Merge branch 'release/2.6.0' into stable

inlabru-org · Oct 24, 2022 · e1c6600 · e1c6600
2 parents 978b2e5 + 6aa3dab
commit e1c6600
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Showing 99 changed files with 6,533 additions and 1,649 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -22,3 +22,4 @@
 ^revdep$
 ^data-raw$
 ^inst/misc/Lambert_ocean_orig.png$
+^sf$
diff --git a/.github/workflows/R-CMD-check-no-suggests.yaml b/.github/workflows/R-CMD-check-no-suggests.yaml
@@ -23,26 +23,28 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-20.04, r: 'release'}
+          - {os: ubuntu-20.04, r: 'oldrel-1'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
           extra-repositories: "https://inla.r-inla-download.org/R/testing"
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - name: Install system dependencies on MacOS (X11, gdal)
         if: runner.os == 'macOS'
         run: |
@@ -51,6 +53,11 @@ jobs:
           brew install proj@9
           brew install gdal
 
+      - name: Install system dependencies on Linux (GL)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y && sudo apt-get install -y libglu1-mesa-dev
+
       - name: Has inla? Check.
         run: |
           options(width = 100)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -23,26 +23,28 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-20.04, r: 'release'}
+          - {os: ubuntu-20.04, r: 'oldrel-1'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
           extra-repositories: "https://inla.r-inla-download.org/R/testing"
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - name: Install system dependencies on MacOS (X11, gdal)
         if: runner.os == 'macOS'
         run: |
@@ -51,6 +53,11 @@ jobs:
           brew install proj@9
           brew install gdal
 
+      - name: Install system dependencies on Linux (GL)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update -y && sudo apt-get install -y libglu1-mesa-dev
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: '"all"'

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,3 +1,5 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches:
@@ -14,25 +16,29 @@ name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: "ubuntu-latest"
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
+          use-public-rspm: true
           r-version: "release"
           extra-repositories: "https://inla.r-inla-download.org/R/testing"
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          dependencies: '"all"'
-          extra-packages: |
-             pkgdown
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
       - name: Session info
         run: |
@@ -41,19 +47,27 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
       # Enable tmate debugging of manually-triggered workflows if the input option was provided
       # https://mxschmitt.github.io/action-tmate/
-      - name: Setup tmate session
+      - name: Setup tmate debugging session
         uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
         with:
           limit-access-to-actor: true
 
-      - name: Deploy package
+      - name: Mermaid update
         run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+          source("vignettes/web/mermaid_updater.R")
+        shell: Rscript {0}
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.lintr b/.lintr
@@ -1,11 +1,10 @@
-linters: with_defaults(
+linters: linters_with_defaults(
     line_length_linter = NULL, # 866
     object_name_linter = NULL, # 618
     commented_code_linter = NULL, # 121
     object_usage_linter = NULL, # 54
     object_length_linter = NULL, # 28
-    cyclocomp_linter = NULL, # 27
-    dummy_linter = NULL
+    cyclocomp_linter = NULL # 27
   )
 exclusions: list(
     "data/gorillas.rda",

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: inlabru
 Type: Package
 Title: Bayesian Latent Gaussian Modelling using INLA and Extensions
-Version: 2.5.3
+Version: 2.6.0
 Authors@R: c(
   person("Finn", "Lindgren", email = "finn.lindgren@gmail.com",
          role = c("aut", "cre", "cph"),
@@ -22,7 +22,7 @@ Authors@R: c(
   person("Seaton", "Andy", email = "andy.e.seaton@gmail.com", role = c("ctb"),
          comment = "Andy Seaton provided testing and bugfixes"),
   person("Suen", "Man Ho", email = "M.H.Suen@sms.ed.ac.uk", role = c("ctb", "cph"),
-         comment = "Man Ho Suen contributed features for aggregated responses and vignett updates"),
+         comment = "Man Ho Suen contributed features for aggregated responses and vignette updates"),
   person("Roudier", "Pierre", email = "", role = c("ctb", "cph"),
          comment = "Pierre Roudier contributed general quantile summaries"),
   person("Meehan", "Tim", email = "tmeeha@gmail.com", role = c("ctb", "cph"),
@@ -60,6 +60,7 @@ Imports:
     rgdal (>= 1.5.8),
     rgeos,
     rlang,
+    sf,
     utils,
     withr
 Suggests:
@@ -79,7 +80,6 @@ Suggests:
     rgl,
     rmarkdown,
     scales,
-    sf,
     shiny,
     sn,
     spatstat.geom,
@@ -88,8 +88,10 @@ Suggests:
     spatstat (>= 2.0-0),
     sphereplot,
     splancs,
+    terra,
     testthat,
-    tidyr
+    tidyr,
+    DiagrammeR
 Roxygen: list(markdown = TRUE)
 Config/testthat/parallel: true
 Config/testthat/edition: 3
@@ -119,6 +121,8 @@ Collate:
     'effect.R'
     'environment.R'
     'fmesher_crs.R'
+    'fmesher_sf_mesh.R'
+    'fmesher_sp_mesh.R'
     'fmesher_utils.R'
     'ggplot.R'
     'inla.R'
@@ -133,6 +137,7 @@ Collate:
     'prediction.R'
     'rgl.R'
     'sampling.R'
+    'sf_utils.R'
     'shapefile.R'
     'spatstat.R'
     'spde.R'