Merge f0440d0 into 720574b

.github/workflows/cmake_release.yml

@@ -49,9 +49,7 @@ 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
+        chmod +x ./resources/make_dynadjust_gcc.sh
+        ./resources/make_dynadjust_gcc.sh --no-install --auto --do-not-clone
 
     

.github/workflows/test_coverage.yml

@@ -50,10 +50,8 @@ 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
+        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

.travis.yml

@@ -22,17 +22,13 @@ 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
+   - chmod +x ./resources/make_dynadjust_gcc.sh
+   - ./resources/make_dynadjust_gcc.sh --no-install --auto --no-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.*" 

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
 

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)

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());

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."