code style improvements

README.md

@@ -1,5 +1,5 @@
 [![Build Status](https://travis-ci.org/OpenDA-Association/OpenDA.svg?branch=master)](https://travis-ci.org/OpenDA-Association/OpenDA)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/e78fb37c00fa4d689eb3a40d4b786d94)](https://www.codacy.com/app/OpenDA_Association/OpenDA?utm_source=github.com&utm_medium=referral&utm_content=OpenDA-Association/OpenDA&utm_campaign=Badge_Grade)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/465833e082b54b279105a280b36c75b8)](https://www.codacy.com/gh/OpenDA-Association/OpenDA?utm_source=github.com&utm_medium=referral&utm_content=OpenDA-Association/OpenDA&utm_campaign=Badge_Grade)
 
 # OpenDA
 
@@ -12,35 +12,34 @@ OpenDA is an Open Source project. Contributions are welcome from anyone wishing
 
 Data-assimilation methods
 
-- Ensemble KF (EnKF)
-- Ensemble SquareRoot KF (EnSR)
-- Steady State KF
-- Particle Filter
-- 3DVar
-- DudEnKF (still under research)
-- DudEnSR (still under research)
+-   Ensemble KF (EnKF)
+-   Ensemble SquareRoot KF (EnSR)
+-   Steady State KF
+-   Particle Filter
+-   3DVar
+-   DudEnKF (still under research)
+-   DudEnSR (still under research)
 
 Parameter estimation (calibration) methods:
 
-- Dud
-- Sparse Dud
-- Simplex
-- Powell
-- Gridded full search
-- Shuffled Comples Evolution (SCE)
-- Generalized Likelihood Uncertainty Estimation (GLUE)
-- (L)BFGS
-- Conjugate Gradient: Fleetjer-Reeves, Polak-Ribiere, Steepest Descent
-- Uncertainty Analaysis methods
-- GLUE
-- DELSA
+-   Dud
+-   Sparse Dud
+-   Simplex
+-   Powell
+-   Gridded full search
+-   Shuffled Comples Evolution (SCE)
+-   Generalized Likelihood Uncertainty Estimation (GLUE)
+-   (L)BFGS
+-   Conjugate Gradient: Fleetjer-Reeves, Polak-Ribiere, Steepest Descent
+-   Uncertainty Analaysis methods
+-   GLUE
+-   DELSA
 
 Language interfaces
 
-- C/C++
-- Java
-- Fortran77/90
+-   C/C++
+-   Java
+-   Fortran77/90
 
 These files are part of the OpenDA software. For more information see our website at
-http://www.openda.org
-
+<http://www.openda.org>

algorithms/java/src/org/openda/algorithms/LeastSquaresCostFunction.java

@@ -19,7 +19,8 @@
 */
 package org.openda.algorithms;
 
-import org.openda.interfaces.*;
+import org.openda.interfaces.IStochVector;
+import org.openda.interfaces.IVector;
 
 public interface LeastSquaresCostFunction extends ICostFunction{
 
@@ -43,7 +44,7 @@ public interface LeastSquaresCostFunction extends ICostFunction{
 
     /**
      * Use background term for cost function, i.e. add Jb = (p-p0)'/B(p-p0)
-     * @param boolean to turn backgroundterm on(true) of off(false)
+     * @param onIsTrue to turn backgroundterm on(true) of off(false)
      */
     public abstract void setBackgroundTerm(boolean onIsTrue);
 

contributing.md

@@ -1,4 +1,3 @@
-
 # Contributing to OpenDA
 
 This document briefly describes the policy for contributing changes to OpenDA.
@@ -9,8 +8,9 @@ share your code with the OpenDA community this document applies.
 ## Share your code with the OpenDA community
 
 For OpenDA we distinguish two methods for contributing:
-1. Create a fork on github and then a pull request. When you contribute for the first time, then this is probably what you want.
-2. Ask a core-developer of OpenDA to create a branch where you can push you contributions. If you do not know who the core-developers of OpenDA are then you can contact one at info@openda.org
+
+1.  Create a fork on github and then a pull request. When you contribute for the first time, then this is probably what you want.
+2.  Ask a core-developer of OpenDA to create a branch where you can push you contributions. If you do not know who the core-developers of OpenDA are then you can contact one at info@openda.org
 
 ## Repository structure
 
@@ -19,34 +19,53 @@ As a general rule all code changes are first committed to a branch. These branch
 ## Step by step
 
 ### Fork scenario
-1. Create a fork on github
-2. Clone your newly created fork `git clone https://github.com/<your account>/OpenDA.git`
-3. Create a branch with a name that describes your intended developments. `git checkout -b my_branch`
-4. Write and test your code in your branch.
-5. Commit to your local copy and push to your fork of OpenDA
-   * `git add bla`
-   * `git commit -m "my description"`
-   * `git push origin my_branch`
-6. Once finished or more regularly: merge changes in OpenDA into your work
-  * Update your fork of OpenDA on github
-  * `git fetch origin master` to update your local copy (from your fork)
-  * `git merge master`
-7. Push changes to the server again `git push origin my_branch` (to your fork)
-8. Create a pull request on github
+
+1.  Create a fork on github
+
+2.  Clone your newly created fork `git clone https://github.com/<your account>/OpenDA.git`
+
+3.  Create a branch with a name that describes your intended developments. `git checkout -b my_branch`
+
+4.  Write and test your code in your branch.
+
+5.  Commit to your local copy and push to your fork of OpenDA
+
+    -   `git add bla`
+    -   `git commit -m "my description"`
+    -   `git push origin my_branch`
+
+6.  Once finished or more regularly: merge changes in OpenDA into your work
+
+    -   Update your fork of OpenDA on github
+    -   `git fetch origin master` to update your local copy (from your fork)
+    -   `git merge master`
+
+7.  Push changes to the server again `git push origin my_branch` (to your fork)
+
+8.  Create a pull request on github
 
 ### Directly on main repository scenario
-1. Clone your OpenDA repository `git clone https://github.com/OpenDA-Association/OpenDA.git`
-3. Create a branch with a name that describes your intended developments.  `git checkout -b my_branch`
-4. Write and test your code in your branch.
-5. Commit to local copy and push to your fork of OpenDA
-  * `git add bla`
-  * `git commit -m "my description"`
-  * `git push origin my_branch`
-6. Once finished or more regularly: merge changes in OpenDA into your work
-  * `git fetch origin master` to update your local copy
-  * `git merge master`
-7. Push changes to OpenDA on github again `git pus origin my_branch`
-8. Create a pull request on github
+
+1.  Clone your OpenDA repository `git clone https://github.com/OpenDA-Association/OpenDA.git`
+
+2.  Create a branch with a name that describes your intended developments.  `git checkout -b my_branch`
+
+3.  Write and test your code in your branch.
+
+4.  Commit to local copy and push to your fork of OpenDA
+
+    -   `git add bla`
+    -   `git commit -m "my description"`
+    -   `git push origin my_branch`
+
+5.  Once finished or more regularly: merge changes in OpenDA into your work
+
+    -   `git fetch origin master` to update your local copy
+    -   `git merge master`
+
+6.  Push changes to OpenDA on github again `git pus origin my_branch`
+
+7.  Create a pull request on github
 
 ## Questions
 

core/java/src/org/openda/exchange/dataobjects/AsciiKeywordDataObject.java

@@ -72,7 +72,7 @@
 public class AsciiKeywordDataObject implements IDataObject{
 
     private static final Logger logger = LoggerFactory.getLogger(AsciiKeywordDataObject.class);
-    MessageFormat logFormatter = new MessageFormat("");
+    private MessageFormat logFormatter = new MessageFormat("");
 
     private String fileName = null;
 	private static final String keyWordPrefix ="#oda:";
@@ -230,9 +230,7 @@ public void finish() {
         	//write to file
 		File outputFile = new File(fileName);
 		try{
-			if(outputFile.isFile()){
-				if ( ! outputFile.delete() ) throw new RuntimeException("Cannot delete " + outputFile);
-			}
+			if(outputFile.isFile() && ! outputFile.delete() ) throw new RuntimeException("Cannot delete " + outputFile);
 		}catch (Exception e) {
 			logger.error("DictionaryDataObject: trouble removing file " + this.fileName +" :\n" + e.getMessage());
 		}

core/java/test/org/openda/blackbox/wrapper/testData/noiseModel/bin/compute.sh

@@ -1,6 +1,6 @@
 #! /bin/bash
 
-echo "compute.sh on instanceDir" $1
+echo "compute.sh on instanceDir $1"
 echo "compute on instanceDir" $1 > compute-out.txt
 
 echo "COMPLETED" >> compute-out.txt

core/java/test/org/openda/blackbox/wrapper/testData/restartFirstPart/bin/compute.sh

@@ -1,6 +1,6 @@
 #! /bin/bash
 
-echo "compute.sh on instanceDir" $1
-echo "compute on instanceDir" $1 > compute-out.txt
+echo "compute.sh on instanceDir" "$1"
+echo "compute on instanceDir" "$1" > compute-out.txt
 
 echo "COMPLETED" >> compute-out.txt

core/java/test/org/openda/blackbox/wrapper/testData/restartSecondPart/bin/compute.sh

@@ -1,6 +1,6 @@
 #! /bin/bash
 
-echo "compute.sh on instanceDir" $1
-echo "compute on instanceDir" $1 > compute-out.txt
+echo "compute.sh on instanceDir" "$1"
+echo "compute on instanceDir" "$1" > compute-out.txt
 
 echo "COMPLETED" >> compute-out.txt

core/native/install_cygwin_dll.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
 cygdlls=$(ls .libs/cyg*.dll 2>/dev/null)
-if [ x$cygdlls != x ]; then
-cp $cygdlls $2
+if [ "x$cygdlls" != x ]; then
+cp "$cygdlls" "$2"
 fi

core/native/linux_install.sh

@@ -44,7 +44,7 @@ else
         fi
 fi	
 #defaults for 64/32bit (=look at architecture of this computer)
-export RAWARCH=`uname -m`
+export RAWARCH=$(uname -m)
 if [ "$RAWARCH" == "x86_64" ]; then
    export ARCH=64
 else
@@ -56,11 +56,11 @@ export IGNORENETCDF="no"
 
 #test for windows mingw
 export OSTYPE="unknown"
-export TMPVAR=`uname -s|grep -i mingw`
+export TMPVAR=$(uname -s|grep -i mingw)
 if [ ! -z  "$TMPVAR" ]; then
 	OSTYPE="win"
 fi
-export TMPVAR=`uname -s|grep -i linux`
+export TMPVAR=$(uname -s|grep -i linux)
 if [ ! -z  "$TMPVAR" ]; then
 	OSTYPE="linux"
 fi
@@ -102,7 +102,7 @@ if [ "$FORT" == "ifort" ];then
 	fi
 fi
 if [ "$FORT" == "gnu" ];then
-	export GFORTRANPATH=`which gfortran 2>/dev/null`
+	export GFORTRANPATH=$(which gfortran 2>/dev/null)
 	if [ ! -z "$GFORTRANPATH" ]; then
 		export MYFORT="$GFORTRANPATH"
 	else
@@ -133,7 +133,7 @@ if [ -z "$NETCDF_ROOT" ]; then
 		echo "Netcdf already compiled"
 	else
 		echo "Starting compilation of Netcdf"
-		pushd $BASE/external/netcdf
+		pushd "$BASE/external/netcdf"
 		./netcdf_install.sh $ARCH $FORT shared | tee netcdf_install.log
 		popd
 	fi
@@ -156,7 +156,7 @@ if [ -z "$MPI_ROOT" ]; then
 		echo "Mpich2 already compiled"
 	else
 		echo "Starting compilation of mpich2"
-		pushd $BASE/external/mpi
+		pushd "$BASE/external/mpi"
 		./mpi_install.sh $ARCH $FORT shared | tee mpi_install.log
 		popd
 	fi
@@ -189,8 +189,8 @@ fi
 #
 # OpenDA settings
 #
-pushd $BASE
-$BASE/autoreconf_fix.sh
+pushd "$BASE"
+"$BASE/autoreconf_fix.sh"
 popd
 
 # compile in a temporary direcory to avoid mixing sources and objects
@@ -214,7 +214,7 @@ else
 fi
 
 if [ -d "$BASE/$SYSTEM" ];then
-	rm -rf $BASE/$SYSTEM
+	rm -rf "$BASE/$SYSTEM"
 fi
 
 
@@ -247,10 +247,10 @@ if [ ! -d "$BASE/../native_bin/$SYSTEM" ]; then
 	mkdir -p $BASE/../native_bin/$SYSTEM
 fi
 #mpi
-rsync -ruav $BASE/external/mpi/$SYSTEM/ $BASE/../native_bin/$SYSTEM/
+rsync -ruav "$BASE/external/mpi/$SYSTEM/ $BASE/../native_bin/$SYSTEM/"
 #workaround: !!! teamcity does not like +'s and mpicxx is indentical
-rm -f $BASE/../native_bin/$SYSTEM/bin/mpic++
+rm -f "$BASE/../native_bin/$SYSTEM/bin/mpic++"
 #netcdf
-rsync -ruav $BASE/external/netcdf/$SYSTEM/ $BASE/../native_bin/$SYSTEM/
+rsync -ruav "$BASE/external/netcdf/$SYSTEM/ $BASE/../native_bin/$SYSTEM/"
 #openda
-rsync -ruav $BASE/$SYSTEM/ $BASE/../native_bin/$SYSTEM/
+rsync -ruav "$BASE/$SYSTEM/ $BASE/../native_bin/$SYSTEM/"

core/native/src/cta/cta_mem.c

@@ -35,7 +35,7 @@ void * CTA_Malloc(size_t size){
    void *ptr = malloc(size);
 #ifdef DEBUG
    if (! ptr){
-      printf("CTA_Malloc: Warning: malloc returns NULL. (size=%zd)\n",size);
+      printf("CTA_Malloc: Warning: malloc returns NULL. (size=%zu)\n",size);
    }
    else {
 //      memset(ptr,'@', size);  
@@ -49,7 +49,7 @@ void * CTA_Realloc(void *ptr, size_t size){
    void *ptrOut = realloc(ptr, size);
 #ifdef DEBUG
    if (! ptrOut){
-      printf("CTA_Malloc: Warning: malloc returns NULL. (size=%zd)\n",size);
+      printf("CTA_Malloc: Warning: malloc returns NULL. (size=%zu)\n",size);
    }
 #endif
   return ptrOut;

core/native/update_simona.sh

@@ -59,15 +59,15 @@ if [ check_env ] ; then
    do
       for file in $group.a $group.la $group.so $group.so.0 $group.so.0.0.0
       do
-          if [ -e $ODA_COSTA_LIB/$file ] ; then
+          if [ -e "$ODA_COSTA_LIB/$file" ] ; then
              cp -vfup "$ODA_COSTA_LIB/$file" "$SIM_COSTA_LIB/$file.$UI_NAME"
           fi
       done
    done
 
    # Perform a simake.pl in the src/external/costa directory
    echo "Running simake.pl..."
-   cd $SIM_COSTA
+   cd "$SIM_COSTA"
    simake.pl
 fi
 

core/tests/native_advec1d/clean.sh

@@ -1,4 +1,4 @@
 #! /bin/sh
 rm -f openda_logfile.txt
-rm *_results.m
-rm -f *.log
+rm ./*_results.m
+rm -f ./*.log

core/tests/native_heat/clean.sh

@@ -1,7 +1,7 @@
 #! /bin/sh
 
-rm -f *_results.m
-rm -f *.log
+rm -f ./*_results.m
+rm -f ./*.log
 rm -f openda_logfile.txt
 rm -rf enkf_nc/*
 rm -rf denkf_nc/*

core/tests/native_oscillator/clean.sh

@@ -1,7 +1,7 @@
 #! /bin/bash
-rm -f *-results.txt 
-rm -f *_results.m 
+rm -f ./*-results.txt 
+rm -f ./*_results.m 
 rm -f openda_logfile.txt
-rm -f *.log
-rm -f *.orp
+rm -f ./*.log
+rm -f ./*.orp
 rm -f netcdf_output/*.nc

core/tests/native_parallel/masterworker/run.sh

@@ -9,7 +9,7 @@ if [ "$BINDIR" == "not set" ]; then
 fi
 
 mpiexec -np 2 Application.sh -p PolluteEnKFOpenDaConfigMW.oda : \
-        -np 2 $BINDIR/pollute2d_worker pollute2d_worker_config.xml : \
+        -np 2 "$BINDIR/pollute2d_worker pollute2d_worker_config.xml" : \
         -np 1 Application.sh -p PolluteEnKFOpenDaConfigMW.oda : \
-        -np 2 $BINDIR/pollute2d_worker pollute2d_worker_config.xml
+        -np 2 "$BINDIR/pollute2d_worker pollute2d_worker_config.xml"