From a920a14dc09769fb02bb9ec751581ecb3b52aa9b Mon Sep 17 00:00:00 2001
From: rogerfraser <roger.fraser@delwp.vic.gov.au>
Date: Fri, 23 Jul 2021 09:40:00 +1000
Subject: [PATCH 1/8] Fix inconsistency in parsing station names from DynaML
 files

---
 dynadjust/dynadjust/dnaimport/dnaparser_pimpl.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dynadjust/dynadjust/dnaimport/dnaparser_pimpl.cxx b/dynadjust/dynadjust/dnaimport/dnaparser_pimpl.cxx
index 3650aab2..f5254361 100644
--- a/dynadjust/dynadjust/dnaimport/dnaparser_pimpl.cxx
+++ b/dynadjust/dynadjust/dnaimport/dnaparser_pimpl.cxx
@@ -1137,7 +1137,7 @@ void StationCoord_pimpl::pre()
 
 void StationCoord_pimpl::Name(const ::std::string& Name)
 {
-	_parent_dnaStn->SetName(Name);
+	//_parent_dnaStn->SetName(Name);
 }
 
 void StationCoord_pimpl::XAxis(const ::std::string& XAxis)

From 39cdaf9c7e9e42b5c8d1ceef809b0d615da088b8 Mon Sep 17 00:00:00 2001
From: rogerfraser <roger.fraser@delwp.vic.gov.au>
Date: Wed, 28 Jul 2021 10:10:25 +1000
Subject: [PATCH 2/8] Cleanup temporary download folder on exit

---
 resources/install_dynadjust_prerequisites.sh | 60 ++++++++++++++++----
 1 file changed, 50 insertions(+), 10 deletions(-)

diff --git a/resources/install_dynadjust_prerequisites.sh b/resources/install_dynadjust_prerequisites.sh
index 98538d18..077de5a8 100755
--- a/resources/install_dynadjust_prerequisites.sh
+++ b/resources/install_dynadjust_prerequisites.sh
@@ -6,7 +6,14 @@
 #   
 #################################################################################
 
-
+_distro_centos="CentOS Linux"
+_distro_debian="Debian"
+_distro_fedora="Fedora"
+_distro_opensusel="openSUSE Leap"
+_distro_opensuse="openSUSE"
+_distro_rhels="Red Hat Enterprise Linux Server"
+_distro_rhel="Red Hat Enterprise Linux"
+_distro_ubuntu="Ubuntu"
 
 #################################################################################
 # Capture system variables and set defaults
@@ -27,6 +34,7 @@ _system=$(uname -sroi)
 _script="install_dynadjust_prerequisites.sh"
 _mode=0
 _distribution=
+_create_downloads_dir=0
 #################################################################################
 
 
@@ -48,8 +56,14 @@ function help {
     echo ""
     usage
     echo -e "options:"
-    echo -e "  -d [ --distro ] arg    The linux distribution, e.g. \"Ubuntu\", \"Fedora\", etc. "
-    echo -e "                         If not provided, try to get from /etc/os-release."
+    echo -e "  -d [ --distro ] arg    The linux distribution. Recognised distros include:"
+    echo -e "                           - ${_distro_centos}"
+    echo -e "                           - ${_distro_debian}"
+    echo -e "                           - ${_distro_fedora}"
+    echo -e "                           - ${_distro_opensuse}"
+    echo -e "                           - ${_distro_rhel}"
+    echo -e "                           - ${_distro_ubuntu}"
+    echo -e "                         If not provided, I will try to get the distro from /etc/os-release."
     echo -e "  -m [ --mode ] arg      Mode of installing prerequisites:"
     echo -e "                           0: interactive (default)"
     echo -e "                           1: package manager"
@@ -99,20 +113,26 @@ function args_check {
     if [[ ! -z $_distribution ]]; then
         # Set distro based on first character
         if [[ "$firstletter" = "C" ]]; then
-            _distro="CentOS Linux"
+            _distro=${_distro_centos}
         elif [[ "$firstletter" = "R" ]]; then
-            _distro="Red Hat Enterprise Linux Server"
+            _distro=${_distro_rhel}
         elif [[ "$firstletter" = "F" ]]; then
-            _distro="Fedora"
+            _distro=${_distro_fedora}
         elif [[ "$firstletter" = "O" ]]; then
-            _distro="openSUSE"
+            _distro=${_distro_opensuse}
         elif [[ "$firstletter" = "U" ]]; then
-            _distro="Ubuntu"
+            _distro=${_distro_ubuntu}
         elif [[ "$firstletter" = "D" ]]; then
-            _distro="Debian"
+            _distro=${_distro_debian}
         else
             # error
-            echo -e "\nUnknown value: --distro $_distribution"
+            echo -e "\nerror: Unknown distribution: \"$_distribution\"\n"
+            echo -e "  If your Linux distribution is based on a distro in the supported"
+            echo -e "  list (e.g. Mint is based on Ubuntu), try running:"
+            echo -e "    $ ${_script} -d base-distro\n"
+            echo -e "  If this fails to work, please submit an issue at:"
+            echo -e "  https://github.com/icsm-au/DynAdjust/issues including this message"
+            echo -e "  and your distribution."
             help
             exit 1 # error
         fi
@@ -397,6 +417,13 @@ elif [[ $REPLY == 2 ]]; then
         sudo mkdir /opt/xerces-c/3.1.4
     fi    
 
+    if [[ ! -d "$DOWNLOADS_FOLDER_FULLPATH" ]]; then
+        mkdir "$DOWNLOADS_FOLDER_FULLPATH"
+        _create_downloads_dir=1
+    else
+        #echo -e "\n ${DOWNLOADS_FOLDER} exists"
+    fi
+
     # 2. download:
     echo "Downloading xerces-c 3.1.4..."
     echo " "
@@ -435,6 +462,11 @@ elif [[ $REPLY == 2 ]]; then
     if [[ -e "$XERCES_TMP_FILE" ]]; then
         rm -f "$XERCES_TMP_FILE"
     fi
+
+    if [[ _create_downloads_dir -eq 1 ]]; then
+        #echo -e "\n ${DOWNLOADS_FOLDER} removed"
+        rm -R "$DOWNLOADS_FOLDER_FULLPATH"    
+    fi
     
 else
     echo " "
@@ -513,6 +545,9 @@ elif [[ $REPLY == 2 ]]; then
 
     if [[ ! -d "$DOWNLOADS_FOLDER_FULLPATH" ]]; then
         mkdir "$DOWNLOADS_FOLDER_FULLPATH"
+        _create_downloads_dir=1
+    else
+        #echo -e "\n ${DOWNLOADS_FOLDER} exists"
     fi
 
     # 2. download:
@@ -550,6 +585,11 @@ elif [[ $REPLY == 2 ]]; then
         rm -f "$XSD_TMP_FILE"
     fi 
 
+    if [[ _create_downloads_dir -eq 1 ]]; then
+        #echo -e "\n ${DOWNLOADS_FOLDER} removed"
+        rm -R "$DOWNLOADS_FOLDER_FULLPATH"    
+    fi
+
 else
     echo " "
     echo "Skipping xsd installation."

From 22878bb04ac6bbfa7ed559278295bf5315ed3266 Mon Sep 17 00:00:00 2001
From: rogerfraser <roger.fraser@delwp.vic.gov.au>
Date: Thu, 29 Jul 2021 17:42:40 +1000
Subject: [PATCH 3/8] Address discontinuity renaming issue found in beta
 release v1.2.1

---
 dynadjust/include/io/dnaiosnxread.cpp | 26 ++++++++------------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/dynadjust/include/io/dnaiosnxread.cpp b/dynadjust/include/io/dnaiosnxread.cpp
index 10ee6fd7..618819be 100644
--- a/dynadjust/include/io/dnaiosnxread.cpp
+++ b/dynadjust/include/io/dnaiosnxread.cpp
@@ -405,24 +405,14 @@ void dna_io_snx::format_station_names(v_discontinuity_tuple* stn_discontinuities
 				year = _it_discont_site->date_start.year();
 				ss << siteOccurrence_.at(site).site_name << "_";
 
-				if (year == DISCONT_TIME_IMMEMORIAL)
-				{
-					// format using the start epoch
-					// year (4 chars)
-					ss << siteOccurrence_.at(site).formatted_date.substr(4, 4);
-					// doy (3 chars)
-					ss << siteOccurrence_.at(site).formatted_date.substr(0, 3);
-				}
-				else
-				{
-					// format using the discontinuity date
-					ss << year;
-					if  (doy < 100)
-						ss << "0";
-					if (doy < 10)
-						ss << "0";
-					ss << doy;
-				}
+				// format date using the start of the window defining the 
+				// period up to which a discontinuity has been identified
+				ss << year;
+				if  (doy < 100)
+					ss << "0";
+				if (doy < 10)
+					ss << "0";
+				ss << doy;
 				
 				siteOccurrence_.at(site).formatted_name = ss.str();
 				//TRACE("Site %s\n", siteOccurrence_.at(site).formatted_name.c_str());

From bac562f96561d8625cb71a316cc92e939b347f0d Mon Sep 17 00:00:00 2001
From: rogerfraser <roger.fraser@delwp.vic.gov.au>
Date: Thu, 29 Jul 2021 17:59:09 +1000
Subject: [PATCH 4/8] Streamline build behaviour across clone and no-clone
 options

---
 .github/workflows/cmake_release.yml |   7 +-
 .github/workflows/test_coverage.yml |   7 +-
 .travis.yml                         |  11 +-
 Dockerfile                          |   5 +-
 resources/make_dynadjust_gcc.sh     | 158 +++++++++++++++++++++-------
 5 files changed, 132 insertions(+), 56 deletions(-)

diff --git a/.github/workflows/cmake_release.yml b/.github/workflows/cmake_release.yml
index ab95656f..f5cf67ac 100644
--- a/.github/workflows/cmake_release.yml
+++ b/.github/workflows/cmake_release.yml
@@ -49,9 +49,8 @@ jobs:
     # Build and test using shell script
     - name: Build
       run: |
-        cd ..
-        cp ./DynAdjust/resources/make_dynadjust_gcc.sh ./
-        chmod +x ./make_dynadjust_gcc.sh
-        ./make_dynadjust_gcc.sh --no-install --auto --do-not-clone
+        cd ./DynAdjust
+        chmod +x ./resources/make_dynadjust_gcc.sh
+        ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone
 
     
diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
index e3000fcd..16265f0d 100644
--- a/.github/workflows/test_coverage.yml
+++ b/.github/workflows/test_coverage.yml
@@ -50,10 +50,9 @@ jobs:
     # Build and test using shell script
     - name: Build and test
       run: |
-        cd ..
-        cp ./DynAdjust/resources/make_dynadjust_gcc.sh ./
-        chmod +x ./make_dynadjust_gcc.sh
-        ./make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
+        cd ./DynAdjust
+        chmod +x ./resources/make_dynadjust_gcc.sh
+        ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
     
     # Submit to coveralls
     - name: Submit coverage to Coveralls
diff --git a/.travis.yml b/.travis.yml
index 6c378469..f4c108d2 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,17 +22,14 @@ before_install:
   - sudo sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list'
   - sudo apt-get update
   - sudo apt-get install -y intel-mkl-64bit-2018.3-051
-#  - bash resources/install_dynadjust_prerequisites.sh -m 1
 
 script:
-   - cd ..
-   - cp ./DynAdjust/resources/make_dynadjust_gcc.sh ./
-   - bash make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
+   - cd ./DynAdjust
+   - chmod +x ./resources/make_dynadjust_gcc.sh
+   - ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
   
 after_success:
-   - cd ./DynAdjust/dynadjust/
-#  - coveralls --root . -E ".*CMakeFiles.*" 
-#  - coveralls --root . --verbose --exclude-pattern ".*feature_tests.*" --exclude-pattern ".*CompilerId.*" --gcov-options '\-lp'
+   - cd ./dynadjust/
    - coveralls 
      --gcov /usr/bin/gcov
      --exclude-pattern ".*feature_tests.*" 
diff --git a/Dockerfile b/Dockerfile
index 0807e75d..619f830b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,6 +21,7 @@ RUN apt-get update &&\
  apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB && \
  sh -c 'echo deb https://apt.repos.intel.com/mkl all main > /etc/apt/sources.list.d/intel-mkl.list' && \
  apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install cpio intel-mkl-64bit-2018.3-051 &&\
- chmod +x ./DynAdjust/resources/make_dynadjust_gcc.sh &&\
- ./DynAdjust/resources/make_dynadjust_gcc.sh
+ cd ./DynAdjust
+ chmod +x ./resources/make_dynadjust_gcc.sh &&\
+ ./resources/make_dynadjust_gcc.sh
   
diff --git a/resources/make_dynadjust_gcc.sh b/resources/make_dynadjust_gcc.sh
index 80c867db..cb1a14b6 100755
--- a/resources/make_dynadjust_gcc.sh
+++ b/resources/make_dynadjust_gcc.sh
@@ -30,7 +30,7 @@ _binaries=(dnaimportwrapper dnaimport dnageoidwrapper dnageoid dnareftranwrapper
 # display example message
 function example {
     echo -e "examples:"
-	echo -e "  $_script --auto --do-not-clone --test --no-install"
+	echo -e "  $_script --auto --no-clone --test --no-install"
 }
 
 # display usage message
@@ -43,15 +43,21 @@ function help {
     echo ""
     usage
     echo -e "options:"
-    echo -e "  -a [ --auto ]          Run automatically with no user interaction."
-    echo -e "  -b [ --binary ] arg    Build a specific binary (e.g. \"dnaimport\" or \"dnaadjustwrapper\")."
-    echo -e "                         By default, \"all\" binaries are built."
-    echo -e "  -c [ --do-not-clone ]  By default, the latest version will be cloned from GitHub."
-    echo -e "                         Set this option if a clone should not be made."
-    echo -e "  -d [ --debug ]         Compile debug version."
-    echo -e "  -n [ --no-install ]    Do not install binaries."
-    echo -e "  -t [ --test ]          Run cmake tests."
-    echo -e "  -h [ --help ]          Prints this help message.\n"
+    echo -e "  -a [ --auto ]        Run automatically with no user interaction."
+    echo -e "  -b [ --binary ] arg  Build a specific binary (e.g. \"dnaimport\" or \"dnaadjustwrapper\")."
+    echo -e "                       By default, \"all\" binaries are built."
+    echo -e "  -c [ --no-clone ]    By default, the latest version will be cloned from GitHub"
+	echo -e "                       into the current directory, using:"
+	echo -e "                         git clone https://github.com/icsm-au/DynAdjust.git"
+    echo -e "                       Provide this option if building source from a local copy, e.g.:"
+	echo -e "                         $ wget https://github.com/icsm-au/DynAdjust/archive/refs/tags/v1.1.0.tar.gz -O DynAdjust-1.1.0.tar.gz"
+    echo -e "                         $ tar xzvf DynAdjust-1.1.0.tar.gz"
+    echo -e "                         $ cd DynAdjust-1.1.0/"
+	echo -e "                         $ bash ./resources/make_dynadjust_gc.sh (this script)"
+    echo -e "  -d [ --debug ]       Compile debug version."
+    echo -e "  -n [ --no-install ]  Do not install binaries."
+    echo -e "  -t [ --test ]        Run cmake tests."
+    echo -e "  -h [ --help ]        Prints this help message.\n"
     example
     echo ""
 }
@@ -69,7 +75,7 @@ do
    -d  | --debug )  
    					_debug=1 # compile debug variant
 			        ;;
-   -c  | --do-not-clone )
+   -c  | --no-clone )
    					_clone=1 # do not clone from GitHub
 			        ;;
    -t  | --test )   
@@ -128,10 +134,20 @@ else
 	echo -e " - run interactively (ask for user input)."
 fi
 
+# get current directory
+_cwd="$PWD"
+
 if [[ $_clone -eq 1 ]]; then
-	echo -e " - do not clone a fresh copy from GitHub."
+	echo -e " - do not clone, but build from local source."
+	# As per help, the user is expected to be in this directory once
+	# a local copy has been extracted.
+	_clone_dir="$_cwd"
+
 else
 	echo -e " - clone a fresh copy from GitHub."
+	# set directory to which git will clone the latest
+	# DynAdjust repo
+	_clone_dir="$_cwd/DynAdjust"
 fi
 
 if [[ $_test -eq 1 ]]; then
@@ -144,11 +160,6 @@ else
 	echo -e " - install binaries to /opt/dynadjust/gcc/x_x_x."
 fi
 
-
-# get current directory
-_cwd="$PWD"
-# set dynadjust clone dir
-_clone_dir="$_cwd/DynAdjust"
 # set dynadjust root dir
 _root_dir="$_clone_dir/dynadjust"
 # set dynadjust root dir
@@ -165,10 +176,10 @@ eval BIN_FOLDER_FULLPATH="$BIN_FOLDER"
 # opt installation folder
 OPT_DYNADJUST_PATH=/opt/dynadjust
 OPT_DYNADJUST_GCC_PATH=/opt/dynadjust/gcc
-DYNADJUST_INSTALL_PATH=/opt/dynadjust/gcc/1_1_0
+DYNADJUST_INSTALL_PATH=/opt/dynadjust/gcc/1_2_1
 
 # version info
-_version="1.1.0"
+_version="1.2.1"
 
 echo -e "\n==========================================================================="
 echo -e "Build and installation of DynAdjust $_version...\n"
@@ -212,22 +223,31 @@ else
 fi
 
 # INSTALL DYNADJUST
-# 1. create install dirs:
-if [[ $_install -eq 0 ]]; then
-	if [[ ! -d "$BIN_FOLDER_FULLPATH" ]]; then
-		echo " "
-		echo "Making $BIN_FOLDER_FULLPATH"
-		mkdir "$BIN_FOLDER_FULLPATH"
-	fi
-fi
-
-# 2. clone from GitHub:
+# 1. clone from GitHub (if required):
 if [[ $_clone -eq 0 ]]; then
 	echo " "
 	echo "Cloning DynAdjust..."
 	git clone "$_clone_url" || echo -e "Okay, let's assume we already have a previously cloned version.\n"
 fi
 
+# check if root directory exists
+if [[ -d "$_root_dir" ]]; then
+    # Good, directory exists
+	echo -e "\nSuccessfully found root directory: $_root_dir\n"
+else
+    echo -e "\nerror: can't find root directory: $_root_dir\n"
+	echo -e "  If building from a local copy, please ensure this script is executed"
+	echo -e "  from the parent directory containing the following directories:"
+	echo -e "    ./dynadjust"
+	echo -e "    ./resources"
+	echo -e "    ./sampleData\n"
+	echo -e "  For example:"
+	echo -e "    $ tar xzvf DynAdjust-1.1.0.tar.gz"
+	echo -e "    $ cd DynAdjust-1.1.0/"
+	echo -e "    $ ./resources/make_dynadjust_gcc.sh\n"
+	exit 1 # error
+fi
+
 if [[ -d "$_build_dir" ]]; then
     echo "Cleaning out directory $_build_dir"
     cd "$_build_dir"
@@ -279,6 +299,7 @@ esac
 
 echo -e "\n==========================================================================="
 
+
 # Make!
 if [[ $_binary = "all" ]]; then
 	echo -e "Building DynAdjust $_version...\n"
@@ -309,26 +330,44 @@ esac
 #
 # determine if user needs prompting
 case ${_auto} in
-    0) # install binaries
-        echo " "
-		read -r -p "Install DynAdjust to $OPT_DYNADJUST_PATH [Y/n]: " optresponse;;
-    *) # proceed without asking
+    0)  # Interactive mode (check if the user has 
+	    # already decided not to install)
+		if [[ $_install -eq 1 ]]; then
+			# user did not want to install, so don't ask
+			optresponse="n"
+		else
+			echo " "
+			read -r -p "Install DynAdjust to $OPT_DYNADJUST_PATH [Y/n]: " optresponse
+		fi
+        ;;
+    *)  # proceed without asking. Assume installation
         optresponse="y"
-		# set install option
+		
+		# user did not want to install, so alter the 
+		# response accordingly
 		if [[ $_install -eq 1 ]]; then
 			optresponse="n"
 		fi
 		;;
 esac
 
+_lib_ext="so"
+
 if [[ "$optresponse" =~ ^([nN][oO]|[nN])$ ]]
 then    
     echo " "
 else
 
-    _lib_ext="so"
+	# create install dirs:
+	if [[ $_install -eq 0 ]]; then
+		if [[ ! -d "$BIN_FOLDER_FULLPATH" ]]; then
+			echo " "
+			echo "Making $BIN_FOLDER_FULLPATH"
+			mkdir "$BIN_FOLDER_FULLPATH"
+		fi
+	fi
 
-	# 1 GET OS, DISTRO AND TOOLS
+    # 1 GET OS, DISTRO AND TOOLS
 	if [[ "$OSTYPE" == "darwin"* ]]; then
 		# Mac OSX
 		_lib_ext="dylib"
@@ -423,12 +462,53 @@ fi
 # return to the original "current directory"
 cd "$_cwd"
 
-echo "Done."
-echo " "
+echo -e "Done.\n"
 
 if [[ $_install -eq 0 ]]; then
 	echo "Don't forget to add the bin directory to path in ~/.bash_profile"
 	echo "For example:"
-	echo "    EXPORT PATH=$PATH:$HOME/bin"
+	echo -e "    EXPORT PATH=$PATH:$HOME/bin\n"
+else
+	echo "DynAdjust binaries can be located as follows:"
+	if [[ -e "${_build_dir}/dynadjust/dynadjust/dynadjust" ]]; then
+		echo " +[dynadjust]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dynadjust"
+	fi
+	if [[ -e "${_build_dir}/dynadjust/dnaadjustwrapper/dnaadjust" ]]; then
+		echo " +[dnaadjust]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnaadjustwrapper/dnaadjust"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnaadjust/libdnaadjust.$_lib_ext"
+	fi
+
+	if [[ -e "${_build_dir}/dynadjust/dnaimportwrapper/dnaimport" ]]; then
+		echo " +[dnaimport]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnaimport/libdnaimport.$_lib_ext"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnaimportwrapper/dnaimport"
+	fi
+
+	if [[ -e "${_build_dir}/dynadjust/dnareftranwrapper/dnareftran" ]]; then
+		echo " +[dnareftran]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnareftranwrapper/dnareftran"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnareftran/libdnareftran.$_lib_ext"
+	fi
+
+	if [[ -e "${_build_dir}/dynadjust/dnageoidwrapper/dnageoid" ]]; then
+		echo " +[dnageoid]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnageoidwrapper/dnageoid"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnageoid/libdnageoid.$_lib_ext"
+	fi
+
+	if [[ -e "${_build_dir}/dynadjust/dnasegmentwrapper/dnasegment" ]]; then
+		echo " +[dnasegment]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnasegmentwrapper/dnasegment"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnasegment/libdnasegment.$_lib_ext"
+	fi
+
+	if [[ -e "${_build_dir}/dynadjust/dnaplotwrapper/dnaplot" ]]; then
+		echo " +[dnaplot]"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnaplotwrapper/dnaplot"
+		echo "  ./dynadjust/build_gcc/dynadjust/dnaplot/libdnaplot.$_lib_ext"
+	fi
+	
 	echo " "
 fi

From e3c718201c7212400444ffdf7994310aa3f2a78a Mon Sep 17 00:00:00 2001
From: Roger Fraser <roger.fraser@delwp.vic.gov.au>
Date: Thu, 29 Jul 2021 20:29:27 +1000
Subject: [PATCH 5/8] Update .travis.yml

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index f4c108d2..57b0628a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,7 +24,6 @@ before_install:
   - sudo apt-get install -y intel-mkl-64bit-2018.3-051
 
 script:
-   - cd ./DynAdjust
    - chmod +x ./resources/make_dynadjust_gcc.sh
    - ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
   

From 3e03ad0f9dcc5c4cc9bb47af90e49ad050a338eb Mon Sep 17 00:00:00 2001
From: Roger Fraser <roger.fraser@delwp.vic.gov.au>
Date: Thu, 29 Jul 2021 20:31:20 +1000
Subject: [PATCH 6/8] Update test_coverage.yml

---
 .github/workflows/test_coverage.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test_coverage.yml b/.github/workflows/test_coverage.yml
index 16265f0d..eb8abd69 100644
--- a/.github/workflows/test_coverage.yml
+++ b/.github/workflows/test_coverage.yml
@@ -50,7 +50,6 @@ jobs:
     # Build and test using shell script
     - name: Build and test
       run: |
-        cd ./DynAdjust
         chmod +x ./resources/make_dynadjust_gcc.sh
         ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
     

From a76d1c199d6514e675a980041c8ef68fec841de7 Mon Sep 17 00:00:00 2001
From: Roger Fraser <roger.fraser@delwp.vic.gov.au>
Date: Thu, 29 Jul 2021 20:31:42 +1000
Subject: [PATCH 7/8] Update cmake_release.yml

---
 .github/workflows/cmake_release.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/cmake_release.yml b/.github/workflows/cmake_release.yml
index f5cf67ac..37524dd0 100644
--- a/.github/workflows/cmake_release.yml
+++ b/.github/workflows/cmake_release.yml
@@ -49,7 +49,6 @@ jobs:
     # Build and test using shell script
     - name: Build
       run: |
-        cd ./DynAdjust
         chmod +x ./resources/make_dynadjust_gcc.sh
         ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone
 

From f0440d092759c1149136e6ace3284972a7126882 Mon Sep 17 00:00:00 2001
From: Roger Fraser <roger.fraser@delwp.vic.gov.au>
Date: Thu, 29 Jul 2021 20:34:28 +1000
Subject: [PATCH 8/8] Update .travis.yml

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 57b0628a..38a66a35 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,7 +25,7 @@ before_install:
 
 script:
    - chmod +x ./resources/make_dynadjust_gcc.sh
-   - ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone --test
+   - ./resources/make_dynadjust_gcc.sh --no-install --auto --no-clone --test
   
 after_success:
    - cd ./dynadjust/