Merge branch 'master' into update-pkgdown

Author: florence-bockting

.Rbuildignore

@@ -24,3 +24,4 @@ vignettes/loo2-non-factorized_cache/*
 ^release-prep\.R$
 ^_pkgdown\.yml$
 ^pkgdown$
+^touchstone$

.gitattributes

@@ -1,4 +1,6 @@
 * text=auto
 data/* binary
-src/* text=lf
-R/* text=lf
+src/* text eol=lf
+R/* text eol=lf
+*.rda binary
+

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/R-CMD-check.yaml

@@ -30,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pkgdown.yaml

@@ -23,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/test-coverage.yaml

@@ -7,7 +7,9 @@ on:
 
 name: test-coverage.yaml
 
-permissions: read-all
+permissions:
+  contents: read
+  id-token: write
 
 jobs:
   test-coverage:
@@ -16,7 +18,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -34,17 +36,18 @@ jobs:
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v6
         with:
-          # Fail if error if not on PR, or if on PR and token is given
+          # Fail if error if not on PR, or if on PR and token is given--dependabot is treated like fork
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
-          file: ./cobertura.xml
-          plugin: noop
+          files: ./cobertura.xml
+          plugins: noop
           disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+          use_oidc: true
 
       - name: Show testthat output
         if: always()
@@ -55,7 +58,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.github/workflows/touchstone-comment.yaml

@@ -0,0 +1,46 @@
+name: Continuous Benchmarks (Comment)
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.run_id }}
+  cancel-in-progress: true
+
+on:
+  workflow_run:
+    workflows: ["Continuous Benchmarks (Receive)"]
+    types: [completed]
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      pull-requests: write
+    if: ${{ github.event.workflow_run.event == 'pull_request' }}
+    steps:
+      - name: Download Touchstone artifact
+        id: download
+        uses: actions/download-artifact@v8
+        with:
+          name: pr
+          github-token: ${{ github.token }}
+          repository: ${{ github.repository }}
+          run-id: ${{ github.event.workflow_run.id }}
+
+      # defensive since issues could cause commenting in random places
+      - name: Read PR number
+        id: pr
+        shell: bash
+        run: |
+          number="$(tr -cd '0-9' < ./NR)"
+          test -n "$number"
+          echo "number=$number" >> "$GITHUB_OUTPUT"
+
+      - name: Create or update sticky PR comment
+        id: comment
+        uses: marocchino/sticky-pull-request-comment@v3
+        with:
+          GITHUB_TOKEN: ${{ github.token }}
+          number_force: ${{ steps.pr.outputs.number }}
+          header: touchstone
+          path: ./info.txt
+          skip_unchanged: true

.github/workflows/touchstone-receive.yaml

@@ -0,0 +1,43 @@
+name: Continuous Benchmarks (Receive)
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      config: ${{ steps.read_touchstone_config.outputs.config }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - id: read_touchstone_config
+        run: |
+          echo "config=$(jq -c . ./touchstone/config.json)" >> $GITHUB_OUTPUT
+
+  build:
+    needs: prepare
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - ${{ fromJson(needs.prepare.outputs.config) }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: lorenzwalthert/touchstone/actions/receive@main
+        with:
+          r-version: ${{ matrix.config.r }}

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.8.0
-Date: 2024-07-03 16:27:12 UTC
-SHA: 23e68bf5fb8aa9d000358f3bbbf52cf7ee92a99c
+Version: 2.9.0
+Date: 2025-12-22 18:21:47 UTC
+SHA: fd95b46e4868019ff05034384f28f12960f69f33

DESCRIPTION

@@ -1,11 +1,11 @@
 Type: Package
 Package: loo
 Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
-Version: 2.8.0.9000
-Date: 2024-07-03
+Version: 2.9.0.9000
+Date: 2025-12-22
 Authors@R: c(
-    person("Aki", "Vehtari", , "Aki.Vehtari@aalto.fi", role = "aut"),
-    person("Jonah", "Gabry", , "jsg2201@columbia.edu", role = c("cre", "aut")),
+    person("Aki", "Vehtari", email = "Aki.Vehtari@aalto.fi", role = "aut"),
+    person("Jonah", "Gabry", email = "jgabry@gmail.com", role = c("cre", "aut")),
     person("Måns", "Magnusson", role = "aut"),
     person("Yuling", "Yao", role = "aut"),
     person("Paul-Christian", "Bürkner", role = "aut"),
@@ -14,9 +14,11 @@ Authors@R: c(
     person("Ben", "Goodrich", role = "ctb"),
     person("Juho", "Piironen", role = "ctb"),
     person("Bruno", "Nicenboim", role = "ctb"),
-    person("Leevi", "Lindgren", role = "ctb")
+    person("Leevi", "Lindgren", role = "ctb"),
+    person("Visruth", "Srimath Kandali", role = "ctb"),
+    person("Florence", "Bockting", role = "ctb")
   )
-Maintainer: Jonah Gabry <jsg2201@columbia.edu>
+Maintainer: Jonah Gabry <jgabry@gmail.com>
 Description: Efficient approximate leave-one-out cross-validation (LOO)
     for Bayesian models fit using Markov chain Monte Carlo, as described
     in Vehtari, Gelman, and Gabry (2017) <doi:10.1007/s11222-016-9696-4>.
@@ -36,7 +38,7 @@ Imports:
     checkmate,
     matrixStats (>= 0.52),
     parallel,
-    posterior (>= 1.5.0),
+    posterior (>= 1.7.0),
     stats
 Suggests:
     bayesplot (>= 1.7.0),