Major update to FFX uses of Groovy to accomodate JDKs 8, 9 and 10. We…

… now depend on the 2.5.0 release version of Groovy, and the PicoCLI version of CLIBuilder
mjschnie · Jun 8, 2018 · 223d469 · 223d469
1 parent 77c16ff
commit 223d469
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Showing 85 changed files with 214 additions and 502 deletions.
diff --git a/bin/ffx b/bin/ffx
@@ -109,29 +109,27 @@ fi
 # Detect JVM version; disallow 1.7 or below, warn for JDK 9+ that experimental flags are in use.
 if [ $hasAwkSed ]; then
     JVERS="`java -version 2>&1 | awk '/version/ {print $3;}' | sed 's/\"//g'`"
-    JVFIRST="`echo "$JVERS" | awk 'BEGIN { FS = "."; } { print $1 }'`"
+    JVFIRST="`echo "$JVERS" | awk 'BEGIN { FS = "[.-]"; } { print $1 }'`"
     JVSEC="`echo "$JVERS" | awk 'BEGIN { FS = "."; } { print $2 }'`"
 
     USE_EXPTL_FLAGS=''
-    if [ $JVFIRST -gt 9 ]; then
-        echo " FFX does not currently support Java 10+ (JDK 1.8 is preferred) - detected ${JVERS}" 1>&2
+    if [ $JVFIRST -gt 10 ]; then
+        echo " Illegal Java version detected (${JVERS}). Please use JRE 1.8, JDK 9 or JDK 10." 1>&2
         exit 1
     elif [ $JVFIRST -eq 9 ]; then
         USE_EXPTL_FLAGS='1'
-    elif [ $JVSEC -eq 9 ]; then
+    elif [ $JVFIRST -eq 10 ]; then
         USE_EXPTL_FLAGS='1'
     elif [ $JVSEC -lt 8 ]; then
-        echo " Illegal Java version detected. Must use JDK 1.8 or JDK 9, found ${JVERS}" 1>&2
+        echo " Illegal Java version detected (${JVERS}). Please use JRE 1.8, JDK 9 or JDK 10." 1>&2
         exit 1
     fi
 
     if [ $USE_EXPTL_FLAGS ]; then
-        echo " WARNING: JDK 9 detected: support is experimental." 1>&2
-        echo '' 1>&2
         EXTRA_JVM_ARGUMENTS="${EXTRA_JVM_ARGUMENTS} --illegal-access=permit --add-opens=java.desktop/java.awt=ALL-UNNAMED --add-exports=java.base/java.lang=ALL-UNNAMED --add-exports=java.desktop/sun.awt=ALL-UNNAMED --add-exports=java.desktop/sun.java2d=ALL-UNNAMED"
     fi
 else
-    echo " The JRE version could not be autodetected. JRE 1.8 is preferred, and JRE 9 is experimental."
+    echo " The JRE version could not be autodetected. Please use JRE 1.8, JDK 9 or JDK 10."
 fi
 
 # For Cygwin, switch paths to Windows format before running java

diff --git a/bin/ffxc b/bin/ffxc
@@ -113,29 +113,27 @@ fi
 # Detect JVM version; disallow 1.7 or below, warn for JDK 9+ that experimental flags are in use.
 if [ $hasAwkSed ]; then
     JVERS="`java -version 2>&1 | awk '/version/ {print $3;}' | sed 's/\"//g'`"
-    JVFIRST="`echo "$JVERS" | awk 'BEGIN { FS = "."; } { print $1 }'`"
+    JVFIRST="`echo "$JVERS" | awk 'BEGIN { FS = "[.-]"; } { print $1 }'`"
     JVSEC="`echo "$JVERS" | awk 'BEGIN { FS = "."; } { print $2 }'`"
 
     USE_EXPTL_FLAGS=''
-    if [ $JVFIRST -gt 9 ]; then
-        echo " FFX does not currently support Java 10+ (JDK 1.8 is preferred) - detected ${JVERS}" 1>&2
-        exit 1
+    if [ $JVFIRST -gt 10 ]; then
+        echo " Illegal Java version detected (${JVERS}). Please use JRE 1.8, JDK 9 or JDK 10." 1>&2
+#       exit 1
     elif [ $JVFIRST -eq 9 ]; then
         USE_EXPTL_FLAGS='1'
-    elif [ $JVSEC -eq 9 ]; then
+    elif [ $JVFIRST -eq 10 ]; then
         USE_EXPTL_FLAGS='1'
     elif [ $JVSEC -lt 8 ]; then
-        echo " Illegal Java version detected. Must use JDK 1.8 or JDK 9, found ${JVERS}" 1>&2
+        echo " Illegal Java version detected (${JVERS}). Please use JRE 1.8, JDK 9 or JDK 10." 1>&2
         exit 1
     fi
 
     if [ $USE_EXPTL_FLAGS ]; then
-        echo " WARNING: JDK 9 detected: support is experimental." 1>&2
-        echo '' 1>&2
         EXTRA_JVM_ARGUMENTS="${EXTRA_JVM_ARGUMENTS} --illegal-access=permit --add-opens=java.desktop/java.awt=ALL-UNNAMED --add-exports=java.base/java.lang=ALL-UNNAMED --add-exports=java.desktop/sun.awt=ALL-UNNAMED --add-exports=java.desktop/sun.java2d=ALL-UNNAMED"
     fi
 else
-    echo " The JRE version could not be autodetected. JRE 1.8 is preferred, and JRE 9 is experimental."
+    echo " The JRE version could not be autodetected. Please use JRE 1.8, JDK 9 or JDK 10."
 fi
 
 # For Cygwin, switch paths to Windows format before running java

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/Anneal.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/Anneal.groovy
@@ -5,6 +5,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.algorithms.integrators.IntegratorEnum
 import ffx.algorithms.thermostats.ThermostatEnum

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/ApplyTorsions.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/ApplyTorsions.groovy
@@ -5,6 +5,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.potential.MolecularAssembly
 import ffx.potential.bonded.Polymer

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/CrystalMin.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/CrystalMin.groovy
@@ -6,6 +6,7 @@ import static org.apache.commons.math3.util.FastMath.abs
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.potential.ForceFieldEnergy
 import ffx.potential.MolecularAssembly

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/Dynamics.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/Dynamics.groovy
@@ -4,6 +4,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import edu.rit.pj.Comm
 

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/DynamicsOpenMM.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/DynamicsOpenMM.groovy
@@ -5,6 +5,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.algorithms.integrators.Integrator
 import ffx.algorithms.integrators.IntegratorEnum

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/Histogram.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/Histogram.groovy
@@ -4,6 +4,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.potential.ForceFieldEnergy
 

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/ManyBody.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/ManyBody.groovy
@@ -4,6 +4,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import edu.rit.pj.Comm
 
@@ -14,7 +15,6 @@ import ffx.potential.bonded.Residue.ResidueType
 import ffx.potential.bonded.ResidueEnumerations.CommonAminoAcid3
 import ffx.potential.bonded.Rotamer
 import ffx.potential.bonded.RotamerLibrary
-import static ffx.potential.extended.ExtUtils.prop
 
 /**
  * The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/Minimize.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/Minimize.groovy
@@ -8,6 +8,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.numerics.Potential
 import ffx.numerics.PowerSwitch

diff --git a/...ain/groovy/ffx/potential/MutatePDB.groovy → ...in/groovy/ffx/algorithms/MutatePDB.groovy b/...ain/groovy/ffx/potential/MutatePDB.groovy → ...in/groovy/ffx/algorithms/MutatePDB.groovy
@@ -1,10 +1,11 @@
 
-package ffx.potentials
+package ffx.algorithms
 
 import org.apache.commons.configuration.CompositeConfiguration
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.algorithms.RotamerOptimization
 import ffx.potential.ForceFieldEnergy

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/Scheduler.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/Scheduler.groovy
@@ -3,6 +3,7 @@ package ffx.algorithms
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder;
 
 /**
  * Run a Parallel Java Job Scheduler on a cluster with multiple nodes.

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/TestOSRWBias.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/TestOSRWBias.groovy
@@ -5,6 +5,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import ffx.potential.DualTopologyEnergy
 import ffx.potential.ForceFieldEnergy

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/Thermodynamics.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/Thermodynamics.groovy
@@ -8,6 +8,7 @@ import org.apache.commons.io.FilenameUtils
 
 import groovy.cli.Option
 import groovy.cli.Unparsed
+import groovy.cli.picocli.CliBuilder
 
 import edu.rit.pj.Comm
 

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/biojLoader.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/biojLoader.groovy
@@ -41,6 +41,8 @@ import org.apache.commons.io.FilenameUtils
 import org.biojava.bio.structure.Structure
 import org.biojava.bio.structure.io.PDBFileReader
 
+import groovy.cli.picocli.CliBuilder
+
 import ffx.algorithms.AlgorithmFunctions
 import ffx.algorithms.AlgorithmUtils
 import ffx.potential.MolecularAssembly

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/cluster.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/cluster.groovy
@@ -38,6 +38,8 @@
 
 package ffx.algorithms
 
+import groovy.cli.picocli.CliBuilder
+
 import ffx.potential.parsers.CoordinateFileFilter
 import ffx.potential.parsers.PDBFileFilter
 import static ffx.algorithms.ClusterStructures.ClustAlg.AV_LINK

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/crystalSearch.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/crystalSearch.groovy
@@ -42,6 +42,8 @@
 import org.apache.commons.io.FilenameUtils
 import org.apache.commons.math3.geometry.euclidean.threed.Rotation
 
+import groovy.cli.picocli.CliBuilder
+
 import ffx.algorithms.Minimize
 import ffx.crystal.Crystal
 import ffx.potential.ForceFieldEnergy

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/generateRotamers.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/generateRotamers.groovy
@@ -36,8 +36,11 @@
  * exception statement from your version.
  */
 
+
 import org.apache.commons.io.FilenameUtils
 
+import groovy.cli.picocli.CliBuilder
+
 import ffx.algorithms.GenerateRotamers
 import ffx.potential.bonded.Polymer
 import ffx.potential.bonded.Residue

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/loopBuilder.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/loopBuilder.groovy
@@ -40,6 +40,8 @@
 
 import org.apache.commons.io.FilenameUtils
 
+import groovy.cli.picocli.CliBuilder
+
 import edu.rit.mp.DoubleBuf
 import edu.rit.mp.IntegerBuf
 import edu.rit.pj.Comm

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/mbMiner.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/mbMiner.groovy
diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/mmGKSA.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/mmGKSA.groovy
@@ -37,6 +37,8 @@
  * exception statement from your version.
  */
 
+import groovy.cli.picocli.CliBuilder
+
 import ffx.algorithms.MMgksa
 import ffx.potential.MolecularAssembly
 import ffx.potential.bonded.Atom

diff --git a/modules/algorithms/src/main/groovy/ffx/algorithms/monteCarlo.groovy b/modules/algorithms/src/main/groovy/ffx/algorithms/monteCarlo.groovy
@@ -41,6 +41,8 @@
 
 import org.apache.commons.io.FilenameUtils
 
+import groovy.cli.picocli.CliBuilder
+
 import edu.rit.pj.Comm
 
 import ffx.algorithms.mc.CoordShakeMove