Merge pull request #28 from chris-allan/test-cases

Add basic test cases

appveyor.yml

@@ -1,13 +1,19 @@
 version: 0.2.4.{build}
 
-build:
-  verbosity: minimal
+image: Ubuntu
+stack: jdk 11
+
+install:
+  - sh: sudo apt-get update
+  - sh: sudo apt-get install -y libblosc1
+
+build: off
 
 build_script:
-  - gradlew build
+  - ./gradlew build
 
 after_test:
-  - gradlew distZip
+  - ./gradlew distZip
 
 artifacts:
   - path: 'build\distributions\*.zip'

build.gradle

@@ -1,7 +1,6 @@
 plugins {
     id 'application'
     id 'eclipse'
-    id 'java'
     id 'checkstyle'
 }
 
@@ -18,24 +17,42 @@ repositories {
     maven {
         url 'https://artifacts.openmicroscopy.org/artifactory/repo/'
     }
+    maven {
+        url 'https://repo.glencoesoftware.com/repository/n5-zarr-snapshots/'
+    }
+    maven {
+        url 'https://repo.glencoesoftware.com/repository/bioformats2raw2ometiff/'
+    }
     maven {
         url 'https://saalfeldlab.github.io/maven'
     }
 }
 
 dependencies {
-    compile ('info.picocli:picocli:3.9.3')
-    compile ('ome:formats-bsd:6.2.1')
+    implementation 'info.picocli:picocli:4.2.0'
+    implementation 'ome:formats-bsd:6.4.0'
     // be careful here, this is a newer version of org.json:json than formats-gpl uses
-    compile ('org.json:json:20190722')
-    compile ('org.janelia.saalfeldlab:n5:2.1.6')
-    compile ('org.janelia.saalfeldlab:n5-blosc:1.0.1')
-    compile ('org.janelia.saalfeldlab:n5-zarr:0.0.2-beta')
+    implementation 'org.json:json:20190722'
+    implementation 'org.janelia.saalfeldlab:n5:2.1.6'
+    implementation 'org.janelia.saalfeldlab:n5-blosc:1.0.1'
+    implementation 'org.janelia.saalfeldlab:n5-zarr:0.0.3-SNAPSHOT'
+    testImplementation 'junit:junit:4.12'
+    testImplementation 'com.glencoesoftware:bioformats2raw:0.2.3-SNAPSHOT'
 }
 
-applicationDistribution.from("$projectDir") {
-    include 'LICENSE.txt'
-    include 'bin/*'
+test {
+    useJUnit()
+}
+
+distributions {
+    main {
+        contents {
+            from("$projectDir") {
+                include 'README.md'
+                include 'LICENSE.txt'
+            }
+        }
+    }
 }
 
 checkstyle {

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,5 @@
-#Tue Feb 12 11:26:51 GMT 2019
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.2.1-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.2.1-bin.zip

gradlew

@@ -1,25 +1,43 @@
-#!/usr/bin/env bash
+#!/usr/bin/env sh
 
 ##############################################################################
 ##
 ##  Gradle start up script for UN*X
 ##
 ##############################################################################
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
 
 APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
+# 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"'
+
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
 
-warn ( ) {
+warn () {
     echo "$*"
 }
 
-die ( ) {
+die () {
     echo
     echo "$*"
     echo
@@ -30,6 +48,7 @@ die ( ) {
 cygwin=false
 msys=false
 darwin=false
+nonstop=false
 case "`uname`" in
   CYGWIN* )
     cygwin=true
@@ -40,26 +59,11 @@ case "`uname`" in
   MINGW* )
     msys=true
     ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
 esac
 
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
 # Determine the Java command to use to start the JVM.
@@ -85,7 +89,7 @@ location of your Java installation."
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
     MAX_FD_LIMIT=`ulimit -H -n`
     if [ $? -eq 0 ] ; then
         if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
@@ -150,11 +154,19 @@ if $cygwin ; then
     esac
 fi
 
-# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
-function splitJvmOpts() {
-    JVM_OPTS=("$@")
+# Escape application args
+save () {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
 }
-eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
-JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
 
-exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
+exec "$JAVACMD" "$@"

gradlew.bat

@@ -8,14 +8,14 @@
 @rem Set local scope for the variables with windows NT shell
 if "%OS%"=="Windows_NT" setlocal
 
-@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=
-
 set DIRNAME=%~dp0
 if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@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"
+
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
@@ -49,7 +49,6 @@ goto fail
 @rem Get command-line arguments, handling Windows variants
 
 if not "%OS%" == "Windows_NT" goto win9xME_args
-if "%@eval[2+2]" == "4" goto 4NT_args
 
 :win9xME_args
 @rem Slurp the command line arguments.
@@ -60,11 +59,6 @@ set _SKIP=2
 if "x%~1" == "x" goto execute
 
 set CMD_LINE_ARGS=%*
-goto execute
-
-:4NT_args
-@rem Get arguments from the 4NT Shell from JP Software
-set CMD_LINE_ARGS=%$
 
 :execute
 @rem Setup the command line