Build JAR on R build

.github/workflows/jar-and-R-ci.yaml → .github/workflows/ci.yml

@@ -2,88 +2,12 @@ name: CI
 
 on:
   push:
-    paths:
-      - java-r5rcore/**
-      - r-package/**
-      - .github/workflows/**
 
-jobs:
-  build-jar:
-    env:
-      GH_TOKEN: ${{ github.token }}
-
-    runs-on: ubuntu-latest
-
-    # don't build on merges to master
-    if: ${{ !github.ref_protected }}
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-#        with:
-#          use-public-rspm: true # this no longer works as of September 2025
-
-      - name: Install R packages
-        run: |
-          # this specification is necessary for some reason as of September 2025
-          options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/latest"))
-          install.packages(c('devtools', 'remotes'))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-        working-directory: r-package
+  pull_request:
 
-      - name: Install system dependencies
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-        working-directory: r-package
-
-      - name: Set up JDK 21
-        uses: actions/setup-java@v3
-        with:
-          java-version: '21'
-          distribution: 'temurin'
-      - name: Validate Gradle wrapper
-        uses: gradle/wrapper-validation-action@v2
-      - name: Build with Gradle
-        uses: gradle/gradle-build-action@749f47bda3e44aa060e82d7b3ef7e40d953bd629
-        with:
-          arguments: build
-          build-root-directory: java-r5rcore
-
-      - name: Create pull request
-        # https://github.com/actions/checkout/pull/1184
-        run: |
-          NEW_JAR="java-r5rcore/build/libs/java-r5rcore-*.jar"
-          TARGET_JAR="r-package/inst/jar/r5r.jar"
-
-          new_sha=$(sha256sum $NEW_JAR | awk '{print $1}')
-          # ensure file exists and then compute sha
-          old_sha=$( [ -f "$TARGET_JAR" ] && sha256sum "$TARGET_JAR" | awk '{print $1}' || echo "" )
-
-          echo "NEW: $new_sha"
-          echo "OLD: $old_sha"
-
-          # Only push if sha different
-          if [ "$new_sha" != "$old_sha" ]; then
-            git config user.name "github-actions[bot]"
-            git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
-
-            echo "JAR changed — updating."
-            mv $NEW_JAR $TARGET_JAR
-            git add $TARGET_JAR
-            git commit -m "Rebuild JAR for commit ${GITHUB_SHA}"
-            git push
-          else
-            echo "JAR unchanged — skipping commit."
-          fi
 
+jobs:
   R-CMD-check:
-    needs: build-jar
-
     runs-on: ${{ matrix.config.os }}
 
     name: R-CMD-check ${{ matrix.config.os }} (R ${{ matrix.config.r }})
@@ -103,15 +27,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
+          submodules: true
 
-      - name: Sync to latest HEAD including rebuilt JAR
-        run: |
-          git fetch origin "${{ github.ref_name }}"
-          git checkout "${{ github.ref_name }}"
-          git pull origin "${{ github.ref_name }}"
+      # ensure our gradle wrapper is correct, https://github.com/gradle/actions/blob/main/docs/wrapper-validation.md
+      - uses: gradle/actions/wrapper-validation@v5
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -147,8 +69,6 @@ jobs:
           working-directory: r-package
 
   R-CMD-check-CRAN:
-    needs: build-jar
-
     runs-on: ${{ matrix.config.os }}
 
     name: R-CMD-check-CRAN
@@ -164,15 +84,10 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-
-      - name: Sync to latest HEAD including rebuilt JAR
-        run: |
-          git fetch origin "${{ github.ref_name }}"
-          git checkout "${{ github.ref_name }}"
-          git pull origin "${{ github.ref_name }}"
+          submodules: true
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -194,20 +109,14 @@ jobs:
           NOT_CRAN: false
 
   test-coverage:
-    needs: build-jar
-
     runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
+          submodules: true
 
-      - name: Sync to latest HEAD including rebuilt JAR
-        run: |
-          git fetch origin "${{ github.ref_name }}"
-          git checkout "${{ github.ref_name }}"
-          git pull origin "${{ github.ref_name }}"
 
       - uses: r-lib/actions/setup-r@v2
 

.gitignore

@@ -2,6 +2,8 @@ java-api/out
 java-api/target
 java-r5/target
 r-package/.Rproj.user
+r-package/inst/jar/*
+!r-package/inst/jar/.gitkeep
 r-package/.Rhistory
 R5.jar
 r5r_core.jar
@@ -15,15 +17,16 @@ poa_osm.pbf.mapdb
 poa_osm.pbf.mapdb.p
 /r-package/inst/extdata/spo/spo_osm.pbf.mapdb
 /r-package/inst/extdata/spo/spo_osm.pbf.mapdb.p
-java-r5rcore/out/artifacts/r5r_jar/r5r.jar
-java-r5rcore/out/production/r5r/org/ipea/r5r/DetailedItineraryPlanner.class
-java-r5rcore/out/production/r5r/org/ipea/r5r/R5RCore.class
-java-r5rcore/out/production/r5r/org/ipea/r5r/RDataFrame.class
-java-r5rcore/out/production/r5r/org/ipea/r5r/TravelTimeMatrixComputer.class
-java-r5rcore/out
-java-r5rcore/libs
+r-package/java/out/artifacts/r5r_jar/r5r.jar
+r-package/java/out/production/r5r/org/ipea/r5r/DetailedItineraryPlanner.class
+r-package/java/out/production/r5r/org/ipea/r5r/R5RCore.class
+r-package/java/out/production/r5r/org/ipea/r5r/RDataFrame.class
+r-package/java/out/production/r5r/org/ipea/r5r/TravelTimeMatrixComputer.class
+r-package/java/out
+r-package/java/libs
+r-package/java/build
 .DS_Store
-java-r5rcore/target
+r-package/java/target
 .*.swp
 jpa-buddy.xml
 r5-*.jar

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "r-package/java/r5"]
+	path = r-package/java/r5
+	url = https://github.com/conveyal/r5.git

configure

@@ -0,0 +1,6 @@
+#!/usr/bin/env sh
+
+(
+  cd src
+  ./gradlew build
+)

r-package/.Rbuildignore

@@ -13,6 +13,16 @@
 ^inst/extdata/.*/.*\.mapdb\.p$
 ^\.github$
 ^inst/img
-^inst/jar/r5-.*\.jar$
+# The JAR will be included in the binary package, because it is not in .Rinstignore
+^inst/jar$
 ^man/figures
 ^cran-comments\.md$
+^java/r5r/build$
+^java/r5/build$
+^java/build$
+^java/r5r/.gradle$
+^java/r5/.gradle$
+^java/.gradle$
+
+# lots of big files used in r5 tests, which we don't need to run
+^java/r5/src/test$

r-package/.Rinstignore

@@ -0,0 +1,3 @@
+^extdata/.*/.*\.dat$
+^extdata/.*/.*\.log$
+^extdata/.*/.*\.mapdb\.p$

r-package/DESCRIPTION

@@ -73,10 +73,12 @@ Suggests:
     patchwork,
     rJavaEnv,
     rmarkdown,
-    testthat
+    testthat,
+    devtools
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
 SystemRequirements: Java JDK (>= 21.0)
+Biarch: true

r-package/NAMESPACE

@@ -5,13 +5,11 @@ export(arrival_travel_time_matrix)
 export(build_network)
 export(check_transit_availability)
 export(detailed_itineraries)
-export(download_r5)
 export(expanded_travel_time_matrix)
 export(find_snap)
 export(get_gtfs_errors)
 export(isochrone)
 export(pareto_frontier)
-export(r5r_cache)
 export(r5r_sitrep)
 export(read_fare_structure)
 export(setup_fare_structure)