Merge pull request #83 from jjmccollum/82-change-ancestralstatelogger…

…-to-ancestralsequencelogger-in-beast-output

82 change ancestralstatelogger to ancestralsequencelogger in beast output

.github/workflows/beast.yml

@@ -42,7 +42,7 @@ jobs:
         cd .beast
         cp /home/runner/work/teiphy/teiphy/beast2/release/Linux/*.tgz .
         tar zxvf *.tgz
-        ~/.beast/beast/bin/packagemanager -add BEASTLabs
+        ~/.beast/beast/bin/packagemanager -add BEAST_CLASSIC
         ~/.beast/beast/bin/packagemanager -add BDSKY
     - name: Phylogenetics Run
       run: |

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "teiphy"
-version = "0.1.9"
+version = "0.1.10"
 description = "Converts TEI XML collations to NEXUS and other formats"
 authors = ["Joey McCollum and Robert Turnbull"]
 license = "MIT"

teiphy/templates/beast_template.xml

@@ -292,10 +292,10 @@
             <log spec="TreeWithMetaDataLogger" id="treeWithMetaDataLogger" branchratemodel="@clock" tree="@tree"/>
         </logger>
         <operatorschedule spec="OperatorSchedule" id="operatorSchedule"/>
-        <logger id="ancestralStateLogger" fileName="$(tree).ancestral.trees" logEvery="10000" mode="tree">
+        <logger id="ancestralSequenceLogger" fileName="$(tree).ancestral.trees" logEvery="10000" mode="tree">
             <!-- Start character ancestral state loggers -->
             {%- for vu in variation_units %}
-            <log spec="beastlabs.evolution.likelihood.AncestralStateLogger" id="morphTreeLikelihood.character.{{ loop.index }}.anclogger" data="@filter.{{ loop.index }}" taxonset="@taxa" siteModel="@morphSiteModel.{{ loop.index }}" branchRateModel="@clock" tree="@tree" useAmbiguities="true" useTipLikelihoods="true"/>
+            <log spec="beastclassic.evolution.likelihood.AncestralSequenceLogger" id="morphTreeLikelihood.character.{{ loop.index }}.anclogger" tag="morphTreeLikelihood.character.{{ loop.index }}" data="@filter.{{ loop.index }}" siteModel="@morphSiteModel.{{ loop.index }}" branchRateModel="@clock" tree="@tree" useAmbiguities="true" useTipLikelihoods="true"/>
             {%- endfor %}
         </logger>
     </run>