Migrate to terra and sf. Partially migrate to fmesher

.Rbuildignore

@@ -1,7 +1,10 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^\.git*
-README.md
-.travis.yml
-vignettes/disaggregation_cache/*
-cran-comments.md
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.git*
+README.md
+.travis.yml
+vignettes/disaggregation_cache/*
+cran-comments.md
+^\.github$
+.github/workflows/R-CMD-check-HTML5.archyaml
+vignettes/spatio_temporal_disaggregation.Rmd

vignettes/.gitignore → .github/.gitignore

@@ -1,2 +1 @@
 *.html
-*.R

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

@@ -0,0 +1,75 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      'build' 
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-12, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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"
+
+      - name: Install system dependencies on MacOS (X11, gdal)
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install pkg-config
+          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"'
+          extra-packages: |
+             rcmdcheck
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        with:
+          args: 'c("--no-manual", "--as-cran")'

.github/workflows/R-CMD-check-HTML5.yaml

@@ -0,0 +1,58 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches: [html5]
+  pull_request:
+    branches: [html5]
+
+name: R-CMD-check-html5
+
+
+jobs:
+  HTML5-check:
+    runs-on: ubuntu-latest
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          extra-repositories: "https://inla.r-inla-download.org/R/stable"
+
+
+      - name: Install pdflatex
+        run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies on MacOS (X11, gdal)
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install pkg-config
+          brew install proj@8
+          brew install gdal
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"all"'
+          extra-packages: |
+             rcmdcheck
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--as-cran"'
+          build_args: 'character()'
+          #error-on: '"note"'

.github/workflows/R-CMD-check-no-suggests.yaml

@@ -0,0 +1,96 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+#
+# Largely copied from: https://github.com/inlabru-org/inlabru/blob/devel/.github/workflows/R-CMD-check-no-suggests.yaml
+# Want to test without suggests to ensure things don't fail on cran when INLA isn't there.
+
+on:
+  push:
+    branches:
+      '**' 
+  pull_request:
+    branches:
+      - devel
+      - master
+
+name: R-CMD-check-no-suggests
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      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: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          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: |
+          brew install --cask xquartz
+          brew install pkg-config
+          brew install proj@9
+          brew install gdal
+
+      - name: Has inla? Check.
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          "INLA" %in% pkgs
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"hard"'
+          extra-packages: |
+            rcmdcheck
+            testthat
+
+      - name: Has inla? Check, and remove.
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          "INLA" %in% pkgs
+          if ("INLA" %in% pkgs) {
+            remove.packages("INLA")
+          }
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+        with:
+          build_args: 'c("--no-manual", "--no-build-vignettes")'
+          args: 'c("--no-manual", "--ignore-vignettes", "--as-cran")'
+
+
+
+

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

@@ -0,0 +1,69 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      '**' 
+  pull_request:
+    branches:
+      - devel
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      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"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          extra-repositories: "https://inla.r-inla-download.org/R/stable"
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies on MacOS (X11, gdal)
+        if: runner.os == 'macOS'
+        run: |
+          brew install --cask xquartz
+          brew install pkg-config
+          brew install proj@8
+          brew install gdal
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"all"'
+          extra-packages: |
+             rcmdcheck
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        with:
+          args: 'c("--no-manual", "--as-cran")'

.gitignore

@@ -1,9 +1,11 @@
-inst/doc
-.Rproj.user
-.Rhistory
-.Rproj
-.RData
-*.o
-*.so
-vignettes/disaggregation_cache/*
-vignettes/disaggregation_files/*
+inst/doc
+.Rproj.user
+.Rhistory
+.Rproj
+.RData
+*.o
+*.so
+vignettes/disaggregation_cache/*
+vignettes/disaggregation_files/*
+.github/workflows/R-CMD-check-HTML5.archyaml
+vignettes/spatio_temporal_disaggregation.Rmd