Main to Stable 2026.7.1

.gitattributes

@@ -0,0 +1,11 @@
+# Handle line endings automatically for files detected as text
+# and leave all files detected as binary untouched.
+*     text=auto
+
+# Binaries
+*.nc    binary
+*.png   binary
+
+# Fortran namelist file identification
+*.nl text diff=fortran-free-form
+*.nl linguist-language=fortran-free-form

.github/pull_request_template.md

@@ -25,17 +25,24 @@ Code Reviewer: <!-- CR id, filled by SSD -->
 
 - [ ] I have performed a self-review of my own code
 - [ ] My code follows the project's style guidelines
-- [ ] Comments have been included that aid undertanding and enhance the
+- [ ] Comments have been included that aid understanding and enhance the
       readability of the code
 - [ ] My changes generate no new warnings
 
 ## Testing
 
-- [ ] I have tested this change locally, using the Moci rose-stem suite
+- [ ] I have tested this change locally, using the Moci rose-stem suite.  Required for any changes to
+  * Coupled_Drivers application
+  * Postprocessing application
+  * Unittests
 - [ ] If any tests fail (rose-stem or CI) the reason is understood and
       acceptable (eg. kgo changes)
 - [ ] I have added tests to cover new functionality as appropriate (eg. system
       tests, unit tests, etc.)
+
+  ### trac.log
+
+<!-- Paste your trac.log from testing output here -->
 
 <!-- Describe other testing performed (if applicable) -->
 

CONTRIBUTORS.md

@@ -5,4 +5,9 @@
 | james-bruten-mo | James Bruten    | Met Office  | 2025-12-09 |
 | Pierre-siddall  | Pierre Siddall  | Met Office  | 2025-01-19 |
 | ericaneininger  | Erica Neininger | Met Office  | 2026-02-04 |
-| dcalve          | Daley Calvert   | Met Office  | 2026-02-04 |
+| dcalve          | Daley Calvert   | Met Office  | 2026-02-04 |
+| harry-shepherd  | Harry Shepherd  | Met Office  | 2026-02-27 |
+| marcstring      | Marc Stringer   | NCAS        | 2026-04-01 |
+| jonseddon       | Jon Seddon      | Met Office  | 2026-05-11 |
+| jonnyhtw        | Jonny Williams  | NCAS        | 2026-05-13 |
+

Coupled_Drivers/cice_driver.py

@@ -26,7 +26,6 @@
 import re
 import datetime
 import time
-import subprocess
 import time2days
 import inc_days
 import common

Coupled_Drivers/common.py

@@ -234,6 +234,10 @@ def exec_subproc_timeout(cmd, timeout_sec=10):
     the commands to be run, and an integer timeout_sec for how long to
     wait for the command to run. Returns the return code from the process
     and the standard out from the command or 'None' if the command times out.
+
+    This function is now DEPRECATED in favour of the exec_shellout function in
+    mocilib
+
     '''
     process = subprocess.Popen(cmd, shell=False,
                                stdin=subprocess.PIPE,
@@ -260,6 +264,10 @@ def exec_subproc(cmd, verbose=True):
     Execute given shell command. Takes a list containing the commands to be
     run, and a logical verbose which if set to true will write the output of
     the command to stdout.
+
+    This function is now DEPRECATED in favour of the exec_shellout function in
+    mocilib
+
     '''
     process = subprocess.Popen(cmd, shell=False,
                                stdin=subprocess.PIPE,
@@ -281,6 +289,10 @@ def __exec_subproc_true_shell(cmd, verbose=True):
     exec_subproc does not work correctly. Takes a list containing the commands
     to be run, and a logical verbose which if set to true will write the
     output of the command to stdout.
+
+    This function is now DEPRECATED in favour of the exec_shellout function in
+    mocilib
+
     '''
     process = subprocess.Popen(cmd, shell=True,
                                stdin=subprocess.PIPE,

Coupled_Drivers/mct_driver.py

@@ -28,6 +28,7 @@
 import dr_env_lib.mct_def
 import dr_env_lib.env_lib
 import cpmip_controller
+
 try:
     import f90nml
 except ImportError:

Coupled_Drivers/rivers_driver.py

@@ -26,6 +26,7 @@
 import error
 import dr_env_lib.rivers_def
 import dr_env_lib.env_lib
+
 try:
     import f90nml
 except ImportError:

Documentation/mocilib/mocilib.md

@@ -0,0 +1,21 @@
+# MOCIlib
+
+MOCIlib is intended as a library to hold an assorted range on utility functions that can be used throughout new development and maintainance of MOCI along with their associated unit tests to ensure robust and unified approach to MOCI's functionality.
+
+## shellout
+
+The shelllout module contains the relevant functions to execute and handle shell commands in a safe manner.
+
+exec_subprocess is a function to execute a shell subprocess and takes the several parameters as follows:
+
+```python
+def exec_subprocess(cmd, verbose=False, timeout=None, current_working_directory=os.getcwd())
+```
+
+cmd - the command to be executed by exec_subprocess given as a string.
+
+verbose - a boolean (True or False) to determine if the standard output (stdout) stream is output during the execution of the shell command.
+
+timeout - an integer number determining the number of seconds a shell command can run for before a TimeoutExpired error is raised.
+
+current_working_directory - The working directory which the shell command will be executed in given as a string.

Infrastructure_Builds/infrastructure_suite/bin/create_oasis_module.sh

@@ -31,7 +31,7 @@ if [ -z "$SUITE_REVISION" ]; then
     SUITE_REVISION='Revision: undefined'
     revision='undefined'
 else
-    revision=$(echo $SUITE_REVISION | grep -oP '\d+')
+    revision=$SUITE_REVISION
 fi
 
 oasis_mod_version_path=$OASIS_MOD_NAME/$OASIS_MOD_VERSION/$revision

Infrastructure_Builds/infrastructure_suite/bin/create_prgenv_module.sh

@@ -28,7 +28,7 @@ if [ -z "$SUITE_REVISION" ]; then
     SUITE_REVISION='Revision: undefined'
     revision='undefined'
 else
-    revision=$(echo $SUITE_REVISION | grep -oP '\d+')
+    revision=$SUITE_REVISION
 fi
 
 module_file_path=$MODULE_BASE/modules/$PRG_ENV_NAME/$PRG_ENV_VERSION
@@ -73,17 +73,6 @@ set version $PRG_ENV_VERSION
 
 EOF
 
-for mod in $MODULE_STR; do
-    if [[ $mod == *'PrgEnv'* ]]; then
-	line="module swap PrgEnv-cray $mod"
-    else
-	line="module load $mod"
-    fi
-    cat <<EOF >>$module_file
-$line
-EOF
-done
-
 # now do the oasis and xios modules
 if [ "XIOS_ONLY" = "True" ]; then
     line="module load $XIOS_MODULE_PATH";

Infrastructure_Builds/infrastructure_suite/bin/create_xios_module.sh

@@ -31,7 +31,7 @@ if [ -z "$SUITE_REVISION" ]; then
     SUITE_REVISION='Revision: undefined'
     revision='undefined'
 else
-    revision=$(echo $SUITE_REVISION | grep -oP '\d+')
+    revision=$SUITE_REVISION
 fi
 
 xios_mod_version_path=$XIOS_MOD_NAME/$XIOS_MOD_VERSION/$revision

Infrastructure_Builds/infrastructure_suite/bin/extract_oasis.sh

@@ -7,7 +7,7 @@
 #
 # ENVIRONMENT VARIABLES (COMPULSORY):
 #    EXTRACT_OASIS
-#    HPC_HOST_OASIS
+#    HPC_HOST
 #    OASIS_BRANCH
 #    OASIS_REPOSITORY
 #
@@ -27,7 +27,7 @@ if [ "$EXTRACT_OASIS" = "True" ]; then
 	exit 999
     fi
 
-    if [ -z "$HPC_HOST_OASIS" ]; then
+    if [ -z "$HPC_HOST" ]; then
 	hpc_build="False"
     else
 	hpc_build="True"
@@ -55,31 +55,31 @@ if [ "$hpc_build" = "True" ] && [ -z "$CYLC_SUITE_RUN_DIR" ]; then
     # manually
     # upload to the HPC
     ssh $user@$HPC_HOST "mkdir -p $OASIS_BUILD_DIR/";
-    scp -r $oasis_extract_dir $user@$HPC_HOST_OASIS:$OASIS_BUILD_DIR/;
+    scp -r $oasis_extract_dir $user@$HPC_HOST:$OASIS_BUILD_DIR/;
     # cleanup, only if we have extracted the code from GIT
     if [ "$EXTRACT_OASIS" = "True" ]; then
 	rm -rf $oasis_extract_dir
     fi
     # upload build scripts to hpc
-    scp bin/oasis_build.sh $user@$HPC_HOST_OASIS:$OASIS_BUILD_DIR/
+    scp bin/oasis_build.sh $user@$HPC_HOST:$OASIS_BUILD_DIR/
     # pass
     if [ "$BUILD_TEST" = "True" ]; then
 	# upload our test executables to the HPC
-	scp src/*.F90 $user@$HPC_HOST_OASIS:$OASIS_BUILD_DIR/oasis3-mct/examples/tutorial/
+	scp src/*.F90 $user@$HPC_HOST:$OASIS_BUILD_DIR/oasis3-mct/examples/tutorial/
 	# upload the run script
-	scp bin/run_tutorial_mo_xc40.sh $user@$HPC_HOST_OASIS:$OASIS_BUILD_DIR/oasis3-mct/examples/tutorial/
+	scp bin/run_tutorial_mo_xc40.sh $user@$HPC_HOST:$OASIS_BUILD_DIR/oasis3-mct/examples/tutorial/
 	# upload the other files to make the test run
 	for i_file in namcouple_TP script_ferret_FRECVOCN.jnl script_ferret_FSENDOCN_to_File.jnl
 	do
-	    scp file/$i_file $user@$HPC_HOST_OASIS:$OASIS_BUILD_DIR/oasis3-mct/examples/tutorial/data_oasis3
+	    scp file/$i_file $user@$HPC_HOST:$OASIS_BUILD_DIR/oasis3-mct/examples/tutorial/data_oasis3
 	done
     fi
 else
     # we are running in a suite context and only need to upload the oasis
     # source code
-    scp -r $oasis_extract_dir $user@$HPC_HOST_OASIS:$OASIS_BUILD_DIR/;
+    scp -r $oasis_extract_dir $user@$HPC_HOST:$OASIS_BUILD_DIR/;
     if [ $? -ne 0 ]; then
-	1>&2 echo "Unable to succesfully upload oasis source to $HPC_HOST_OASIS"
+	1>&2 echo "Unable to succesfully upload oasis source to $HPC_HOST"
 	exit 999;
     fi
     # cleanup, only if we have extracted the code from GIT
@@ -89,5 +89,5 @@ else
 fi
 
 #End of script test, check that the code is avaliable
-ssh $user@$HPC_HOST_OASIS ls $OASIS_BUILD_DIR/oasis3-mct
+ssh $user@$HPC_HOST ls $OASIS_BUILD_DIR/oasis3-mct
 [ $? -eq 0 ] || exit 1

Infrastructure_Builds/infrastructure_suite/bin/extract_xios.sh

@@ -19,6 +19,10 @@ fcm co $XIOS_URL/$XIOS_VERSION@$XIOS_REV
 XIOS_VERSION_BASE="$(basename $XIOS_VERSION)"
 mv $XIOS_VERSION_BASE $XIOSPATH
 
+if [[ "$XIOS_REV" == "1873" ]]; then
+   sed -i 's/#include <mpi.h>/#include <stdint.h>\n#include <mpi.h>/g' $XIOSPATH/src/mpi.hpp
+fi
+
 #End of script test
 ls $XIOSPATH
 [ $? -eq 0 ] || exit 1

Infrastructure_Builds/infrastructure_suite/suite.rc → Infrastructure_Builds/infrastructure_suite/flow.cylc

@@ -1,54 +1,40 @@
 #!jinja2
 
-{% set HPC_HOST_OASIS = DEPLOYMENT_HOST if DEPLOYMENT_HOST is defined else HPC_HOST_OASIS %}
+{% set HPC_HOST = DEPLOYMENT_HOST if DEPLOYMENT_HOST is defined else HPC_HOST %}
 
-MODULE_STR = {{ MODULES|join(' ') }}
-{% set MODULE_STR =  MODULES|join(' ')  %}
-{% set MODULE_CMD = 'for mod in '+MODULE_STR+'; do module load $mod; module swap $mod; done; module list' %}
 
-
-[cylc]
+[scheduler]
     UTC mode = True
+    install = src/, file/
     [[events]]
-        timeout handler = "rose suite-hook --shutdown"
-	timeout = PT6H
+        stall timeout handlers = "rose suite-hook --shutdown"
 
-[scheduling]
-    [[dependencies]]
-	graph = """
-                prepare_hpc_host => extract_xios_background => build_xios => create_xios_module => create_prgenv_module => run_xios_toy_attached & run_xios_toy_server
+[scheduling] 
+    [[graph]]
+	 R1 = """
+         prepare_hpc_host => extract_xios_background => build_xios => create_xios_module => create_prgenv_module => run_xios_toy_attached & run_xios_toy_server
 {% if not XIOS_ONLY %}
                 prepare_hpc_host => extract_oasis => build_oasis => run_oasis_tutorial => create_oasis_module => build_xios
 {% endif %}
                 """
-
 [runtime]
     [[root]]
         script = 'rose task-run --verbose'
     [[LINUX_SERVER]]
-        [[[job]]]
-            batch system = slurm
-            execution time limit = PT15M
+        execution time limit = PT15M
+	platform = slurm
         [[[directives]]]
             --ntasks=1
             --mem=1G
             --qos=normal
-            --partition=rhel7
     [[LOCALHOST]]
-        [[[remote]]]
-            host={{ROSE_ORIG_HOST}}
-        [[[job]]]
-            batch system = background
+        platform=localhost
     [[HPC]]
 	env-script = "{{MODULE_CMD}}"
-        [[[job]]]
-            batch system = pbs
-        [[[remote]]]
-            host = $(rose host-select {{ HPC_HOST_OASIS }})
+	platform = {{HPC_HOST}}
     [[HPC_SERIAL]]
         inherit = None, HPC
-        [[[job]]]
-            execution time limit = PT10M
+	execution time limit = PT10M
         [[[environment]]]
             ROSE_TASK_N_JOBS = 1
         [[[directives]]]
@@ -72,7 +58,7 @@ MODULE_STR = {{ MODULES|join(' ') }}
             --mem=8G
         [[[environment]]]
             HPC_HOST_USERNAME={{HPC_HOST_USERNAME}}
-            HPC_HOST_OASIS={{HPC_HOST_OASIS}}
+            HPC_HOST={{HPC_HOST}}
 	    EXTRACT_OASIS={{EXTRACT_OASIS}}
 {% if EXTRACT_OASIS == true %}
 	    OASIS_BRANCH={{OASIS_BRANCH}}
@@ -82,8 +68,7 @@ MODULE_STR = {{ MODULES|join(' ') }}
 {% endif %}
     [[build_oasis]]
         inherit = None, HPC_SERIAL, OASIS
-        [[[job]]]
-            execution time limit = PT20M
+	execution time limit = PT20M
         [[[environment]]]
 	    BUILD_MCT={{BUILD_MCT}}
 	    BUILD_TEST={{BUILD_TEST}}
@@ -130,18 +115,15 @@ MODULE_STR = {{ MODULES|join(' ') }}
         [[[environment]]]
             XIOSPATH=$CYLC_SUITE_RUN_DIR/share/xios
     [[extract_xios_background]]
-        inherit = XIOS
-        [[[remote]]]
-            host = login.exz
-        [[[job]]]
-            execution time limit = PT10M
+        inherit = XIOS, HPC_SERIAL
         [[[environment]]]
             ROSE_TASK_APP=extract_xios
             XIOS_VERSION={{XIOS_VERSION}}
 	    XIOS_REV={{XIOS_REV}}
 	    XIOS_URL={{XIOS_URL}}
     [[build_xios]]
         inherit = None, HPC, XIOS
+	execution time limit = PT2H
 	env-script = """
 		     {{MODULE_CMD}};
 {% if not XIOS_ONLY %}
@@ -153,8 +135,6 @@ MODULE_STR = {{ MODULES|join(' ') }}
 		     """
         [[[environment]]]
             XIOS_ONLY={{XIOS_ONLY}}
-        [[[job]]]
-            execution time limit = PT2H
 	[[[directives]]]
 	    -l select=1:ncpus=8
     [[create_xios_module]]
@@ -176,6 +156,7 @@ MODULE_STR = {{ MODULES|join(' ') }}
 {% endif %}
     [[RUN_XIOS_TOY]]
         env-script = """
+                     {{MODULE_CMD}};
                      eval $(cat $CYLC_SUITE_RUN_DIR/share/load_prgenv_mod.sh);
                      module use $TEST_PRGENV_MODULE_PATH
                      module load $TEST_PRGENV_MODULE_NAME
@@ -206,7 +187,7 @@ MODULE_STR = {{ MODULES|join(' ') }}
 		     """
         [[[environment]]]
             XIOS_ONLY={{XIOS_ONLY}}
-	    MODULE_STR={{MODULE_STR}}
+	    MODULE_STR={{MODULE_CMD}}
 {% if not XIOS_ONLY %}
 	    PRG_ENV_VERSION={{GC_PRG_ENV_VERSION}}
 	    PRG_ENV_NAME={{GC_PRG_ENV_NAME}}