Test PR for jenkins CI pipeline

README.md

@@ -139,4 +139,4 @@ States Government.
 
 ## UPP Terms of Use Notice
 
-The UPP Terms of Use Notice is available at: https://github.com/NOAA-EMC/UPP/wiki/UPP-Terms-of-Use-Notice
+The UPP Terms of Use Notice is available at: https://github.com/NOAA-EMC/UPP/wiki/UPP-Terms-of-Use-Notice

ci/Jenkinsfile

@@ -0,0 +1,124 @@
+pipeline {
+  agent none
+  stages {
+    stage('UPP Regression Tests') {
+       agent {
+        label 'built-in'   
+       }
+      steps {
+        script {
+          for (label in pullRequest.labels) {
+            if ((label.matches("orion"))) {
+                 env.CHOICE_NODE='orion'
+            }  
+            else if ((label.matches("hera"))) {
+                env.CHOICE_NODE='hera'
+            }  
+            else if ((label.matches("hercules"))) {
+                env.CHOICE_NODE='hercules'
+            }  
+            else if ((label.matches("jet"))) {
+                env.CHOICE_NODE='jet'
+            } 
+            else { 
+                env.CHOICE_NODE='none'
+            }
+         }
+// Why do I need another if..block, because it just works this way.
+
+            if (CHOICE_NODE == 'orion') {
+                echo "Starting up orion ${CHOICE_NODE}...this might take 5-10 minutes...please be patient."
+            } 
+             else if (CHOICE_NODE == 'jet') {
+                echo "Starting up jet ${CHOICE_NODE}...this might take 5-10 minutes...please be patient."
+            }
+             else if (CHOICE_NODE == 'hercules') {
+                 echo "Starting up hera ${CHOICE_NODE}...this might take 5-10 minutes...please be patient."
+            }
+             else if (CHOICE_NODE == 'hera') {
+                 echo "Starting up hera ${CHOICE_NODE}...this might take 5-10 minutes...please be patient."
+            }
+             else {
+                echo "${CHOICE_NODE} is NOT a platform, moving on..."
+            }
+       }    
+    }
+  } 
+  stage('Run UPP RTs on Hera') {
+        agent {
+          label "hera"
+        }
+        environment {
+        ACCNR = 'epic'
+        NODE_PATH = '/scratch2/NAGAPE/epic/UPP/jenkins-ci'
+      }
+      steps {
+
+        cleanWs()
+        checkout scm
+        sh '''
+        echo $(pwd)
+        cd ci/
+        cp /scratch1/NCEPDEV/nems/Fernando.Andrade-maldonado/scripts/rt.sh .
+        ./rt.sh -a ${ACCNR} -h /scratch2/NAGAPE/epic/UPP/test_suite/ -r `pwd`/rundir -t `pwd`/../
+        python ./rt-status.py
+        '''
+      }
+    }        
+    stage('Run UPP RTs on Orion') {
+        agent {
+          label "orion"
+        }
+        environment {
+        ACCNR = 'epic'
+        NODE_PATH = '/work/noaa/epic/UPP/jenkins-ci/orion'
+      }
+      steps {
+
+        cleanWs()
+        checkout scm
+        sh '''
+        echo $(pwd)
+        cd ci/
+        cp /work/noaa/epic-ps/nandoam/scripts/rt.sh .
+        ./rt.sh -a ${ACCNR} -h /work/noaa/epic/UPP/ -r `pwd`/rundir -t `pwd`/../
+        python ./rt-status.py
+        '''
+      }
+    }    
+    stage('Run UPP RTs on Hercules') {
+        agent {
+          label "hercules"
+        }
+        environment {
+        ACCNR = 'epic'
+        NODE_PATH = '/work/noaa/epic/UPP/jenkins-ci/hercules'
+      }
+      steps {
+
+        cleanWs()
+        checkout scm
+        sh '''
+
+        ''' 
+        }
+    } 
+        stage('Run UPP RTs on Jet') {
+        agent {
+          label "jet"
+        }
+        environment {
+        ACCNR = 'hfv3gfs'
+        NODE_PATH = '/mnt/lfs4/HFIP/hfv3gfs/role.epic/'
+      }
+      steps {
+
+        cleanWs()
+        checkout scm
+        sh '''
+
+        '''
+      }
+    }
+  }  
+}

ci/rt-status.py

@@ -0,0 +1,56 @@
+# check the UPP RT rundir for .diff files that would indicate a change in test results
+
+'''
+Updates
+Aug/29/2023 - Fernando Andrade-Maldonado: Script creation
+
+'''
+
+import os
+
+# files used in result comparison
+tests = [
+    'nmmb',
+    'gfs',
+    'fv3gefs',
+    'fv3r',
+    'rap',
+    'hrrr',
+    'fv3hafs',
+    'rtma'
+]
+
+# look for .diff files
+# every case has its own directory in rundir
+# loop through every test case sub directory and files, then match with the test name
+def check_for_diff(tests):
+    changed = False
+    for case_dir in os.listdir('./rundir'):
+        for file in os.listdir('./rundir/{}'.format(case_dir)):
+            if file.endswith('.diff'):
+                diff_case = ''
+                for test in tests:
+                    if test in case_dir:
+                        diff_case = test
+                if case_dir.endswith('pe_test'):
+                    # the rap pe test currently has a false positive bug with WRFPRS
+                    if 'rap' in case_dir and file == 'WRFPRS.GrbF16.diff':
+                        with open('./rundir/{}/{}'.format(case_dir, file)) as f:
+                            data = f.readlines()
+                            if len(data) == 1 and '708:195469472:CDCON:convective cloud layer:rpn_corr=-nan:rpn_rms=undefined' in data[0]:
+                                continue
+                    print('There are changes in results for case {}_pe_test in {}'.format(diff_case, file.replace(".diff", "")))
+                else:
+                    print('There are changes in results for case {} in {}'.format(diff_case, file.replace(".diff", "")))
+                changed = True
+    if changed:
+        print('Refer to .diff files in rundir: {}/rundir for details on differences in results for each case.'.format(os.getcwd()))
+    else:
+        print('No changes in test results detected.')
+
+
+def main():
+    check_for_diff(tests)
+
+if __name__ == "__main__":
+    main()

docs/Doxyfile.in

@@ -93,14 +93,6 @@ ALLOW_UNICODE_NAMES    = NO
 
 OUTPUT_LANGUAGE        = English
 
-# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all generated output in the proper direction.
-# Possible values are: None, LTR, RTL and Context.
-# The default value is: None.
-
-OUTPUT_TEXT_DIRECTION  = None
-
 # If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
 # descriptions after the members that are listed in the file and class
 # documentation (similar to Javadoc). Set to NO to disable this.
@@ -1111,44 +1103,6 @@ USE_HTAGS              = NO
 
 VERBATIM_HEADERS       = YES
 
-# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see:
-# http://clang.llvm.org/) for more accurate parsing at the cost of reduced
-# performance. This can be particularly helpful with template rich C++ code for
-# which doxygen's built-in parser lacks the necessary type information.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse_libclang=ON option for CMake.
-# The default value is: NO.
-
-CLANG_ASSISTED_PARSING = NO
-
-# If clang assisted parsing is enabled and the CLANG_ADD_INC_PATHS tag is set to
-# YES then doxygen will add the directory of each input to the include path.
-# The default value is: YES.
-
-CLANG_ADD_INC_PATHS    = YES
-
-# If clang assisted parsing is enabled you can provide the compiler with command
-# line options that you would normally use when invoking the compiler. Note that
-# the include paths will already be set by doxygen for the files and directories
-# specified with INPUT and INCLUDE_PATH.
-# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
-
-CLANG_OPTIONS          =
-
-# If clang assisted parsing is enabled you can provide the clang parser with the
-# path to the directory containing a file called compile_commands.json. This
-# file is the compilation database (see:
-# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
-# options used when the source files were built. This is equivalent to
-# specifying the -p option to a clang tool, such as clang-check. These options
-# will then be passed to the parser. Any options specified with CLANG_OPTIONS
-# will be added as well.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse_libclang=ON option for CMake.
-
-CLANG_DATABASE_PATH    =
-
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -1590,17 +1544,6 @@ HTML_FORMULA_FORMAT    = png
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANSPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are not
-# supported properly for IE 6.0, but are supported on all modern browsers.
-#
-# Note that when changing this option you need to delete any form_*.png files in
-# the HTML output directory before the changes have effect.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_TRANSPARENT    = YES
-
 # The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
 # to create new LaTeX commands to be used in formulas as building blocks. See
 # the section "Including formulas" for details.
@@ -1809,7 +1752,7 @@ COMPACT_LATEX          = NO
 # The default value is: a4.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-PAPER_TYPE             = a4wide
+PAPER_TYPE             = a4
 
 # The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
 # that should be included in the LaTeX output. The package can be specified just
@@ -1904,16 +1847,6 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
-# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source
-# code with syntax highlighting in the LaTeX output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_SOURCE_CODE      = NO
-
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. See
 # https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
@@ -1994,16 +1927,6 @@ RTF_STYLESHEET_FILE    =
 
 RTF_EXTENSIONS_FILE    =
 
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF output.
-#
-# Note that which sources are shown also depends on other settings such as
-# SOURCE_BROWSER.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_SOURCE_CODE        = NO
-
 #---------------------------------------------------------------------------
 # Configuration options related to the man page output
 #---------------------------------------------------------------------------
@@ -2100,15 +2023,6 @@ GENERATE_DOCBOOK       = NO
 
 DOCBOOK_OUTPUT         = docbook
 
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
 #---------------------------------------------------------------------------
 # Configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -2287,15 +2201,6 @@ EXTERNAL_PAGES         = NO
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 
-# If the CLASS_DIAGRAMS tag is set to YES, doxygen will generate a class diagram
-# (in HTML and LaTeX) for classes with base or super classes. Setting the tag to
-# NO turns the diagrams off. Note that this option also works with HAVE_DOT
-# disabled, but it is recommended to install and use dot, since it yields more
-# powerful graphs.
-# The default value is: YES.
-
-CLASS_DIAGRAMS         = YES
-
 # You can include diagrams made with dia in doxygen documentation. Doxygen will
 # then run dia to produce the diagram and insert it in the documentation. The
 # DIA_PATH tag allows you to specify the directory where the dia binary resides.
@@ -2328,23 +2233,6 @@ HAVE_DOT               = NO
 
 DOT_NUM_THREADS        = 0
 
-# When you want a differently looking font in the dot files that doxygen
-# generates you can specify the font name using DOT_FONTNAME. You need to make
-# sure dot is able to find the font, which can be done by putting it in a
-# standard location or by setting the DOTFONTPATH environment variable or by
-# setting DOT_FONTPATH to the directory containing the font.
-# The default value is: Helvetica.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTNAME           = Helvetica
-
-# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of
-# dot graphs.
-# Minimum value: 4, maximum value: 24, default value: 10.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_FONTSIZE           = 10
-
 # By default doxygen will tell dot to use the default font as specified with
 # DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set
 # the path where dot can find it using this tag.
@@ -2581,18 +2469,6 @@ DOT_GRAPH_MAX_NODES    = 50
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not seem
-# to support this out of the box.
-#
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-# The default value is: NO.
-# This tag requires that the tag HAVE_DOT is set to YES.
-
-DOT_TRANSPARENT        = NO
-
 # Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
 # makes dot run faster, but since only newer versions of dot (>1.8.10) support

jobs/J_NCEPPOST

@@ -147,7 +147,11 @@ env
 #########################################################
 # Execute the Script
 #########################################################
-$SCRgfs/ex${RUN}_atmos_nceppost.sh
+if [ $WAFSF = "YES" ] ; then
+    $SCRgfs/exwafs_atmos_nceppost.sh
+else
+    $SCRgfs/ex${RUN}_atmos_nceppost.sh
+fi
 
 ##############################
 # Remove the Temporary working directory