everything works?

prioritizr · Apr 24, 2024 · 1f8c51c · 1f8c51c
1 parent dd0317b
commit 1f8c51c
Show file tree

Hide file tree

Showing 145 changed files with 19,331 additions and 0 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,43 @@
+^doc$
+^Meta$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^gurobi\.log$
+^revdep$
+^docs$
+^appveyor\.yml$
+.gitkeep
+^Makefile$
+cran-comments.md
+CRAN-RELEASE
+_pkgdown.yml
+check.log
+test.log
+gp.log
+spell.log
+benchmark.log
+examples.log
+README.Rmd
+inst/extdata/dictionary.txt
+^_pkgdown\.yml$
+^debug*
+.editorconfig
+.travis.yml
+^simulation.R$
+^\.github$
+.covrignore
+^CRAN-RELEASE$
+config.status
+config.log
+^autom4te.cache*
+^windows$
+gmp_test
+gmp_test.cpp
+mpfr_test
+mpfr_test.cpp
+errors.txt
+inst/WORDLIST
+^CRAN-SUBMISSION$
+^pkgdown$
+codecov.yml
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check-macos.yaml b/.github/workflows/R-CMD-check-macos.yaml
@@ -0,0 +1,76 @@
+# 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:
+  schedule:
+    - cron: 0 0 * * 1 # schedule to run at midnight on Monday each week
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: macOS
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-14, r: 'release'}
+
+    env:
+      _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
+      _R_CHECK_FORCE_SUGGESTS_: false
+      _R_CHECK_TIMINGS_: 10
+      _R_CHECK_CRAN_INCOMING_REMOTE_: false
+
+    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 }}
+          use-public-rspm: true
+
+      - name: Install system dependencies
+        run: |
+          brew install gmp
+          brew install mpfr
+          brew install gdal
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 4
+          extra-packages: |
+            any::rcmdcheck
+            cran/XML
+          needs: |
+            check
+
+      - name: Session information
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+          cat("Platform:\n")
+          cat(system("uname -m"))
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml
@@ -0,0 +1,100 @@
+# 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:
+  schedule:
+    - cron: 0 0 * * 1 # schedule to run at midnight on Monday each week
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: Ubuntu
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-20.04, r: 'release'}
+          - {os: ubuntu-20.04, r: 'devel'}
+          - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only'}
+
+    env:
+      _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
+      _R_CHECK_FORCE_SUGGESTS_: false
+      _R_CHECK_TIMINGS_: 10
+      _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CI: true
+
+    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 }}
+          use-public-rspm: true
+
+      - name: Install system dependencies
+        run: |
+          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt update
+          sudo apt-get install \
+            libgdal-dev libgeos-dev libproj-dev \
+            libgmp3-dev libmpfr-dev libudunits2-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            any::rcmdcheck
+            any::covr
+            any::remotes
+            cran/XML
+          needs: |
+            check
+
+      - name: Install spatial R packages
+        run: |
+          options(repos = "https://cloud.r-project.org/")
+          install.packages("sf")
+          install.packages("lwgeom")
+        shell: Rscript {0}
+
+      - name: Session information
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Environmental variables
+        if: matrix.config.pkgs == 'depends only'
+        run: |
+          echo "_R_CHECK_DEPENDS_ONLY_=true" >> $GITHUB_ENV
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran", "--no-build-vignettes")'
+          upload-snapshots: true
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Test coverage
+        if: runner.os == 'Linux' && matrix.config.r == 'release'
+        run: covr::codecov()
+        shell: Rscript {0}
diff --git a/.github/workflows/R-CMD-check-windows.yaml b/.github/workflows/R-CMD-check-windows.yaml
@@ -0,0 +1,77 @@
+# 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:
+  schedule:
+    - cron: 0 0 * * 1 # schedule to run at midnight on Monday each week
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: Windows
+
+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'}
+
+    env:
+      _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
+      _R_CHECK_FORCE_SUGGESTS_: false
+      _R_CHECK_TIMINGS_: 10
+      _R_CHECK_CRAN_INCOMING_REMOTE_: false
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CI: true
+
+    steps:
+      # configure git to prevent it from automatically converting line-endings
+      # this is important to avoid WARNINGS during CRAN checks
+      # that are false-positives, see:
+      # https://msmith.de/2020/03/12/r-cmd-check-github-actions.html
+      - name: Configure git
+        run: git config --global core.autocrlf false
+
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            any::rcmdcheck
+            any::XML
+          needs: |
+            check
+
+      - name: Session information
+        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:
+          upload-snapshots: true
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,56 @@
+Meta
+doc
+# C++ compiled files
+*.o
+*.so
+*.dll
+
+# temporary files
+approximation.R
+simulation.R
+vignettes/simulation_files/figure-html/*png
+src/Makevars
+gmp_test
+gmp_test.cpp
+mpfr_test
+mpfr_test.cpp
+errors.txt
+
+# R profile files
+*.Rproj.user
+*.Rhistory
+.Rproj.user
+
+# log files
+gurobi.log
+test.log
+check.log
+spell.log
+gp.log
+benchmark.log
+examples.log
+
+# system files
+.directory
+
+# debugging files
+debug*R
+config.status
+config.log
+autom4te.cache/*
+
+# do not ignore the following files
+!.gitkeep
+!*/
+!inst/doc/*.html
+!inst/doc/*.Rmd
+!inst/doc/.gitkeep
+
+# devtools files
+doc/*
+Meta/*
+.build.timestamp
+.DS_Store
+*.tmp
+/doc/
+/Meta/