From 8581dfda6b7ace8d958620a10ed19206d0bcd177 Mon Sep 17 00:00:00 2001 From: Nico Neureiter Date: Tue, 21 Jul 2026 15:51:09 +0200 Subject: [PATCH 1/4] Add contacTrres to packages.yaml --- packages.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/packages.yaml b/packages.yaml index ac939e2..6cc7df4 100644 --- a/packages.yaml +++ b/packages.yaml @@ -123,3 +123,9 @@ packages: maven: io.github.tgvaughan:remaster stage: compile_tested notes: Migration WIP on `beast2.8-migration` branch (Maven, v3.0.0). + + - name: contacTrees + path: ../contacTrees + github: NicoNeureiter/contacTrees + maven: io.github.niconeureiter:contactrees + stage: maven_central From ac94ac52fde2624f307e8265c59f3aedc7973744 Mon Sep 17 00:00:00 2001 From: Nico Neureiter Date: Tue, 21 Jul 2026 16:09:00 +0200 Subject: [PATCH 2/4] Add contacTrees reports --- CHECKLIST.md | 5 +- reports/README.md | 1 + reports/contacTrees.md | 155 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 160 insertions(+), 1 deletion(-) create mode 100644 reports/contacTrees.md diff --git a/CHECKLIST.md b/CHECKLIST.md index b549200..2b6441b 100644 --- a/CHECKLIST.md +++ b/CHECKLIST.md @@ -9,7 +9,7 @@ are at the bottom of this page. -_Last regenerated: 2026-05-15T12:13:16.575206+12:00_ +_Last regenerated: 2026-07-21T16:02:08.207735+02:00_ ## Release & build status @@ -31,6 +31,7 @@ _Last regenerated: 2026-05-15T12:13:16.575206+12:00_ | [GammaSpikeModel](https://github.com/jordandouglas/GammaSpikeModel) | compile-tested | โ€” | 1.3.0-SNAPSHOT | โœ… | โœ… | โŒ | ๐ŸŸก | ๐Ÿ”ด | ๐ŸŸข | 262 | | [BDMM-Prime](https://github.com/tgvaughan/BDMM-Prime) | compile-tested | โ€” | 3.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | โ€” | ๐ŸŸข | โœ… | | [remaster](https://github.com/tgvaughan/remaster) | compile-tested | โ€” | 3.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | ๐Ÿ”ด | โ€” | 10 | +| [contacTrees](https://github.com/NicoNeureiter/contacTrees) | Maven Central | [2.0.0](https://central.sonatype.com/artifact/io.github.niconeureiter/contactrees) | 2.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | ๐ŸŸก | ๐ŸŸก | 27 | Traffic-light columns: ๐Ÿ”ด any legacy lineage / non-migrated content, ๐ŸŸก no legacy but some unnecessarily-concrete Inputs (Code), or stray legacy `parameter.*` declarations / references to `@Deprecated` classes (XML / FxT), ๐ŸŸข clean, โ€” = 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 `` bodies); also degrades the XML / FxT light to ๐ŸŸก when non-zero. 0 = โœ…. Per-package reports list each hit and the spec replacement. @@ -55,6 +56,7 @@ Traffic-light columns: ๐Ÿ”ด any legacy lineage / non-migrated content, ๐ŸŸก no l | GammaSpikeModel | โœ… 4 | โœ… 12 | โœ… 3 | โœ… 4 | โ€” | โ€” | 0 / 11 / 17 | 2 / 2 / 2 | 7 / 30 | | BDMM-Prime | โœ… 7 | โœ… 7 | โœ… 3 | โœ… 24 | โ€” | โœ… 3 | โ€” | 2 / 2 / 2 | โœ… | | remaster | โ€” | โ€” | โœ… 2 | โœ… 5 | โ€” | โœ… 2 | 4 / 7 / 25 | โ€” | โœ… | +| contacTrees | โœ… 4 | โœ… 21 | โœ… 2 | โœ… 4 | โ€” | โœ… 6 | 31 / 31 / 31 | 3 / 3 / 3 | โœ… | Legend: โœ… = clean, โŒ = missing, `legacy / total` = classes still on a legacy base, `โ€”` = artefact type not used by this package (treated as complete). FxTemplates show `clean / spec / total` โ€” `clean` = uses spec types and no legacy `parameter.RealParameter`-style attrs; `spec` = body references `beast.base.spec.*` at all. @@ -83,6 +85,7 @@ Per package, for each kind: `spec / mixed / legacy / neutral ยท total`. | GammaSpikeModel | 3 / 0 / 0 / 1 ยท 4 | 4 / 0 / 0 / 8 ยท 12 | 0 / 0 / 0 / 3 ยท 3 | 4 / 0 / 0 / 0 ยท 4 | โ€” | โ€” | | BDMM-Prime | 2 / 0 / 0 / 5 ยท 7 | 0 / 0 / 0 / 7 ยท 7 | 0 / 0 / 0 / 3 ยท 3 | 2 / 0 / 0 / 22 ยท 24 | โ€” | 0 / 0 / 0 / 3 ยท 3 | | remaster | โ€” | โ€” | 0 / 0 / 0 / 2 ยท 2 | 0 / 0 / 0 / 5 ยท 5 | โ€” | 0 / 0 / 0 / 2 ยท 2 | +| contacTrees | 0 / 0 / 0 / 4 ยท 4 | 0 / 0 / 0 / 21 ยท 21 | 0 / 0 / 0 / 2 ยท 2 | 3 / 0 / 0 / 1 ยท 4 | โ€” | 0 / 0 / 0 / 6 ยท 6 | ## Diagnostics diff --git a/reports/README.md b/reports/README.md index 0e4854b..5bee999 100644 --- a/reports/README.md +++ b/reports/README.md @@ -23,3 +23,4 @@ for the high-level cross-package status table. | [GammaSpikeModel](GammaSpikeModel.md) | compile-tested | โŒ | `13bd1b2` | `1.3.0-SNAPSHOT` | | [BDMM-Prime](BDMM-Prime.md) | compile-tested | โŒ | `ee37e1b` | `3.0.0` | | [remaster](remaster.md) | compile-tested | โŒ | `896c7b7` | `3.0.0` | +| [contacTrees](contacTrees.md) | Maven Central | `2.0.0` | `0c20eda` | `2.0.0` | diff --git a/reports/contacTrees.md b/reports/contacTrees.md new file mode 100644 index 0000000..e24bfdd --- /dev/null +++ b/reports/contacTrees.md @@ -0,0 +1,155 @@ +# contacTrees โ€” what's left + +> **Scanned at:** 2026-07-21T16:02:07.591752 +> **Commit:** `0c20eda` on `master` โ€” [view on GitHub](https://github.com/NicoNeureiter/contacTrees/commit/0c20eda49ae00f26846a45d390c7fe56b1a92c29) +> **Pom version:** `2.0.0` +> **Maven Central:** `io.github.niconeureiter:contactrees:2.0.0` +> **Stage hint:** Maven Central + +## Summary + +- **Java classes:** 3 on spec, 0 mixed, 0 legacy of 89 total +- **Example XMLs:** 31 on spec / 31 on `version="2.8"` / 31 total + - skipped: 4 untracked by git +- **BEAUti fxtemplates:** 3 clean / 3 use spec / 3 total +- **Input rule:** all Inputs use the right carrier โœ… +- **Maven Central:** 2.0.0 + +## Java migration + +No Java classes flagged as legacy or mixed โ€” all relevant types are on spec or have no parameter involvement. โœ… + +## Example XMLs + +All example XMLs target `version="2.8"` and use spec types with no legacy parameter declarations. โœ… + +## FxTemplates + +All BEAUti fxtemplates use spec types with no legacy `parameter.*` declarations. โœ… + +## Deprecated class references in XMLs + +> Every entry below points at a class annotated `@Deprecated` in the spec sources. Replace each `spec=`/`` reference with the suggested spec replacement, or drop it entirely if the surrounding `` wrapper or `` is now unused. Short-name hits (no dots) resolve to deprecated classes whose simple name is unambiguous within the scanned packages. + +**`fxtemplates/ContacTrees.xml`** (9): + +| Where | Hit | Replacement | +|---|---|---| +| `map=` | `beast.base.inference.distribution.Uniform` | `beast.base.spec.inference.distribution.Uniform` | +| `map=` | `beast.base.inference.distribution.Normal` | `beast.base.spec.inference.distribution.Normal` | +| `map=` | `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | +| `map=` | `beast.base.inference.distribution.Exponential` | `beast.base.spec.inference.distribution.Exponential` | +| `map=` | `beast.base.inference.distribution.Gamma` | `beast.base.spec.inference.distribution.Gamma` | +| `map=` | `beast.base.inference.distribution.Beta` | `beast.base.spec.inference.distribution.Beta` | +| `map=` | `beast.base.inference.distribution.LaplaceDistribution` | `beast.base.spec.inference.distribution.Laplace` | +| `map=` | `beast.base.inference.distribution.InverseGamma` | `beast.base.spec.inference.distribution.InverseGamma` | +| `map=` | `beast.base.inference.distribution.Prior` | `beast.base.spec.inference.distribution.TensorDistribution` | + +**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeHop.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_NarrowExchange.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeHopGibbs.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_Uniform.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_Scale.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_AddRemoveConversion.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeSlide.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_ScaleRoot.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_ConversionSplit.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/2taxa_AddRemoveConversion.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_AddRemoveConversionGibbs.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_CFConversionSwap.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_GibbsSampleMovesPerConversion.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_WideExchange.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeFlip.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/10taxa_WilsonBalding.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/operatorTests/2taxa_ConversionSplit.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + +**`src/test/resources/examples/ACGsimulations/simulateACGs2taxon.xml`** (1): + +| Where | Hit | Replacement | +|---|---|---| +| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | + From 005a32a37032704f31ab1e356c78ad003a4fa16a Mon Sep 17 00:00:00 2001 From: Nico Neureiter Date: Tue, 21 Jul 2026 16:35:00 +0200 Subject: [PATCH 3/4] updated contacTrees report --- CHECKLIST.md | 4 +- reports/README.md | 2 +- reports/contacTrees.md | 130 +---------------------------------------- 3 files changed, 5 insertions(+), 131 deletions(-) diff --git a/CHECKLIST.md b/CHECKLIST.md index 2b6441b..f45472a 100644 --- a/CHECKLIST.md +++ b/CHECKLIST.md @@ -9,7 +9,7 @@ are at the bottom of this page. -_Last regenerated: 2026-07-21T16:02:08.207735+02:00_ +_Last regenerated: 2026-07-21T16:30:34.397365+02:00_ ## Release & build status @@ -31,7 +31,7 @@ _Last regenerated: 2026-07-21T16:02:08.207735+02:00_ | [GammaSpikeModel](https://github.com/jordandouglas/GammaSpikeModel) | compile-tested | โ€” | 1.3.0-SNAPSHOT | โœ… | โœ… | โŒ | ๐ŸŸก | ๐Ÿ”ด | ๐ŸŸข | 262 | | [BDMM-Prime](https://github.com/tgvaughan/BDMM-Prime) | compile-tested | โ€” | 3.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | โ€” | ๐ŸŸข | โœ… | | [remaster](https://github.com/tgvaughan/remaster) | compile-tested | โ€” | 3.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | ๐Ÿ”ด | โ€” | 10 | -| [contacTrees](https://github.com/NicoNeureiter/contacTrees) | Maven Central | [2.0.0](https://central.sonatype.com/artifact/io.github.niconeureiter/contactrees) | 2.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | ๐ŸŸก | ๐ŸŸก | 27 | +| [contacTrees](https://github.com/NicoNeureiter/contacTrees) | Maven Central | [2.0.0](https://central.sonatype.com/artifact/io.github.niconeureiter/contactrees) | 2.0.0 | โœ… | โœ… | โœ… | ๐ŸŸข | ๐ŸŸข | ๐ŸŸข | โœ… | Traffic-light columns: ๐Ÿ”ด any legacy lineage / non-migrated content, ๐ŸŸก no legacy but some unnecessarily-concrete Inputs (Code), or stray legacy `parameter.*` declarations / references to `@Deprecated` classes (XML / FxT), ๐ŸŸข clean, โ€” = 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 `` bodies); also degrades the XML / FxT light to ๐ŸŸก when non-zero. 0 = โœ…. Per-package reports list each hit and the spec replacement. diff --git a/reports/README.md b/reports/README.md index 5bee999..b320529 100644 --- a/reports/README.md +++ b/reports/README.md @@ -23,4 +23,4 @@ for the high-level cross-package status table. | [GammaSpikeModel](GammaSpikeModel.md) | compile-tested | โŒ | `13bd1b2` | `1.3.0-SNAPSHOT` | | [BDMM-Prime](BDMM-Prime.md) | compile-tested | โŒ | `ee37e1b` | `3.0.0` | | [remaster](remaster.md) | compile-tested | โŒ | `896c7b7` | `3.0.0` | -| [contacTrees](contacTrees.md) | Maven Central | `2.0.0` | `0c20eda` | `2.0.0` | +| [contacTrees](contacTrees.md) | Maven Central | `2.0.0` | `efff8b7` | `2.0.0` | diff --git a/reports/contacTrees.md b/reports/contacTrees.md index e24bfdd..e455b6a 100644 --- a/reports/contacTrees.md +++ b/reports/contacTrees.md @@ -1,7 +1,7 @@ # contacTrees โ€” what's left -> **Scanned at:** 2026-07-21T16:02:07.591752 -> **Commit:** `0c20eda` on `master` โ€” [view on GitHub](https://github.com/NicoNeureiter/contacTrees/commit/0c20eda49ae00f26846a45d390c7fe56b1a92c29) +> **Scanned at:** 2026-07-21T16:30:34.158327 +> **Commit:** `efff8b7` on `master` โ€” [view on GitHub](https://github.com/NicoNeureiter/contacTrees/commit/efff8b7ef5bd7864487a87d9ab74d4e78c1b8d49) > **Pom version:** `2.0.0` > **Maven Central:** `io.github.niconeureiter:contactrees:2.0.0` > **Stage hint:** Maven Central @@ -27,129 +27,3 @@ All example XMLs target `version="2.8"` and use spec types with no legacy parame All BEAUti fxtemplates use spec types with no legacy `parameter.*` declarations. โœ… -## Deprecated class references in XMLs - -> Every entry below points at a class annotated `@Deprecated` in the spec sources. Replace each `spec=`/`` reference with the suggested spec replacement, or drop it entirely if the surrounding `` wrapper or `` is now unused. Short-name hits (no dots) resolve to deprecated classes whose simple name is unambiguous within the scanned packages. - -**`fxtemplates/ContacTrees.xml`** (9): - -| Where | Hit | Replacement | -|---|---|---| -| `map=` | `beast.base.inference.distribution.Uniform` | `beast.base.spec.inference.distribution.Uniform` | -| `map=` | `beast.base.inference.distribution.Normal` | `beast.base.spec.inference.distribution.Normal` | -| `map=` | `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | -| `map=` | `beast.base.inference.distribution.Exponential` | `beast.base.spec.inference.distribution.Exponential` | -| `map=` | `beast.base.inference.distribution.Gamma` | `beast.base.spec.inference.distribution.Gamma` | -| `map=` | `beast.base.inference.distribution.Beta` | `beast.base.spec.inference.distribution.Beta` | -| `map=` | `beast.base.inference.distribution.LaplaceDistribution` | `beast.base.spec.inference.distribution.Laplace` | -| `map=` | `beast.base.inference.distribution.InverseGamma` | `beast.base.spec.inference.distribution.InverseGamma` | -| `map=` | `beast.base.inference.distribution.Prior` | `beast.base.spec.inference.distribution.TensorDistribution` | - -**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeHop.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_NarrowExchange.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeHopGibbs.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_Uniform.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_Scale.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_AddRemoveConversion.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeSlide.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_ScaleRoot.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_ConversionSplit.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/2taxa_AddRemoveConversion.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_AddRemoveConversionGibbs.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_CFConversionSwap.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_GibbsSampleMovesPerConversion.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_WideExchange.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_ConvertedEdgeFlip.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/10taxa_WilsonBalding.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/operatorTests/2taxa_ConversionSplit.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - -**`src/test/resources/examples/ACGsimulations/simulateACGs2taxon.xml`** (1): - -| Where | Hit | Replacement | -|---|---|---| -| `spec=` | `LogNormalDistributionModel` โ†’ `beast.base.inference.distribution.LogNormalDistributionModel` | `beast.base.spec.inference.distribution.LogNormal` | - From 30f4c88af71385d1b9337f39b8ebfb488ea72c9f Mon Sep 17 00:00:00 2001 From: Nico Neureiter Date: Tue, 21 Jul 2026 16:40:56 +0200 Subject: [PATCH 4/4] update BACKLOG.md --- BACKLOG.md | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/BACKLOG.md b/BACKLOG.md index d9a0156..836f654 100644 --- a/BACKLOG.md +++ b/BACKLOG.md @@ -3,15 +3,15 @@ Auto-generated from CBAN's `packages2.7.xml`, `packages-extra-2.7.xml`, and `packages2.8.xml`. Regenerate with `python3 scripts/gen-backlog.py`. -_Last regenerated: 2026-05-13T17:39:18+12:00_ +_Last regenerated: 2026-07-21T16:40:14+02:00_ ## Summary -- v2.7 packages (union of main + extra): **84** -- Migrated to v2.8 (in `packages2.8.xml`): **10** +- v2.7 packages (union of main + extra): **87** +- Migrated to v2.8 (in `packages2.8.xml`): **14** - Built into beast3 core in v2.8: **2** (BEAST.app, BEAST.base) - Tracked in `packages.yaml` but not yet in `packages2.8.xml`: **3** -- Untracked, unmigrated: **69** +- Untracked, unmigrated: **68** ## Tracked in `packages.yaml` but not yet in CBAN packages2.8.xml @@ -31,7 +31,7 @@ These v2.7 packages are not in `packages2.8.xml` and are not currently tracked i |---|---|---|---|---| | 5rf | extra | 0.0.2 | [link](https://github.com/rbouckaert/5rf/) | Rate Class Root Frequency Model | | AlmostDistributions | extra | 0.2.1 | [link](https://github.com/rbouckaert/AlmostDistributions) | Almost-distributions | -| ASM | extra | 0.0.1 | [link](https://github.com/rbouckaert/asm) | Automatic stopping MCMC | +| ASM | main | 0.0.1 | [link](https://github.com/rbouckaert/asm) | Automatic stopping MCMC | | Babel | main | 0.4.2 | [link](https://github.com/rbouckaert/Babel) | BABEL = BEAST analysis backing effective linguistics | | bacter | main | 3.0.1 | [link](https://tgvaughan.github.io/bacter) | Bacterial ARG inference. | | BADTRIP | main | 2.0.0 | [link](https://bitbucket.org/nicofmay/badtrip) | Infer transmission time for non-haplotype data and epi data | @@ -40,17 +40,16 @@ These v2.7 packages are not in `packages2.8.xml` and are not currently tracked i | BDSKY | main | 1.5.1 | [link](https://github.com/BEAST2-Dev/bdsky/) | birth death skyline - handles serially sampled tips, piecewise constant rate changes through time and sampled ancestors | | bdtree | main | 0.0.2 | [link](https://github.com/fkmendes/bdtree) | Birth-death sequential sampling | | BEAST2Lang | extra | 0.0.1 | [link](https://github.com/CompEvol/beast2lang/) | Run a Beast2 model using the definition language | +| BEASTBooster | extra | 0.0.2 | [link](https://github.com/rbouckaert/beastbooster) | BEAST Booster | | beastmap | extra | 0.0.3 | [link](https://github.com/jordandouglas/BeastMap/) | Stochastic mapping and ancestral sequence/state reconstruction | | BEASTvntr | main | 0.2.0 | [link](https://github.com/arjun-1/BEASTvntr) | Variable Number of Tandem Repeat data, such as microsattelites | -| BICEPS | main | 1.1.2 | [link](https://github.com/rbouckaert/biceps/) | Bayesian Integrated Coalescent Epoch PlotS + Yule Skyline | | BREAK_AWAY | main | 1.2.0 | [link](https://github.com/rbouckaert/break-away) | break-away model of phylogegraphy | -| BREATH | extra | 0.0.5 | [link](https://github.com/rbouckaert/transmission) | Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories | +| BREATH | extra | 0.0.6 | [link](https://github.com/rbouckaert/transmission) | Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories | | CA | main | 2.1.0 | [link](https://github.com/BEAST2-Dev/cladeage) | Bayesian estimation of clade ages based on probabilities of fossil sampling | | CCD | main+extra | 1.0.3 | [link](https://github.com/CompEvol/CCD) | Better tree distribution and point estimates, computation of entropy, rogues and more. | | ClaDS | main | 2.3.0 | [link](https://bitbucket.org/bjoelle/clads/) | Implementation of the ClaDS birth-death tree prior with sampled ancestors | | CoalRe | main | 1.0.4 | [link](https://github.com/nicfel/CoalRe/) | Inference of Recombination networks | | CodonSubstModels | main | 2.0.1 | [link](https://github.com/BEAST2-Dev/codonsubstmodels) | Codon substitution models for DNA | -| contacTrees | main | 1.2.0 | [link](https://github.com/NicoNeureiter/contacTrees) | Phylogenetic model with horizontal transfer for linguistics | | contraband | main | 1.0.2 | [link](https://github.com/fkmendes/contraband) | Scalable brownian models for continuous trait evolution | | CorrelatedTrait | extra | 0.0.5 | [link](https://github.com/rbouckaert/CorrelatedTrait) | Analysis for a fixed tree or fixed tree set | | CubeVB | main | 1.0.2 | [link](https://github.com/rbouckaert/cubevb) | Variational Bayes on a cube | @@ -73,8 +72,9 @@ These v2.7 packages are not in `packages2.8.xml` and are not currently tracked i | MSBD | main | 2.0.6 | [link](https://bitbucket.org/bjoelle/msbd/) | MSBD multi-type birth-death tree prior with sampled ancestors | | MultiTypeTree | main | 8.3.0 | [link](https://tgvaughan.github.io/MultiTypeTree) | Structured coalescent inference. | | NS | main | 1.2.2 | [link](https://github.com/BEAST2-Dev/nested-sampling/wiki) | Nested sampling for model selection and posterior inference | +| online | extra | 0.0.2 | [link](https://github.com/rbouckaert/online) | Online and faster parallel phylogenetics | | PhyDyn | main | 1.4.0 | [link](https://github.com/mrc-ide/PhyDyn) | PhyDyn: Epidemiological modelling with BEAST | -| phylodynamics | main | 1.4.0 | [link](https://github.com/BEAST2-Dev/phylodynamics) | BDSIR and Stochastic Coalescent | +| phylodynamics | main | 1.5.0 | [link](https://github.com/BEAST2-Dev/phylodynamics) | BDSIR and Stochastic Coalescent | | phylonco | main | 1.2.1 | [link](https://github.com/bioDS/beast-phylonco) | A package for single cell cancer evolution. | | phylonco.lphybeast | main | 1.2.1 | [link](https://github.com/bioDS/beast-phylonco) | A LPhyBEAST extension for phylonco (requires: LPhy and phylonco-lphy). | | PIQMEE | main | 1.0.0 | [link](https://github.com/boskovav/piqmee) | Birth-death skyline-based method efficiently dealing with duplicate sequences | @@ -89,7 +89,6 @@ These v2.7 packages are not in `packages2.8.xml` and are not currently tracked i | snapper | main | 1.1.5 | [link](https://github.com/rbouckaert/snapper) | Diffusion based SNP and AFLP Phylogenies | | SpeciesNetwork | main | 1.0.0 | [link](https://github.com/zhangchicool/speciesnetwork) | Multispecies network coalescent (MSNC) inference of introgression and hybridization | | speedemon | main | 1.1.0 | [link](https://github.com/rbouckaert/speedemon) | Fast species delimitation under the multispecies coalescent | -| SSM | main | 1.2.2 | [link](https://github.com/BEAST2-Dev/substmodels/) | Standard Nucleotide Substitution Models | | STACEY | main | 1.3.1 | [link](http://indriid.com/software.html) | Species delimitation and species tree estimation | | StarBEAST2 | main | 1.0.0 | [link](https://github.com/genomescale/starbeast2) | Multispecies coalescent inference using multi-locus and fossil data | | starbeast3 | main | 1.2.1 | [link](https://github.com/rbouckaert/starbeast3) | StarBeast3 multispecies coalescent using advanced MCMC operators | @@ -103,13 +102,17 @@ These v2.7 packages are not in `packages2.8.xml` and are not currently tracked i | Package | Latest 2.7 | Latest 2.8 | |---|---|---| +| BDMM-Prime | 2.7.2 | 3.0.0 | | BEAST_CLASSIC | 1.6.4 | 1.7.0 | | BEASTLabs | 2.0.3 | 2.1.0 | +| BICEPS | 1.1.2 | 1.2.0 | +| contacTrees | 1.2.0 | 2.0.0 | | CoupledMCMC | 1.2.2 | 1.3.0 | -| feast | 10.6.1 | 11.0.0 | +| feast | 10.6.1 | 11.0.1 | | gammaspike | 1.2.0 | 1.3.0 | | Mascot | 3.0.7 | 3.1.0 | | MM | 1.2.1 | 1.3.0 | | ORC | 1.2.1 | 1.3.1 | -| ReMASTER | 2.7.4 | 3.0.0 | +| ReMASTER | 2.7.4 | 3.0.1 | | SA | 2.1.1 | 2.3.0 | +| SSM | 1.2.2 | 1.3.0 |