diff --git a/.github/workflows/c_tests.yml b/.github/workflows/c_tests.yml index e0d83ab7..c301547e 100644 --- a/.github/workflows/c_tests.yml +++ b/.github/workflows/c_tests.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout code - uses: actions/checkout@v3 + uses: actions/checkout@v5 - name: Install dependencies run: sudo apt-get update && sudo apt-get install -y cmake build-essential libboost-filesystem-dev libboost-thread-dev libboost-chrono-dev liblz4-dev doxygen diff --git a/.github/workflows/doc_generation-6.0.yml b/.github/workflows/doc_generation-6.0.yml index fcf13f09..2a53791a 100644 --- a/.github/workflows/doc_generation-6.0.yml +++ b/.github/workflows/doc_generation-6.0.yml @@ -29,10 +29,12 @@ jobs: working-directory: '.' doxyfile-path: 'doc/doxygen/DoxyfileCC' - - name: Install Maven - run: | - sudo apt-get update - sudo apt-get install -y maven + # Setup gradle and build Java + - name: Setup Gradle + uses: gradle/actions/setup-gradle@v3 + + - name: Build with Gradle + run: ./gradlew build # generate the javadoc files - name: Set up JDK 17 @@ -41,7 +43,7 @@ jobs: java-version: '17' distribution: 'temurin' - name: Javadoc Action - run: mvn javadoc:javadoc + run: ./gradlew javadoc # clean up the javadoc files including removing timestamps. OPTIONAL. - name: Tidy up the javadocs diff --git a/.github/workflows/java_tests.yml b/.github/workflows/java_tests.yml index 58e3fd3f..124196da 100644 --- a/.github/workflows/java_tests.yml +++ b/.github/workflows/java_tests.yml @@ -8,23 +8,25 @@ jobs: java_test: name: Run JUnit Tests runs-on: ubuntu-latest - container: - image: maven:3.9-eclipse-temurin-17-alpine steps: - name: Check out code - uses: actions/checkout@v3 + uses: actions/checkout@v5 - # Uncomment to set up Java and Maven manually, if desired - # # (and probably comment out the container image above) - # - name: Set up JDK 17 - # uses: actions/setup-java@v3 - # with: - # distribution: temurin - # java-version: 17 - # Install maven by hand (if not in container image) - # - name: Maven Setup - # run: sudo apt-get update && apt-get install -y maven + - name: Set up JDK 17 + uses: actions/setup-java@v3 + with: + distribution: temurin + java-version: 17 + # Setup gradle and build Java + - name: Setup Gradle + uses: gradle/actions/setup-gradle@v3 + + - name: Build with Gradle + run: ./gradlew build + + # Run tests with Gradle - name: Build and run tests - run: mvn --batch-mode test + run: ./gradlew test + \ No newline at end of file diff --git a/CMakeLists.txt b/CMakeLists.txt index 1a0810b5..a0e3a779 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -2,7 +2,7 @@ ### VERSION DEFINITIONS ### cmake_minimum_required(VERSION 3.22) -project(evio VERSION 6.1.3 LANGUAGES C CXX) +project(evio VERSION 6.2.0 LANGUAGES C CXX) set(CMAKE_C_STANDARD 11) set(CMAKE_CXX_STANDARD 20) # C/C++ build options diff --git a/README.md b/README.md index 5c0112a7..7edbe8a6 100644 --- a/README.md +++ b/README.md @@ -49,8 +49,8 @@ libraries are typically system-specific (e.g. using a command like `yum`, `dbn`, ## **Java Library** The Java version of evio (internally `org.jlab.coda.jevio`) can also be used for reading & writing -`.evio` format files. A "fat" jar file with all dependencies is included in the `java/jars` folder, -which should be all most users need to run and execute Java code utilizing the evio library. +`.evio` format files. A "fat" jar file with all dependencies is included in the `java/jars` folder, +the only thing strictly required to run and execute `et` in Java. Java 17 is the default version used, however the Java evio library should be compatible with all java versions 8 and higher (note this has not been rigorously tested). If one wants to create a @@ -58,11 +58,11 @@ new jar file for any reason (e.g. to modify Java versions), do: git clone https://github.com/JeffersonLab/evio/ cd evio - mvn clean install + ./gradlew ### Prerequisites -Requires Maven (`mvn`) and an installation of Java on your system. +Gradle and an installation of Java on your system. **Running on "ifarm" at JLab will not work unless you install java yourself**. Note that the default java versions on the farm will be too old to work. See downloads from [OpenJDK](https://openjdk.org/install/) or [Oracle](https://www.oracle.com/java/technologies/javase/jdk17-archive-downloads.html). diff --git a/build.gradle.kts b/build.gradle.kts new file mode 100644 index 00000000..86528769 --- /dev/null +++ b/build.gradle.kts @@ -0,0 +1,61 @@ +/* + * This file was generated by the Gradle 'init' task. + * + * This project uses @Incubating APIs which are subject to change. + */ + +plugins { + `java-library` + `maven-publish` + // `com.github.spotbugs` + id("com.gradleup.shadow") version "9.2.2" +} + +repositories { + mavenLocal() + maven { + url = uri("https://repo.maven.apache.org/maven2/") + } +} + +dependencies { + api(libs.org.lz4.lz4.java) + api(files("$projectDir/java/jars/disruptor-4.0.0.jar")) + testImplementation(platform("org.junit:junit-bom:5.10.3")) // Makes sure JUnit dependencies below have matching versions + testImplementation("org.junit.jupiter:junit-jupiter") + testRuntimeOnly("org.junit.platform:junit-platform-launcher") + } + +group = "org.jlab.coda" +version = "6.2.0" +description = "Jefferson Lab EVIO Java Library (JEVIO)" +java.sourceCompatibility = JavaVersion.VERSION_17 +java.targetCompatibility = JavaVersion.VERSION_17 + +defaultTasks("build") + +publishing { + publications.create("maven") { + from(components["java"]) + } +} + +tasks.withType() { + options.encoding = "UTF-8" +} + +tasks.withType() { + options.encoding = "UTF-8" +} + +tasks.test { + useJUnitPlatform() + failOnNoDiscoveredTests = false +} + +// spotbugs { +// toolVersion.set("4.7.3") +// effort.set(com.github.spotbugs.snom.Effort.MAX) +// reportLevel.set(com.github.spotbugs.snom.ReportLevel.LOW) +// excludeFilter.set(file("config/spotbugs/exclude.xml")) +// } diff --git a/etc/test_files/testEventsV6_javaAPI.evio b/etc/test_files/testEventsV6_javaAPI.evio index fb2ce47d..4e773cac 100644 Binary files a/etc/test_files/testEventsV6_javaAPI.evio and b/etc/test_files/testEventsV6_javaAPI.evio differ diff --git a/gradle.properties b/gradle.properties new file mode 100644 index 00000000..51540088 --- /dev/null +++ b/gradle.properties @@ -0,0 +1,7 @@ +# This file was generated by the Gradle 'init' task. +# https://docs.gradle.org/current/userguide/build_environment.html#sec:gradle_configuration_properties + +org.gradle.configuration-cache=true +org.gradle.parallel=true +org.gradle.caching=true + diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml new file mode 100644 index 00000000..aa30e14e --- /dev/null +++ b/gradle/libs.versions.toml @@ -0,0 +1,12 @@ +# This file was generated by the Gradle 'init' task. +# https://docs.gradle.org/current/userguide/platforms.html#sub::toml-dependencies-format + +[versions] +com-lmax-disruptor = "4.0.0" +org-junit-jupiter-junit-jupiter = "5.9.3" +org-lz4-lz4-java = "1.8.0" + +[libraries] +com-lmax-disruptor = { module = "com.lmax:disruptor", version.ref = "com-lmax-disruptor" } +org-junit-jupiter-junit-jupiter = { module = "org.junit.jupiter:junit-jupiter", version.ref = "org-junit-jupiter-junit-jupiter" } +org-lz4-lz4-java = { module = "org.lz4:lz4-java", version.ref = "org-lz4-lz4-java" } diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 00000000..8bdaf60c Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 00000000..2e111328 --- /dev/null +++ b/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,7 @@ +distributionBase=GRADLE_USER_HOME +distributionPath=wrapper/dists +distributionUrl=https\://services.gradle.org/distributions/gradle-9.1.0-bin.zip +networkTimeout=10000 +validateDistributionUrl=true +zipStoreBase=GRADLE_USER_HOME +zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew new file mode 100755 index 00000000..adff685a --- /dev/null +++ b/gradlew @@ -0,0 +1,248 @@ +#!/bin/sh + +# +# Copyright © 2015 the original authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# +# SPDX-License-Identifier: Apache-2.0 +# + +############################################################################## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# +############################################################################## + +# Attempt to set APP_HOME + +# Resolve links: $0 may be a link +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac +done + +# This is normally unused +# shellcheck disable=SC2034 +APP_BASE_NAME=${0##*/} +# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) +APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s\n' "$PWD" ) || exit + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&2 + +die () { + echo + echo "$*" + echo + exit 1 +} >&2 + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; +esac + + + +# Determine the Java command to use to start the JVM. +if [ -n "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD=$JAVA_HOME/jre/sh/java + else + JAVACMD=$JAVA_HOME/bin/java + fi + if [ ! -x "$JAVACMD" ] ; then + die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + if ! command -v java >/dev/null 2>&1 + then + die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac +fi + +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + + # Now convert the arguments - kludge to limit ourselves to /bin/sh + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) + fi + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg + done +fi + + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Collect all arguments for the java command: +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments, +# and any embedded shellness will be escaped. +# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be +# treated as '${Hostname}' itself on the command line. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \ + "$@" + +# Stop when "xargs" is not available. +if ! command -v xargs >/dev/null 2>&1 +then + die "xargs is not available" +fi + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' + +exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat new file mode 100644 index 00000000..e509b2dd --- /dev/null +++ b/gradlew.bat @@ -0,0 +1,93 @@ +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem +@rem SPDX-License-Identifier: Apache-2.0 +@rem + +@if "%DEBUG%"=="" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%"=="" set DIRNAME=. +@rem This is normally unused +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if %ERRORLEVEL% equ 0 goto execute + +echo. 1>&2 +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2 +echo. 1>&2 +echo Please set the JAVA_HOME variable in your environment to match the 1>&2 +echo location of your Java installation. 1>&2 + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. 1>&2 +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2 +echo. 1>&2 +echo Please set the JAVA_HOME variable in your environment to match the 1>&2 +echo location of your Java installation. 1>&2 + +goto fail + +:execute +@rem Setup the command line + + + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -jar "%APP_HOME%\gradle\wrapper\gradle-wrapper.jar" %* + +:end +@rem End local scope for the variables with windows NT shell +if %ERRORLEVEL% equ 0 goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +set EXIT_CODE=%ERRORLEVEL% +if %EXIT_CODE% equ 0 set EXIT_CODE=1 +if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE% +exit /b %EXIT_CODE% + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/java/jars/jevio-6.1.3-jar-with-dependencies.jar b/java/jars/jevio-6.2.0-all.jar similarity index 89% rename from java/jars/jevio-6.1.3-jar-with-dependencies.jar rename to java/jars/jevio-6.2.0-all.jar index 5ae1548f..485485d0 100644 Binary files a/java/jars/jevio-6.1.3-jar-with-dependencies.jar and b/java/jars/jevio-6.2.0-all.jar differ diff --git a/java/jars/jevio-6.1.3.jar b/java/jars/jevio-6.2.0.jar similarity index 87% rename from java/jars/jevio-6.1.3.jar rename to java/jars/jevio-6.2.0.jar index 90c33141..0c71b284 100644 Binary files a/java/jars/jevio-6.1.3.jar and b/java/jars/jevio-6.2.0.jar differ diff --git a/pom.xml b/pom.xml deleted file mode 100644 index 02fb83cd..00000000 --- a/pom.xml +++ /dev/null @@ -1,156 +0,0 @@ - - 4.0.0 - org.jlab.coda - jevio - 6.1.3 - Jefferson Lab EVIO Java Library (JEVIO) - Java library for EVIO (Event Input/Output) - jar - - - - - - - - 17 - ${java.version} - ${java.version} - - 1.8.0 - 4.0.0 - - UTF-8 - ${pom.basedir}/java/jars - - - - - - - local-disruptor - file://${project.basedir}/java/jars - true - - - - - - - org.lz4 - lz4-java - ${lz4.version} - - - - - - com.lmax - disruptor - ${disruptor.version} - - - - org.junit.jupiter - junit-jupiter - 5.9.3 - test - - - - - - - - - - org.apache.maven.plugins - maven-install-plugin - 3.1.4 - - - install-local-disruptor - initialize - - install-file - - - ${project.basedir}/java/jars/disruptor-${disruptor.version}.jar - com.lmax - disruptor - ${disruptor.version} - jar - true - - - - - - - - maven-assembly-plugin - 3.6.0 - - - jar-with-dependencies - - - jar-with-dependencies - jar - false - - - runtime - true - - - system - true - false - / - - - - - - - make-assembly - package - - single - - - - - - - - org.apache.maven.plugins - maven-surefire-plugin - 3.0.0-M7 - - - - **/**.java - - - true - - - - - org.apache.maven.plugins - maven-javadoc-plugin - 3.6.2 - - ${java.version} - ${java.version} - doc/javadoc - - - - - - - - diff --git a/settings.gradle.kts b/settings.gradle.kts new file mode 100644 index 00000000..52c5d67b --- /dev/null +++ b/settings.gradle.kts @@ -0,0 +1,7 @@ +/* + * This file was generated by the Gradle 'init' task. + * + * This project uses @Incubating APIs which are subject to change. + */ + +rootProject.name = "jevio"