+ <!-- Prior for sampling proportion for China -->
200
+ <distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
201
+ classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
122
202
  <Uniform name="distr" lower="0" upper="0.15"/>
123
203
  </distribution>
124
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
204
+ <!-- Prior for sampling proportion for France -->
205
+ <distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
206
+ classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
125
207
  <Uniform name="distr" lower="0" upper="0.093"/>
126
208
  </distribution>
127
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
209
+ <!-- Prior for sampling proportion for Germany Epoch -->
210
+ <distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
211
+ classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
128
212
  <Uniform name="distr" lower="0" upper="0.10"/>
129
213
  </distribution>
130
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
214
+ <!-- Prior for sampling proportion for Italy -->
215
+ <distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
216
+ classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
131
217
  <Uniform name="distr" lower="0" upper="0.005"/>
132
218
  </distribution>
133
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
219
+ <!-- Prior for sampling proportion for OtherEuropean -->
220
+ <distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
221
+ classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
134
222
  <Uniform name="distr" lower="0" upper="0.057"/>
135
223
  </distribution>
224
+
136
225
  <plate var="n" range="$(layersRange)">
137
226
  <prior name="distribution" x="@migrationW$(n)">
138
227
  <Normal name="distr" mean="0.0" sigma="1.0"/>
139
228
  </prior>
140
229
  </plate>
141
- <prior name="distribution" x="@gammaShape">
142
- <Exponential name="distr" mean="0.5"/>
230
+
231
+ <prior id="GammaShapePrior" name="distribution" x="@gammaShape">
232
+ <Exponential name="distr">
233
+ <parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
234
+ </Exponential>
143
235
  </prior>
144
- <prior name="distribution" x="@kappa">
145
- <LogNormal name="distr" M="1.0" S="1.25"/>
236
+
237
+ <prior id="KappaPrior" name="distribution" x="@kappa">
238
+ <LogNormal name="distr">
239
+ <parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
240
+ <parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
241
+ </LogNormal>
146
242
  </prior>
243
+
147
244
  </distribution>
148
245
  </distribution>
149
246
 
150
- <operator spec="BactrianScaleOperator" tree="@treeBDMMPrime" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
151
- <operator spec="BactrianNodeOperator" tree="@treeBDMMPrime" weight="30.0"/>
152
- <operator spec="BactrianSubtreeSlide" tree="@treeBDMMPrime" weight="15.0"/>
153
- <operator spec="Exchange" tree="@treeBDMMPrime" weight="15.0"/>
154
- <operator spec="Exchange" tree="@treeBDMMPrime" isNarrow="false" weight="3.0"/>
155
- <operator spec="WilsonBalding" tree="@treeBDMMPrime" weight="3.0"/>
156
- <operator spec="EpochFlexOperator" tree="@treeBDMMPrime" scaleFactor="0.1" weight="2.0"/>
157
- <operator spec="EpochFlexOperator" tree="@treeBDMMPrime" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
158
- <operator spec="TreeStretchOperator" tree="@treeBDMMPrime" scaleFactor="0.01" weight="2.0"/>
159
- <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0" />
160
- <operator spec="BactrianScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
161
- <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0" />
247
+
248
+ <operator id="BDMMPrimeTreeRootScaler" spec="BactrianScaleOperator" tree="@treeBDMMPrime"
249
+ rootOnly="true" scaleFactor="0.25" weight="5.0"/>
250
+
251
+ <operator id="BDMMPrimeUniformOperator" spec="BactrianNodeOperator" tree="@treeBDMMPrime"
252
+ weight="30.0"/>
253
+
254
+ <operator id="BDMMPrimeSubtreeSlideScaler" spec="BactrianSubtreeSlide" tree="@treeBDMMPrime"
255
+ weight="15.0"/>
256
+
257
+ <operator id="BDMMPrimeNarrow" spec="Exchange" tree="@treeBDMMPrime"
258
+ weight="15.0"/>
259
+
260
+ <operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
261
+ isNarrow="false" weight="3.0"/>
262
+
263
+ <operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
264
+ weight="3.0"/>
265
+
266
+ <operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
267
+ scaleFactor="0.1" weight="2.0"/>
268
+
269
+ <operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
270
+ fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
271
+
272
+ <operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
273
+ scaleFactor="0.01" weight="2.0"/>
274
+
275
+ <operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
276
+ scaleFactor="0.25" weight="3.0" />
277
+
278
+ <operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" scaleFactor="0.25"
279
+ weight="10.0" />
280
+
281
+ <operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
282
+ weight="3.0" />
283
+
162
284
  <plate var="n" range="$(layersRange)">
163
285
  <operator spec="BactrianRandomWalkOperator" parameter="@migrationW$(n)" weight="5.0"/>
164
286
  </plate>
165
- <operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
166
- <operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
167
- <operatorschedule spec="OperatorSchedule"/>
168
287
 
169
- <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
288
+ <operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
289
+ weight="1.0"/>
290
+
291
+ <operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
292
+ weight="1.0"/>
293
+
294
+
295
+ <!-- Loggers -->
296
+ <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
170
297
  <log idref="posterior"/>
171
298
  <log idref="likelihood"/>
172
299
  <log idref="prior"/>
173
- <log idref="BDMMPrime"/>
174
- <log idref="ReSP"/>
175
- <log idref="samplingProportionSP"/>
176
- <log idref="migrationRateSP"/>
177
- <log idref="migrationRate"/>
178
- <log spec="TypedTreeStatsLogger" includeRootEdge="true" typeLabel="type" typeSet="@typeSet">
300
+ <log idref="treeLikelihood"/>
301
+ <log idref="gammaShape"/>
302
+ <log idref="kappa"/>
303
+ <log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
304
+ <log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
305
+ typeLabel="type" typeSet="@typeSetBDMMPrime">
179
306
  <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
180
307
  </log>
181
- </logger>
308
+ <log idref="originBDMMPrime"/>
309
+ <log idref="ReSV"/>
310
+ <log idref="becomeUninfectiousRateSV"/>
311
+ <log idref="samplingProportionSV"/>
312
+ <log idref="migrationRateSM"/>
182
313
 
183
- <logger spec="OptionalLogger" enableLogger="true" fileName="TypedTree.trees" logEvery="10000" mode="tree">
184
- <log idref="typeMappedTree"/>
314
+ <log idref="removalProbSV"/>
315
+ <log idref="typeFrequencies"/>
185
316
  </logger>
186
317
 
187
- <logger spec="OptionalLogger" enableLogger="true" fileName="TypedNodeTree.trees" logEvery="10000" mode="tree">
188
- <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
318
+ <logger id="screenlog" spec="Logger" logEvery="1000">
319
+ <log idref="posterior"/>
320
+ <log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
321
+ <log idref="likelihood"/>
322
+ <log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
323
+ <log idref="prior"/>
324
+ <log arg="@prior" id="ESS_prior" spec="util.ESS"/>
325
+ <log idref="BDMMPrime"/>
326
+ <log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
189
327
  </logger>
190
328
 
191
- <logger spec="OptionalLogger" enableLogger="true" fileName="trajectory.traj" logEvery="10000">
192
- <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
329
+ <logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
330
+ <log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
331
+ </logger>
332
+
333
+ <logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
334
+ fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
335
+ <log idref="typeMappedTree"/>
336
+ </logger>
337
+ <logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true"
338
+ fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
339
+ <log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
340
+ </logger>
341
+ <logger id="trajLogger" spec="OptionalLogger" enableLogger="true" fileName="$(filebase).traj" logEvery="10000">
342
+ <log id="typedTraj" spec="SampledTrajectory" bdmmDistrib="@BDMMPrime"
343
+ startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
193
344
  </logger>
194
345
 
346
+ <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
347
+
195
348
  </run>
196
-
349
+
197
350
  </beast>
@@ -80,13 +80,12 @@ def run_beast():
80
80
  cpus=128,
81
81
  mem_per_cpu=12000,
82
82
  )
83
- """
83
+
84
84
  os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
85
85
  job_ids["all-predictors-MLP"] = submit_job(
86
86
  " ".join(
87
87
  [
88
88
  os.environ["BELLA_RUN_BEAST_CMD"],
89
- f"-D ReDimension='{5 * 7}'",
90
89
  f'-D layersRange="0,1,2",nodes="16 8"',
91
90
  all_predictors_data,
92
91
  f"-prefix {output_dir / 'all-predictors-MLP'}{os.sep}",
@@ -94,7 +93,8 @@ def run_beast():
94
93
  ]
95
94
  ),
96
95
  base_log_dir / "all-predictors-MLP",
97
- mem_per_cpu="256000",
96
+ cpus=128,
97
+ mem_per_cpu=12000,
98
98
  )
99
99
 
100
100
  os.makedirs(output_dir / "flights-MLP", exist_ok=True)
@@ -102,7 +102,6 @@ def run_beast():
102
102
  " ".join(
103
103
  [
104
104
  os.environ["BELLA_RUN_BEAST_CMD"],
105
- f"-D ReDimension='{5 * 4}'",
106
105
  f'-D layersRange="0,1,2",nodes="16 8"',
107
106
  flight_predictor_data,
108
107
  f"-prefix {output_dir / 'flights-MLP'}{os.sep}",
@@ -110,9 +109,9 @@ def run_beast():
110
109
  ]
111
110
  ),
112
111
  base_log_dir / "flights-MLP",
113
- mem_per_cpu="256000",
112
+ cpus=128,
113
+ mem_per_cpu=12000,
114
114
  )
115
- """
116
115
 
117
116
  with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
118
117
  json.dump(job_ids, f)
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: bella-companion
3
- Version: 0.0.27
3
+ Version: 0.0.28
4
4
  Summary:
5
5
  Author: gabriele-marino
6
6
  Author-email: gabmarino.8601@gmail.com
@@ -2,7 +2,7 @@ bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
2
  bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
3
3
  bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
4
4
  bella_companion/eucovid/beast_configs/GLM.xml,sha256=YMvcyeSRIGQOhSSoj7FV0R-5wZHcGWwf9bKxamJ0q9k,20739
5
- bella_companion/eucovid/beast_configs/MLP.xml,sha256=qLvfP3qEIa_XEDigXrPGbegKDLddifRvoZjNmoDDmFo,11268
5
+ bella_companion/eucovid/beast_configs/MLP.xml,sha256=SGJVUYyi1ULU7zxx8xn9aiKZNQQ3D9ruyYRsDcFjPzo,16139
6
6
  bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
7
7
  bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
8
8
  bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
@@ -20,7 +20,7 @@ bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5
20
20
  bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
21
21
  bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
22
22
  bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
23
- bella_companion/eucovid/run_beast.py,sha256=Rj_Cf38TtyljP0JRyMn7G5Nt5Jv9T4CM5eJsKKfoy4E,3823
23
+ bella_companion/eucovid/run_beast.py,sha256=FYeqqG2_S3o_NrmYqyyll82CR0sbYtI7QuRv5MIrRVY,3748
24
24
  bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
25
25
  bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
26
26
  bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
@@ -69,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
69
69
  bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
70
70
  bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
71
71
  bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
72
- bella_companion-0.0.27.dist-info/METADATA,sha256=Sl37hKYlQ0qIq5NxxA1wNCmF-Mj109HazWo8EDq_pkk,576
73
- bella_companion-0.0.27.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
74
- bella_companion-0.0.27.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
75
- bella_companion-0.0.27.dist-info/RECORD,,
72
+ bella_companion-0.0.28.dist-info/METADATA,sha256=f_4at3vdN5Z4FMjq-1C71qUa1raHCBL4TaouU3S0TDw,576
73
+ bella_companion-0.0.28.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
74
+ bella_companion-0.0.28.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
75
+ bella_companion-0.0.28.dist-info/RECORD,,