regression test system bug fixes, eliminate MOM6 warnings (#2197), add xr_cnvcld flag to FV3 (#2185)

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "FV3"]
   path = FV3
-  url = https://github.com/NOAA-EMC/fv3atm
+  url = https://github.com/lisa-bengtsson/fv3atm
   branch = develop
 [submodule "WW3"]
   path = WW3
@@ -24,8 +24,10 @@
   branch = emc/develop
 [submodule "MOM6"]
   path = MOM6-interface/MOM6
-  url = https://github.com/NOAA-EMC/MOM6
-  branch = dev/emc
+#  url = https://github.com/NOAA-EMC/MOM6
+#  branch = dev/emc
+  url = https://github.com/marshallward/MOM6
+  branch = emc_fix_warn
 [submodule "CICE"]
   path = CICE-interface/CICE
   url = https://github.com/NOAA-EMC/CICE

tests/atparse.bash

@@ -1,42 +1,106 @@
 #! /usr/bin/env bash
 function atparse {
-    local __set_x
-    [ -o xtrace ] && __set_x='set -x' || __set_x='set +x'
-    set +x
+    # Usage:
+    #     source atparse.bash # defines the "atparse" function; only do this once
+    #     atparse [ var1=value1 [ var2=value2 [...] ] ] < input_file > output_file
+    # This function filters text from stdin to stdout. It scans for text sequences like:
+    #    @[varname]
+    # And replaces them with the value of the corresponding ${varname} variable.
+    # You can provide variables that are not set in bash by providing them on the command line.
+    # If set -u is enabled, it will exit the process when a variable is empty or undefined via set -u.
+
     # Use __ in names to avoid clashing with variables in {var} blocks.
-    local __text __before __after __during
+    local __text # current line of text being parsed, or the current command-line argument being parsed
+    local __before # all text before the next @[...] option
+    local __after # all text after the next @[...] option
+    local __during # the contents of the @[...] option, including the @[ and ]
+    local __set_x=":" # will be "set -x" if the calling script had that option enabled
+    local __set_u=":" # will be "set -u" if the calling script had that option enabled
+    local __set_e=":" # will be "set -e" if the calling script had that option enabled
+    local __abort_on_undefined=NO # YES = script should abort if a variable is undefined, NO otherwise
+
+    # Ensure "set -x -e -u" are all inactive, but remember if they
+    # were active so we can reset them later.
+    if [[ -o xtrace ]] ; then
+        __set_x="set -x"
+    fi
+    if [[ -o errexit ]] ; then
+        __set_e="set -e"
+    fi
+    if [[ -o nounset ]] ; then
+        __set_u="set -u"
+        __abort_on_undefined=YES
+    fi
+    set +eux
+
+    # Allow setting variables on the atparse command line rather than the environment.
+    # They will be local variables in this function.
     for __text in "$@" ; do
         if [[ $__text =~ ^([a-zA-Z][a-zA-Z0-9_]*)=(.*)$ ]] ; then
             eval "local ${BASH_REMATCH[1]}"
             eval "${BASH_REMATCH[1]}="'"${BASH_REMATCH[2]}"'
         else
-            echo "ERROR: Ignoring invalid argument $__text\n" 1>&2
+            echo "ERROR: Ignoring invalid argument $__text" 1>&2
         fi
     done
-    while IFS= read -r __text ; do
+
+    # Loop over all lines of text.
+    while [[ 1 == 1 ]] ; do
+        # Read the next line of text. This will "fail" if no more text
+        # is left OR if the last line lacks an end-of-line character.
+        read -d '' -r __text
+
+        # Stop when "read" reports it is done ($? -ne 0) AND the text is
+        # non-empty (! -n "$__text"). This ensures we read the final line
+        # even if it lacks an end-of-line character.
+        if [[ $? -ne 0 ]] ; then
+            if [[ -n "$__text" ]] ; then
+                # Text remained, but it had no end-of-line.
+                :
+            else
+                break
+            fi
+        fi
+        # Search for strings like @[varname] or @['string'] or @[@]
         while [[ "$__text" =~ ^([^@]*)(@\[[a-zA-Z_][a-zA-Z_0-9]*\]|@\[\'[^\']*\'\]|@\[@\]|@)(.*) ]] ; do
             __before="${BASH_REMATCH[1]}"
             __during="${BASH_REMATCH[2]}"
             __after="${BASH_REMATCH[3]}"
-#            printf 'PARSE[%s|%s|%s]\n' "$__before" "$__during" "$__after"
             printf %s "$__before"
+            # @['string'] inserts string
             if [[ "$__during" =~ ^@\[\'(.*)\'\]$ ]] ; then
                 printf %s "${BASH_REMATCH[1]}"
+            # @[@] inserts @
             elif [[ "$__during" == '@[@]' ]] ; then
                 printf @
+            # @[varname] inserts $varname
             elif [[ "$__during" =~ ^@\[([a-zA-Z_][a-zA-Z_0-9]*)\] ]] ; then
+                # Flag unknown variables at this step only.
+                if [[ ${__abort_on_undefined} == YES ]] ; then
+                    set -u
+                fi
                 eval 'printf %s "$'"${BASH_REMATCH[1]}"'"'
+                if [[ ${__abort_on_undefined} == YES ]] ; then
+                    set +u
+                fi
+            # Unrecognized sequences are inserted verbatim.
             else
                 printf '%s' "$__during"
             fi
+            # Continue until we run out of text in this line.
             if [[ "$__after" == "$__text" ]] ; then
                 break
             fi
             __text="$__after"
         done
+        # Print the corrected text
         printf '%s\n' "$__text"
     done
+
+    # Restore the calling script's shell options.
     eval "$__set_x"
+    eval "$__set_u"
+    eval "$__set_e"
 }
 
 function test_atparse {
@@ -45,14 +109,18 @@ function test_atparse {
     testvar='[testvar]'
     var1='[var1]'
     var2='[var2]'
-    cat<<\EOF | atparse var3='**'
+    var4='[var4]'
+    ( cat<<\EOF ; echo -n "line with no end-of-line character [var4] = @[var4]" ) | atparse var3='**'
 Nothing special here. = @['Nothing special here.']
 [testvar] = @[testvar]
 [var1] [var2] = @[var1] @[var2]
 ** = @[var3]
+[var4] == @[var4]
 @ = @[@] = @['@']
+@[undefined_variable_that_should_exit_script_if_set_minus_u_is_used]
 -n
  eval "export PE$c=\${PE$c:-0}" = @[' eval "export PE$c=\${PE$c:-0}"']
 EOF
+    echo " ... this text should be on the same line as the line with no end-of-line character"
     echo "After block, \$var3 = \"$var3\" should be empty"
 }