Merge branch 'main' into refactor-wet-model

Author: Pierre-siddall

.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

CONTRIBUTORS.md

@@ -5,4 +5,7 @@
 | 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 |
+

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

@@ -254,6 +254,10 @@ 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,
@@ -280,6 +284,10 @@ 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,
@@ -301,6 +309,10 @@ 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