Merge branch 'main' into sm-read-offsets

.github/workflows/docs-ci.yml

@@ -65,6 +65,57 @@ jobs:
           remote_user: ${{ secrets.DOCS_USER }}
           remote_key: ${{ secrets.DEEPHAVEN_CORE_SSH_KEY }}
 
+  typedoc:
+    runs-on: ubuntu-22.04
+    concurrency:
+      group: typedoc-${{ github.workflow }}-${{ github.ref }}
+      # We don't want to cancel in-progress jobs against main because that might leave the upload in a bad state.
+      cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup JDK 11
+        id: setup-java-11
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '11'
+
+      - name: Setup JDK 17
+        id: setup-java-17
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '17'
+
+      - name: Set JAVA_HOME
+        run: echo "JAVA_HOME=${{ steps.setup-java-11.outputs.path }}" >> $GITHUB_ENV
+
+      - name: Run typedoc on JS API
+        uses: burrunan/gradle-cache-action@v1
+        with:
+          job-id: typedoc
+          arguments: --scan :web-client-api:types:typedoc
+          gradle-version: wrapper
+      - name: Upload JavaScript/TypeScript docs
+        if: ${{ github.ref == 'refs/heads/main' }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: typedoc
+          path: 'web/client-api/types/build/documentation/'
+      - name: Deploy JavaScript/TypeScript docs
+        if: ${{ github.ref == 'refs/heads/main' }}
+        uses: burnett01/[email protected]
+        with:
+          switches: -avzr --delete
+          path: web/client-api/types/build/documentation/
+          remote_path: deephaven-core/client-api/javascript/
+          remote_host: ${{ secrets.DOCS_HOST }}
+          remote_port: ${{ secrets.DOCS_PORT }}
+          remote_user: ${{ secrets.DOCS_USER }}
+          remote_key: ${{ secrets.DEEPHAVEN_CORE_SSH_KEY }}
+
   pydoc:
     runs-on: ubuntu-22.04
     concurrency:
@@ -191,3 +242,51 @@ jobs:
           remote_port: ${{ secrets.DOCS_PORT }}
           remote_user: ${{ secrets.DOCS_USER }}
           remote_key: ${{ secrets.DEEPHAVEN_CORE_SSH_KEY }}
+
+  rdoc:
+    runs-on: ubuntu-22.04
+    concurrency:
+      group: rdoc-${{ github.workflow }}-${{ github.ref }}
+      # We don't want to cancel in-progress jobs against main because that might leave the upload in a bad state.
+      cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup JDK 11
+        id: setup-java-11
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '11'
+
+      - name: Set JAVA_HOME
+        run: echo "JAVA_HOME=${{ steps.setup-java-11.outputs.path }}" >> $GITHUB_ENV
+
+      - name: Setup gradle properties
+        run: |
+          .github/scripts/gradle-properties.sh >> gradle.properties
+          cat gradle.properties
+
+      - name: Generate R Docs
+        uses: burrunan/gradle-cache-action@v1
+        with:
+          job-id: rDocs
+          arguments: R:rClientSite
+          gradle-version: wrapper
+
+      - name: Deploy R Docs
+        if: ${{ github.ref == 'refs/heads/main' }}
+        uses: burnett01/[email protected]
+        with:
+          switches: -avzr --delete
+          path: R/rdeephaven/docs/
+          remote_path: deephaven-core/client-api/r/
+          remote_host: ${{ secrets.DOCS_HOST }}
+          remote_port: ${{ secrets.DOCS_PORT }}
+          remote_user: ${{ secrets.DOCS_USER }}
+          remote_key: ${{ secrets.DEEPHAVEN_CORE_SSH_KEY }}
+
+      - name: Upload JVM Error Logs
+        uses: actions/upload-artifact@v3
+        if: failure()

Plot/src/main/java/io/deephaven/plot/datasets/multiseries/MultiOHLCSeries.java

@@ -83,6 +83,26 @@ public OHLCDataSeriesInternal createSeries(String seriesName, final BaseTable t,
                 timeCol, openCol, highCol, lowCol, closeCol);
     }
 
+    public String getTimeCol() {
+        return timeCol;
+    }
+
+    public String getOpenCol() {
+        return openCol;
+    }
+
+    public String getHighCol() {
+        return highCol;
+    }
+
+    public String getLowCol() {
+        return lowCol;
+    }
+
+    public String getCloseCol() {
+        return closeCol;
+    }
+
     ////////////////////////////// CODE BELOW HERE IS GENERATED -- DO NOT EDIT BY HAND //////////////////////////////
     ////////////////////////////// TO REGENERATE RUN GenerateMultiSeries //////////////////////////////
     ////////////////////////////// AND THEN RUN GenerateFigureImmutable //////////////////////////////

Plot/src/main/java/io/deephaven/plot/datasets/multiseries/MultiXYErrorBarSeries.java

@@ -107,6 +107,30 @@ public XYErrorBarDataSeriesInternal createSeries(String seriesName, final BaseTa
                 drawXError, drawYError);
     }
 
+    public boolean getDrawXError() {
+        return drawXError;
+    }
+
+    public boolean getDrawYError() {
+        return drawYError;
+    }
+
+    public String getXLow() {
+        return xLow;
+    }
+
+    public String getXHigh() {
+        return xHigh;
+    }
+
+    public String getYLow() {
+        return yLow;
+    }
+
+    public String getYHigh() {
+        return yHigh;
+    }
+
     ////////////////////////////// CODE BELOW HERE IS GENERATED -- DO NOT EDIT BY HAND //////////////////////////////
     ////////////////////////////// TO REGENERATE RUN GenerateMultiSeries //////////////////////////////
     ////////////////////////////// AND THEN RUN GenerateFigureImmutable //////////////////////////////

Plot/src/main/java/io/deephaven/plot/util/ArgumentValidations.java

@@ -841,7 +841,7 @@ public static void assertColumnsInTable(final Table t, final PlotInfo plotInfo,
         assertNotNull(t, "t", plotInfo);
         assertNotNull(cols, "cols", plotInfo);
         for (String c : cols) {
-            if (!t.getColumnSourceMap().containsKey(c)) {
+            if (!t.hasColumns(c)) {
                 throw new PlotIllegalArgumentException("Column " + c + " could not be found in table.", plotInfo);
             }
         }

R/build.gradle

@@ -38,11 +38,11 @@ def buildRClient = Docker.registerDockerTask(project, 'rClient') {
             include 'rdeephaven/NAMESPACE'
             include 'rdeephaven/README.md'
             include 'rdeephaven/inst/**'
-            include 'rdeephaven/man/**'
             include 'rdeephaven/etc/**'
             include 'rdeephaven/R/**'
             include 'rdeephaven/src/*.cpp'
             include 'rdeephaven/src/Makevars'
+            include 'rdeephaven/vignettes/*.Rmd'
         }
     }
     dockerfile {
@@ -54,18 +54,18 @@ def buildRClient = Docker.registerDockerTask(project, 'rClient') {
                         /out \\
                         ${prefix}/log \\
                         ${prefix}/bin/rdeephaven \\
-                        ${prefix}/src/rdeephaven/{inst,man,etc,src,R,bin}
+                        ${prefix}/src/rdeephaven/{inst,etc,src,R,bin}
                    """)
         copyFile('rdeephaven/DESCRIPTION',  "${prefix}/src/rdeephaven/")
         copyFile('rdeephaven/LICENSE',  "${prefix}/src/rdeephaven/")
         copyFile('rdeephaven/NAMESPACE',  "${prefix}/src/rdeephaven/")
         copyFile('rdeephaven/README.md',  "${prefix}/src/rdeephaven/")
         copyFile('rdeephaven/inst/',  "${prefix}/src/rdeephaven/inst/")
-        copyFile('rdeephaven/man/', "${prefix}/src/rdeephaven/man/")
         copyFile('rdeephaven/etc/', "${prefix}/src/rdeephaven/etc/")
         copyFile('rdeephaven/R/', "${prefix}/src/rdeephaven/R/")
         copyFile('rdeephaven/src/*.cpp', "${prefix}/src/rdeephaven/src/")
         copyFile('rdeephaven/src/Makevars', "${prefix}/src/rdeephaven/src/")
+        copyFile('rdeephaven/vignettes/*.Rmd', "${prefix}/src/rdeephaven/vignettes/")
         copyFile('r-build.sh', "${prefix}/bin/rdeephaven")
         runCommand("PREFIX=${prefix}; " +
                   '''set -eux ; \
@@ -115,7 +115,7 @@ def rClientDoc = Docker.registerDockerTask(project, 'rClientDoc') {
         }
     }
     copyOut {
-        into layout.buildDirectory.dir('man')
+        into layout.projectDirectory.dir('rdeephaven/man')
     }
     dockerfile {
         from('deephaven/r-client:local-build')
@@ -153,18 +153,46 @@ def rClientDoc = Docker.registerDockerTask(project, 'rClientDoc') {
         copyFile('r-doc.sh', "${prefix}/bin/rdeephaven")
     }
     parentContainers = [ project.tasks.getByName('rClient') ]
-    entrypoint = ["${prefix}/bin/rdeephaven/r-doc.sh", '/out']
+    entrypoint = ["${prefix}/bin/rdeephaven/r-doc.sh"]
+    containerOutPath = "${prefix}/src/rdeephaven/man"
 }
 
-task updateRClientDoc {
-    dependsOn rClientDoc
-    doLast {
-        exec {
-            workingDir '.'
-            commandLine 'rm', '-f', 'man/*'
-            commandLine 'tar', '-C', 'rdeephaven', '-zxvf', 'build/man/man.tgz'
+def rClientSite = Docker.registerDockerTask(project, 'rClientSite') {
+    // Only tested on x86-64, and we only build dependencies for x86-64
+    platform = 'linux/amd64'
+    copyIn {
+        from(layout.projectDirectory) {
+            include 'r-site.sh'
+            include 'rdeephaven/man/**'
         }
     }
+    copyOut {
+        into layout.projectDirectory.dir('rdeephaven/docs')
+    }
+    dockerfile {
+        from('deephaven/r-client-doc:local-build')
+        // We need the contents of 'man' to build the docsite
+        copyFile('rdeephaven/man/**', "${prefix}/src/rdeephaven/man/")
+        runCommand("mkdir -p ${prefix}/src/rdeephaven/docs")
+        runCommand('''echo "status = tryCatch(" \
+                           "   {" \
+                           "      install.packages('pkgdown', repos='http://cran.us.r-project.org'); " \
+                           "      0" \
+                           "   }," \
+                           "  error=function(e) 1," \
+                           "  warning=function(w) 2" \
+                           ");" \
+                           "print(paste0('status=', status));" \
+                           "quit(save='no', status=status)" | \
+                        MAKE="make -j`getconf _NPROCESSORS_ONLN`" R --no-save --no-restore
+                   ''')
+        // Keep this after the package installs above;
+        // it is likely it changes more frequently.
+        copyFile('r-site.sh', "${prefix}/bin/rdeephaven")
+    }
+    parentContainers = [ project.tasks.getByName('rClientDoc') ]
+    entrypoint = ["${prefix}/bin/rdeephaven/r-site.sh"]
+    containerOutPath = "${prefix}/src/rdeephaven/docs"
 }
 
 deephavenDocker.shouldLogIfTaskFails testRClient

R/r-build.sh

@@ -18,18 +18,14 @@ fi
 trap 'rm -f src/*.o src/*.so' 1 2 15
 rm -f src/*.o src/*.so
 
-MAKE="make -j${NCPUS}" R --no-save --no-restore <<EOF
-status = tryCatch(
-  {
-     install.packages(".", repos=NULL, type="source")
-     0
-  },
-  error=function(e) 1,
-  warning=function(w) 2
-)
-print(paste0('status=', status))
-quit(save='no', status=status)
-EOF
+MAKE="make -j${NCPUS}"
+cd .. && \
+  rm -f rdeephaven_*.tar.gz && \
+  R CMD build rdeephaven && \
+  R CMD INSTALL --no-multiarch --with-keep.source rdeephaven_*.tar.gz && \
+  rm -f rdeephaven_*.tar.gz && \
+  cd rdeephaven ||
+  exit 1
 
 rm -f src/*.o src/*.so
 

R/r-doc.sh

@@ -2,11 +2,6 @@
 
 set -euo pipefail
 
-if [ "$#" -ne 1 ]; then
-    echo "Usage: $0 output-dir" 1>&2
-    exit 1
-fi
-
 if [ -z "${DH_PREFIX}" ]; then
     echo "$0: Environment variable DH_PREFIX is not set, aborting." 1>&2
     exit 1
@@ -16,8 +11,6 @@ source $DH_PREFIX/env.sh
 
 cd $DH_PREFIX/src/rdeephaven
 
-OUT_DIR="$1"
-
 R --no-save --no-restore <<EOF
 library('roxygen2')
 status = tryCatch(
@@ -30,7 +23,3 @@ status = tryCatch(
 print(paste0('status=', status))
 quit(save='no', status=status)
 EOF
-
-tar -zcf $OUT_DIR/man.tgz man
-
-exit 0

R/r-site.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+set -euo pipefail
+
+if [ -z "${DH_PREFIX}" ]; then
+    echo "$0: Environment variable DH_PREFIX is not set, aborting." 1>&2
+    exit 1
+fi
+
+source $DH_PREFIX/env.sh
+
+cd $DH_PREFIX/src/rdeephaven
+
+R --no-save --no-restore <<EOF
+library('pkgdown')
+status = tryCatch(
+  {
+     pkgdown::build_site()
+     0
+  },
+  error=function(e) 1
+)
+print(paste0('status=', status))
+quit(save='no', status=status)
+EOF

R/rdeephaven/.Rbuildignore

@@ -0,0 +1,5 @@
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^doc$
+^Meta$

R/rdeephaven/.gitignore

@@ -5,3 +5,7 @@ lib/cpp-dependencies/src
 lib/cpp-dependencies/env.sh
 *.o
 *.so
+docs
+inst/doc
+/doc/
+/Meta/

R/rdeephaven/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rdeephaven
 Type: Package
 Title: R Client for Deephaven Core
-Version: 0.30.0
+Version: 0.31.0
 Date: 2023-05-12
 Author: Deephaven Data Labs
 Maintainer: Alex Peters <[email protected]>
@@ -16,6 +16,12 @@ License: Apache License (== 2.0)
 Depends: R (>= 3.5.3)
 Imports: Rcpp (>= 1.0.10), arrow (>= 12.0.0), R6 (>= 2.5.0), dplyr (>= 1.1.0), utils (>= 3.5.3)
 LinkingTo: Rcpp
-Suggests: testthat (>= 3.0.0), lubridate (>= 1.9.0), zoo (>= 1.8-0)
+Suggests: 
+    testthat (>= 3.0.0),
+    lubridate (>= 1.9.0),
+    zoo (>= 1.8-0),
+    knitr,
+    rmarkdown
 Config/testthat/edition: 3
 RoxygenNote: 7.2.3
+VignetteBuilder: knitr