Auto-generated from packages.yaml by the beast3-migration-status
Java tool. Regenerate with mvn -q exec:java (or
java -jar target/*-all.jar) after cloning or updating a tracked
package. For per-package migration status ("what's left for flc?"),
see reports/. Notes on how to read the columns
are at the bottom of this page.
Last regenerated: 2026-05-15T12:13:16.575206+12:00
| Package | Stage | Maven Central | Pom version | JPMS | Release | CI | Code | XML | FxT | Dep refs |
|---|---|---|---|---|---|---|---|---|---|---|
| beast3 | Maven Central | 2.8.0-beta5 | 2.8.0-SNAPSHOT | ✅ | ✅ | ✅ | 🟢 | 🔴 | 🟡 | 618 |
| BEASTLabs | Maven Central | 2.1.0-beta2 | 2.1.0-SNAPSHOT | ✅ | ✅ | ✅ | 🔴 | 🔴 | 🔴 | 173 |
| beast-classic | Maven Central | 1.7.0-beta1 | 1.7.0-SNAPSHOT | ✅ | ✅ | ✅ | 🔴 | 🔴 | 🔴 | 112 |
| CoupledMCMC | Maven Central | 1.3.0-beta1 | 1.3.0-beta1 | ✅ | ✅ | ✅ | 🟢 | 🟢 | 🟢 | ✅ |
| flc | Maven Central | 1.3.0-beta1 | 1.3.0-beta1 | ✅ | ✅ | ✅ | 🟢 | 🟢 | — | ✅ |
| Mascot | Maven Central | 3.1.0-beta1 | 3.1.0-beta1 | ✅ | ✅ | ✅ | 🟡 | 🔴 | 🔴 | 28 |
| morph-models | Maven Central | 1.3.0-beta3 | 1.3.0-beta3 | ✅ | ✅ | ✅ | 🟢 | 🟢 | 🟢 | ✅ |
| sampled-ancestors | Maven Central | 2.3.0-beta1 | 2.3.0-beta1 | ✅ | ✅ | ✅ | 🟢 | 🟢 | 🟢 | ✅ |
| MutableAlignment | compile-tested | — | 0.1.0-SNAPSHOT | ✅ | ✅ | ✅ | 🟢 | 🟢 | — | ✅ |
| ORC | Maven Central | 1.3.1 | 1.3.0-SNAPSHOT | ✅ | ✅ | ❌ | 🟢 | 🟢 | 🟢 | ✅ |
| bModelTest | compile-tested | — | 1.4.0-beta1 | ✅ | ✅ | ❌ | 🟢 | 🟢 | 🟢 | ✅ |
| obama | compile-tested | — | 1.2.0-beta1 | ✅ | ✅ | ❌ | 🔴 | 🔴 | 🟡 | 207 |
| feast | compile-tested | — | 11.0.0 | ✅ | ✅ | ✅ | 🟢 | 🔴 | 🔴 | 9 |
| GammaSpikeModel | compile-tested | — | 1.3.0-SNAPSHOT | ✅ | ✅ | ❌ | 🟡 | 🔴 | 🟢 | 262 |
| BDMM-Prime | compile-tested | — | 3.0.0 | ✅ | ✅ | ✅ | 🟢 | — | 🟢 | ✅ |
| remaster | compile-tested | — | 3.0.0 | ✅ | ✅ | ✅ | 🟢 | 🔴 | — | 10 |
Traffic-light columns: 🔴 any legacy lineage / non-migrated content, 🟡 no legacy but some unnecessarily-concrete Inputs (Code), or stray legacy parameter.* declarations / references to @Deprecated classes (XML / FxT), 🟢 clean, — = artefact type not used by this package (treated as complete).
Dep refs = number of references to @Deprecated classes found in this package's XMLs and fxtemplates (either as spec= attributes or <map> bodies); also degrades the XML / FxT light to 🟡 when non-zero. 0 = ✅. Per-package reports list each hit and the spec replacement.
| Package | Distrs | Ops | Loggers | CalcNodes | Params | StateNodes | XMLs | FxTemplates | Input rule |
|---|---|---|---|---|---|---|---|---|---|
| beast3 | ✅ 38 | ✅ 15 | ✅ 2 | ✅ 38 | ✅ 4 | ✅ 13 | 0 / 0 / 157 (+1 legacy) | 3 / 5 / 5 | ✅ |
| BEASTLabs | 5 / 22 | ✅ 21 | ✅ 5 | 8 / 16 | 2 / 2 | ✅ 8 | 0 / 0 / 20 | 0 / 0 / 3 | 15 / 29 |
| beast-classic | ✅ 9 | ✅ 11 | ✅ 3 | 9 / 22 | ✅ 1 | ✅ 2 | 0 / 0 / 10 | 0 / 1 / 5 | 7 / 15 |
| CoupledMCMC | — | — | ✅ 4 | — | — | — | 1 / 1 / 1 | 1 / 1 / 1 | ✅ |
| flc | — | — | — | ✅ 10 | — | — | 2 / 2 / 2 | — | ✅ |
| Mascot | ✅ 11 | ✅ 6 | ✅ 12 | ✅ 30 | — | ✅ 3 | 1 / 1 / 4 | 0 / 0 / 5 | ✅ |
| morph-models | — | — | — | ✅ 4 | — | ✅ 1 | 2 / 2 / 2 (+4 legacy) | 1 / 1 / 1 | ✅ |
| sampled-ancestors | ✅ 6 | ✅ 13 | ✅ 1 | ✅ 6 | — | ✅ 2 | 3 / 3 / 3 | 1 / 1 / 1 | ✅ |
| MutableAlignment | — | ✅ 1 | ✅ 1 | ✅ 3 | — | ✅ 1 | 1 / 1 / 1 | — | ✅ |
| ORC | ✅ 1 | ✅ 52 | ✅ 1 | — | — | — | 1 / 1 / 1 | 1 / 1 / 1 | ✅ |
| bModelTest | ✅ 3 | ✅ 4 | ✅ 1 | ✅ 5 | — | — | 3 / 3 / 3 | 1 / 1 / 1 | ✅ |
| obama | ✅ 3 | ✅ 2 | ✅ 1 | 11 / 45 | — | — | 0 / 0 / 14 | 0 / 1 / 1 | 9 / 18 |
| feast | ✅ 3 | ✅ 8 | — | ✅ 18 | ✅ 6 | ✅ 5 | 0 / 0 / 9 | 0 / 0 / 1 | ✅ |
| GammaSpikeModel | ✅ 4 | ✅ 12 | ✅ 3 | ✅ 4 | — | — | 0 / 11 / 17 | 2 / 2 / 2 | 7 / 30 |
| BDMM-Prime | ✅ 7 | ✅ 7 | ✅ 3 | ✅ 24 | — | ✅ 3 | — | 2 / 2 / 2 | ✅ |
| remaster | — | — | ✅ 2 | ✅ 5 | — | ✅ 2 | 4 / 7 / 25 | — | ✅ |
Legend: ✅ = clean, ❌ = missing, legacy / total = classes still on a legacy base, — = artefact type not used by this package (treated as complete).
FxTemplates show clean / spec / total — clean = uses spec types and no legacy parameter.RealParameter-style attrs; spec = body references beast.base.spec.* at all.
Input rule shows classes / violations: classes with at least one Input declared too concretely / total violating Inputs. Concrete spec params (RealScalarParam, …) belong on Operators (which write the param) and Loggers (which need getID(), absent from the pure type interfaces); Distributions/CalcNodes/etc. should declare the interface (RealScalar, RealVector, …). 0 = ✅.
Per package, for each kind: spec / mixed / legacy / neutral · total.
mixed classes import both spec and legacy types — usually mid-migration.
| Package | Distributions | Operators | Loggers | CalcNodes | Parameters | StateNodes |
|---|---|---|---|---|---|---|
| beast3 | 38 / 0 / 0 / 0 · 38 | 1 / 0 / 0 / 14 · 15 | 0 / 0 / 0 / 2 · 2 | 7 / 0 / 0 / 31 · 38 | 4 / 0 / 0 / 0 · 4 | 6 / 0 / 0 / 7 · 13 |
| BEASTLabs | 1 / 0 / 5 / 16 · 22 | 0 / 0 / 0 / 21 · 21 | 0 / 0 / 0 / 5 · 5 | 0 / 0 / 8 / 8 · 16 | 0 / 0 / 2 / 0 · 2 | 0 / 0 / 0 / 8 · 8 |
| beast-classic | 0 / 0 / 0 / 9 · 9 | 1 / 0 / 0 / 10 · 11 | 1 / 0 / 0 / 2 · 3 | 4 / 0 / 9 / 9 · 22 | 1 / 0 / 0 / 0 · 1 | 0 / 0 / 0 / 2 · 2 |
| CoupledMCMC | — | — | 0 / 0 / 0 / 4 · 4 | — | — | — |
| flc | — | — | — | 8 / 0 / 0 / 2 · 10 | — | — |
| Mascot | 0 / 0 / 0 / 11 · 11 | 0 / 0 / 0 / 6 · 6 | 0 / 0 / 0 / 12 · 12 | 5 / 0 / 0 / 25 · 30 | — | 0 / 0 / 0 / 3 · 3 |
| morph-models | — | — | — | 4 / 0 / 0 / 0 · 4 | — | 0 / 0 / 0 / 1 · 1 |
| sampled-ancestors | 2 / 0 / 0 / 4 · 6 | 1 / 0 / 0 / 12 · 13 | 0 / 0 / 0 / 1 · 1 | 0 / 0 / 0 / 6 · 6 | — | 0 / 0 / 0 / 2 · 2 |
| MutableAlignment | — | 0 / 0 / 0 / 1 · 1 | 0 / 0 / 0 / 1 · 1 | 3 / 0 / 0 / 0 · 3 | — | 0 / 0 / 0 / 1 · 1 |
| ORC | 1 / 0 / 0 / 0 · 1 | 0 / 0 / 0 / 52 · 52 | 0 / 0 / 0 / 1 · 1 | — | — | — |
| bModelTest | 0 / 0 / 0 / 3 · 3 | 1 / 0 / 0 / 3 · 4 | 0 / 0 / 0 / 1 · 1 | 5 / 0 / 0 / 0 · 5 | — | — |
| obama | 0 / 0 / 0 / 3 · 3 | 0 / 0 / 0 / 2 · 2 | 0 / 0 / 0 / 1 · 1 | 19 / 0 / 11 / 15 · 45 | — | — |
| feast | 0 / 0 / 0 / 3 · 3 | 0 / 0 / 0 / 8 · 8 | — | 15 / 0 / 0 / 3 · 18 | 6 / 0 / 0 / 0 · 6 | 0 / 0 / 0 / 5 · 5 |
| GammaSpikeModel | 3 / 0 / 0 / 1 · 4 | 4 / 0 / 0 / 8 · 12 | 0 / 0 / 0 / 3 · 3 | 4 / 0 / 0 / 0 · 4 | — | — |
| BDMM-Prime | 2 / 0 / 0 / 5 · 7 | 0 / 0 / 0 / 7 · 7 | 0 / 0 / 0 / 3 · 3 | 2 / 0 / 0 / 22 · 24 | — | 0 / 0 / 0 / 3 · 3 |
| remaster | — | — | 0 / 0 / 0 / 2 · 2 | 0 / 0 / 0 / 5 · 5 | — | 0 / 0 / 0 / 2 · 2 |
- MutableAlignment — Maven Central: not published (404)
- bModelTest — Maven Central: not published (404)
- obama — Maven Central: not published (404)
- feast — Maven Central: not published (404)
- GammaSpikeModel — Maven Central: not published (404)
- BDMM-Prime — Maven Central: not published (404)
- remaster — Maven Central: not published (404)
Most cells have an inline legend right below their table. The points below cover what those legends don't.
- Java class counts. Each kind cell shows
legacy / total— classes still extending a legacy base (ParametricDistribution,Prior,RealParameter/IntegerParameter/BooleanParameter).✅ Nmeans none of theNclasses have a legacy base. The Java class kinds detail table splits each kind intospec / mixed / legacy / neutral; NEUTRAL = no migration target either way (e.g., a subclass of a base that has no spec equivalent yet). - XML counts —
spec / v2.8 / total:spec=<beast>root has bothversion="2.8"and abeast.base.spec.*namespace;v2.8= root hasversion="2.8"regardless of namespace;total= every XML with a<beast>root. Files underexamples/legacy*/are reported separately as(+N legacy)and excluded from the totals. - Build / release columns are simple presence checks. The Maven
Central column shows the latest released version, or
—if not published.