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Make spec RandomTree recognise spec MRCAPrior constraints #121

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Merged
walterxie merged 2 commits into from
Jul 23, 2026
Merged

Make spec RandomTree recognise spec MRCAPrior constraints #121

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28c76bf
Make spec RandomTree recognise spec MRCAPrior constraints
alexeid Jul 23, 2026
5b04d92
Make LoggerTest hermetic against leaked JVM-wide logger state
alexeid Jul 23, 2026
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12 changes: 6 additions & 6 deletions beast-base/src/main/java/beast/base/spec/evolution/tree/coalescent/RandomTree.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,15 +33,15 @@
import beast.base.core.Log;
import beast.base.evolution.alignment.Alignment;
import beast.base.evolution.alignment.TaxonSet;
import beast.base.evolution.tree.MRCAPrior;
import beast.base.evolution.tree.Node;
import beast.base.evolution.tree.TraitSet;
import beast.base.evolution.tree.Tree;
import beast.base.evolution.tree.coalescent.PopulationFunction;
import beast.base.inference.StateNode;
import beast.base.inference.StateNodeInitialiser;
import beast.base.inference.distribution.ParametricDistribution;
import beast.base.spec.domain.PositiveReal;
import beast.base.spec.evolution.tree.MRCAPrior;
import beast.base.spec.inference.distribution.ScalarDistribution;
import beast.base.spec.type.RealScalar;
import beast.base.util.HeapSort;
import beast.base.util.Randomizer;
Expand Down Expand Up @@ -87,7 +87,7 @@ public String toString() {
List<Set<String>> taxonSets;

// list of parametric distribution constraining the MRCA of taxon sets, null if not present
List<ParametricDistribution> distributions;
List<ScalarDistribution> distributions;

// hard bound for the set, if any
List<Bound> m_bounds;
Expand Down Expand Up @@ -224,7 +224,7 @@ public void initStateNodes() {
}
usedTaxa.add(taxonID);
}
final ParametricDistribution distr = prior.distInput.get();
final ScalarDistribution distr = prior.distInput.get();
final Bound bounds = new Bound();
if (distr != null) {
List<BEASTInterface> beastObjects = new ArrayList<>();
Expand All @@ -233,8 +233,8 @@ public void initStateNodes() {
beastObjects.get(i).initAndValidate();
}
try {
double tLow = distr.inverseCumulativeProbability(0.0);
double tHi = distr.inverseCumulativeProbability(1.0);
double tLow = ((Number) distr.inverseCumulativeProbability(0.0)).doubleValue();
double tHi = ((Number) distr.inverseCumulativeProbability(1.0)).doubleValue();
bounds.lower = getDate(tLow);
bounds.upper = getDate(tHi);
if (bounds.lower > bounds.upper && tLow < tHi) {
Expand Down
20 changes: 20 additions & 0 deletions beast-base/src/test/java/test/beast/core/LoggerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,28 @@
public class LoggerTest {
Logger logger;

/**
* Logger.sampleOffset is protected static, so it is not reachable from this package
* directly; a subclass can reach it because protected static members are inherited
* regardless of package.
*/
private static class LoggerGlobals extends Logger {
static void reset() {
Logger.sampleOffset = -1;
}
}

@BeforeEach
public void setUp() throws Exception {
// file.name.prefix, Logger.FILE_MODE and Logger.sampleOffset are JVM-wide globals
// that the integration tests set and do not restore (see XMLPathUtil.setUpOutputDir
// and ResumeTest). Whether this class runs before or after them varies between
// surefire runs, which made testFileLog fail intermittently: a stale prefix sends
// the log to <prefix>beast.log while the assertions resolve "beast.log" against the
// working directory, and a stale sampleOffset is added to every logged sample.
System.clearProperty("file.name.prefix");
Logger.FILE_MODE = Logger.LogFileMode.only_new;
LoggerGlobals.reset();
logger = new Logger();
}

Expand Down
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