Bench

.Rbuildignore

@@ -7,3 +7,4 @@
 ^pkgdown$
 ^\.github$
 ^CODE_OF_CONDUCT\.md$
+^bench$

.github/workflows/benchmarks.yml

@@ -0,0 +1,118 @@
+on: push
+
+name: Continuous Benchmarks
+
+jobs:
+  build:
+    runs-on: ${{ matrix.config.os }}
+
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+          # fails: https://github.com/luukvdmeer/sfnetworks/pull/64/checks?check_run_id=798178450
+          # - {os: ubuntu-20.04, r: 'release'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      CRAN: ${{ matrix.config.cran }}
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Brew and macOS config
+        if: runner.os == 'macOS'
+        run: |
+          brew install pkg-config
+          brew install udunits
+          brew install gdal
+          cat <<EOT >> .Renviron
+          PKG_CONFIG_PATH=/usr/local/lib/pkgconfig/
+          PROJ_LIB=/usr/local/opt/proj/share/proj/
+          # for installing XML package from source
+          XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config
+          EOT
+          cat <<EOT >> .Rprofile
+          r <- getOption("repos")
+          r["CRAN"] <- "https://cran.rstudio.com"
+          r["rccp_drat"] <- "https://RcppCore.github.io/drat"
+          config_args <- c("sf" = "--with-proj-lib=/usr/local/lib/", "rgdal" = "--with-proj-lib=/usr/local/lib/ --with-proj-include=/usr/local/include/")
+          options(configure.args = config_args,
+                  install.packages.compile.from.source = "yes",
+                  repos = r)
+          EOT
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+
+          # install spatial dependencies
+          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt update
+          sudo apt install \
+            libudunits2-dev \
+            libgdal-dev \
+            libgeos-dev \
+            libproj-dev
+          git config --global user.email "[email protected]"
+          git config --global user.name "Robin Lovelace"
+
+      - name: Install dependencies
+        run: |
+          library(remotes)
+          deps <- readRDS("depends.Rds")
+          deps[["installed"]] <- vapply(deps[["package"]], remotes:::local_sha, character(1))
+          update(deps)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Checkout repo
+        uses: actions/checkout@master
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@master
+
+      - name: Install dependencies
+        run: |
+          Rscript -e "install.packages(c('remotes', 'jsonlite'))" -e "remotes::install_deps(dependencies = TRUE)"  -e "remotes::install_github('r-lib/bench')"
+          R CMD INSTALL .
+      - name: Fetch existing benchmarks
+        run: Rscript -e 'bench::cb_fetch()'
+
+      - name: Run benchmarks
+        run: Rscript -e 'bench::cb_run()'
+
+      - name: Show benchmarks
+        run: git notes --ref benchmarks show
+
+      - name: Push benchmarks
+        run: Rscript -e "bench::cb_push()"

bench/create.R

@@ -0,0 +1,42 @@
+pkgload::load_all()
+# remotes::install_github("luukvdmeer/sfnetworks@develop")
+# library(sfnetworks)
+
+bench::mark(check = FALSE,
+            as_sfnetwork(roxel[1:10, ]),
+            as_sfnetwork(roxel[1:100, ]),
+            as_sfnetwork(roxel[1:200, ]),
+            as_sfnetwork(roxel)
+            )
+
+# See https://github.com/r-lib/bench/issues/88
+# bench::press(n = c(10, 100, 200, nrow(roxel)),
+#              {
+#                bench::mark(check = FALSE,
+#                  as_sfnetwork(roxel[1:n, ]),
+#                )
+#              }
+#              )
+
+# # comparison with stplanr (commented out to reduce dependencies)
+# library(sfnetworks)
+# system.time({
+#   net = as_sfnetwork(roxel)
+# })
+# system.time({
+#   net2 = stplanr::SpatialLinesNetwork(roxel)
+# })
+# pryr::object_size(net)
+# pryr::object_size(net2)
+#
+# res = bench::press(n = seq(from = 10, to = nrow(roxel), length.out = 5),
+#              {
+#                bench::mark(
+#                  check = FALSE,
+#                  time_unit = "ms",
+#                  stplanr::SpatialLinesNetwork(roxel[1:n, ]),
+#                  sfnetworks::as_sfnetwork(roxel[1:n, ])
+#                )
+#              }
+# )
+# ggplot2::autoplot(res)

bench/shortpath.R

@@ -0,0 +1,55 @@
+pkgload::load_all()
+
+library(sf)
+library(tidygraph)
+
+net = as_sfnetwork(roxel, directed = FALSE)
+
+bench::mark(
+  sp_1_9 = {
+  short_path_1_9 = net %>%
+    activate("edges") %>%
+    dplyr::mutate(weight = edge_length()) %>%
+    tidygraph::convert(to_shortest_path, 1, 9)
+})
+
+#
+# plot(roxel$geometry)
+# plot(sf::st_as_sf(short_path_1_9)$geometry, lwd = 5, add = TRUE)
+
+# sp = function(net, from, to) {
+#   net %>%
+#     activate("edges") %>%
+#     dplyr::mutate(weight = edge_length()) %>%
+#     tidygraph::convert(to_shortest_path, from, to)
+# }
+# sp(net, 1, 9)
+# bench::press(n = seq(from = 9, to = 99, length.out = 5),
+#              {
+#                bench::mark(
+#                  sp(net, 9, n)
+#                )
+#              }
+#              )
+
+# with stplanr # work in progress, not currently working
+# library(stplanr)
+# sln = SpatialLinesNetwork(roxel)
+# p1 = net %>%
+#   activate(nodes) %>%
+#   st_as_sf() %>%
+#   slice(1)
+# p9 = net %>%
+#   activate(nodes) %>%
+#   st_as_sf() %>%
+#   slice(1)
+#
+# stplanr::route_local(sln = sln, from = c(st_coordinates(p1)), to = c(st_coordinates(p9)))
+#
+# bench::press(n = seq(from = 9, to = 99, length.out = 5),
+#              {
+#                bench::mark(
+#                  sp(net, 9, n)
+#                )
+#              }
+# )