Add topo gen workflow

.gitmodules

@@ -1,9 +1,6 @@
-[submodule "domain-tools"]
-	path = domain-tools
-	url = https://github.com/COSIMA/domain-tools.git
-[submodule "topogtools"]
-	path = topogtools
-	url = https://github.com/COSIMA/topogtools.git
 [submodule "om3-scripts"]
 	path = om3-scripts
 	url = https://github.com/COSIMA/om3-scripts.git
+[submodule "bathymetry-tools"]
+	path = bathymetry-tools
+	url = https://github.com/COSIMA/bathymetry-tools.git

LICENSE

@@ -0,0 +1,201 @@
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README.md

@@ -1 +1,24 @@
-# make_OM3_025deg_topo
+# make_OM3_025deg_topo
+
+Make 0.25-degree `topog.nc` MOM bathymetry file from the GEBCO 2024 dataset.
+
+## Workflow Overview
+
+1. **Generate Topography:**  
+   Use `./gen_topog.sh` to generate the topography and associated files. For 0.25-degree resolution or higher, this will require submission via `qsub`.
+
+   First, add gdata for your project & working directory to the `#PBS -l storage=` line in `get_topo.sh`
+
+   Then, use the `qsub` command to submit the script, passing the required input files as arguments. For example:  
+   ```bash
+   qsub -v INPUT_HGRID="/path/to/ocean_hgrid.nc",INPUT_VGRID="/path/to/ocean_vgrid.nc",INPUT_GBCO="/path/to/GEBCO_2024.nc" -P $PROJECT gen_topo.sh
+   ```
+
+2. **Finalize Output Files:**  
+   Once the output files meet your satisfaction, commit and push the changes, then add the git commit hash as metadata in the output `.nc` files by running `finalise.sh`.
+
+## Note on Dependencies  
+
+This workflow relies on the **hh5 conda environments** for running the scripts and generating the outputs. As long as you are a member of the _hh5_ project, this conda environment is loaded as part of the scripts.
+
+--- 

build.sh

@@ -0,0 +1,24 @@
+# Copyright 2024 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0
+# 
+# Build bathymetry-tools executables
+
+module purge
+module load intel-compiler 
+module load netcdf
+
+cd ./bathymetry-tools/
+
+
+# Check if the build directory exists before cleaning
+if [ -d "build" ]; then
+  cmake --build build --target clean
+fi
+
+cmake -B build -DCMAKE_BUILD_TYPE=Release -DNetCDF_Fortran_LIBRARY=$NETCDF_ROOT/lib/Intel/libnetcdff.so -DNetCDF_C_LIBRARY=$NETCDF_ROOT/lib/libnetcdf.so -DNetCDF_Fortran_INCLUDE_DIRS=$NETCDF_ROOT/include/Intel  
+
+cmake --build build
+
+cmake --install build --prefix=./
+
+cd ../

edit_025deg_topog_new_fillfraction.txt

@@ -0,0 +1,11 @@
+editTopo.py edits file version 1
+#
+# This file can be used as an argument for editTopo.py --apply
+#
+# created: Fri Nov  1 12:56:59 2024
+# by: ek4684
+# via: editTopo.py /g/data/tm70/ek4684/domain-tools/C-grid-workflow/fill_fraction_0.5/topog_new_fillfraction.nc --overwrite
+#
+#    i    j  old  new
+  1235  737  0.0  65.28469848632812
+  1227  734  0.0  56.118499755859375

finalise.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env sh
+# Copyright 2024 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
+# SPDX-License-Identifier: Apache-2.0
+#
+# Commit changes and push, then add metadata to note how changes were made 
+
+module load nco
+module load git
+
+echo "About to commit all changes to git repository and push to remote."
+read -p "Proceed? (y/n) " yesno
+case $yesno in
+   [Yy] ) ;;
+      * ) echo "Cancelled."; exit 0;;
+esac
+
+set -x
+set -e
+
+git commit -am "Files used for topo/mask generation on $(date)" || true
+git push || true
+
+ncatted -O -h -a history,global,a,c," | Created on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" topog.nc
+ncatted -O -h -a history,global,a,c," | Updated on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" ocean_mask.nc
+ncatted -O -h -a history,global,a,c," | Created on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" kmt.nc
+ncatted -O -h -a history,global,a,c," | Updated on $(date) using https://github.com/ACCESS-NRI/make_OM3_025deg_topo/tree/$(git rev-parse --short HEAD)" ocean_vgrid.nc
+
+ncatted -O -h -a history,global,a,c," and based on GEBCO_2024 topography" topog.nc
+