From 287eb8bc14a5ef3c0d21987bc8c3c829732ef438 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Wed, 6 May 2026 11:03:06 +0100
Subject: [PATCH 01/11] #96 first pass vertical regridder

---
 lib/ants/cli/ancil_vertical_regrid.py | 155 ++++++++++++++++++++++++++
 pyproject.toml                        |   1 +
 2 files changed, 156 insertions(+)
 create mode 100644 lib/ants/cli/ancil_vertical_regrid.py

diff --git a/lib/ants/cli/ancil_vertical_regrid.py b/lib/ants/cli/ancil_vertical_regrid.py
new file mode 100644
index 0000000..acd126c
--- /dev/null
+++ b/lib/ants/cli/ancil_vertical_regrid.py
@@ -0,0 +1,155 @@
+#!/usr/bin/env python
+# (C) Crown Copyright, Met Office. All rights reserved.
+#
+# This file is part of ANTS and is released under the BSD 3-Clause license.
+# See LICENSE.txt in the root of the repository for full licensing details.
+"""
+A vertical regrid application
+*****************************
+
+Regrids data from a source to a target grid using
+:class:`ants.regrid.GeneralRegridScheme`.  The result is written to an output
+file.  The application supports only vertical regridding.  The
+regrid algorithm can be specified in the ants configuration file as described
+in :class:`ants.config.GlobalConfiguration`. See :mod:`ants.regrid` for further
+details.
+"""
+import ants
+import ants.decomposition as decomp
+import ants.io.save as save
+import ants.utils
+import iris.cube
+from ants.utils.cube import create_time_constrained_cubes
+import numpy as np
+
+
+def load_data(
+    source,
+    target_grid,
+    begin=None,
+    end=None,
+):
+    source_cubes = ants.io.load.load(source)
+    if begin is not None:
+        source_cubes = create_time_constrained_cubes(source_cubes, begin, end)
+
+    vertical_grid = ants.io.load.load_grid(target_grid)
+
+    return source_cubes, vertical_grid
+
+
+def create_target(source_grid, vertical_grid):
+    source = ants.utils.cube.as_cubelist(source_grid)[0]
+    data = np.ones((source.shape[0], source.shape[1], vertical_grid.shape[0]))
+    target_grid = iris.cube.Cube(data)
+    target_grid.add_dim_coord(source.coord("latitude"), 0)
+    target_grid.add_dim_coord(source.coord("longitude"), 1)
+    target_grid.add_dim_coord(vertical_grid.coord("model_level_number"), 2)
+    return target_grid
+
+
+def regrid(sources, target):
+    sources = ants.utils.cube.as_cubelist(sources)
+    results = []
+    scheme = ants.regrid.GeneralRegridScheme(vertical_scheme="Linear")
+    for source in sources:
+        results.append(source.regrid(target, scheme))
+    return results
+
+
+def main(
+    source_path,
+    output_path,
+    target_path,
+    begin,
+    end,
+    save_ukca,
+    netcdf_only,
+):
+    """
+    General regrid application top level call function.
+
+    Loads source data cubes, regrids them to match target data cube
+    co-ordinates, and saves result to output.  In addition to writing the
+    resulting data cube to disk, also returns the regridded data cube.
+
+    Parameters
+    ----------
+
+    source_path : str
+        File path for one or more files which contain the data to be
+        regridded.
+    target_path : str
+        File path for files that provide the grid to which the source data
+        cubes will be mapped.  e.g. a namelist for vertical levels.
+    output_path : str
+        Output file path to write the regridded data to.
+    begin : :obj:`datetime`, optional
+        If provided, all source data prior to this year is discarded.  Default is to
+        include all source data.
+    end : :obj:`datetime`, optional
+        If provided, all source data after this year is discarded.  Default is to
+        include all source data.
+
+
+    Returns
+    -------
+    : :class:`~iris.cube.Cube`
+    A single data cube with the regridded data.
+
+    """
+    source_cubes, vertical_grid = load_data(
+        source_path,
+        target_path,
+        begin,
+        end,
+    )
+    if ants.utils.cube._is_ugrid(vertical_grid):
+        raise ValueError(
+            "Target appears to be a UGrid mesh - the regrid to mesh application in "
+            "UG-ANTS should be used instead."
+        )
+
+    target_cube = create_target(source_cubes, vertical_grid)
+    regridded_cubes = decomp.decompose(regrid, source_cubes, target_cube)
+
+    if save_ukca:
+        save.ukca_netcdf(regridded_cubes, output_path)
+    else:
+        if not netcdf_only:
+            save.ancil(regridded_cubes, output_path)
+        save.netcdf(regridded_cubes, output_path)
+
+    print(regridded_cubes)
+    return regridded_cubes
+
+
+def _get_parser():
+    parser = ants.AntsArgParser(target_grid=True, time_constraints=True)
+    parser.add_argument(
+        "--save-ukca",
+        action="store_true",
+        help="Save to a UKCA-specific netCDF file",
+        required=False,
+    )
+    return parser
+
+
+def cli_interface():
+    parser = _get_parser()
+    args = parser.parse_args()
+
+    source = args.sources
+    main(
+        source,
+        args.output,
+        args.target_grid,
+        args.begin,
+        args.end,
+        args.save_ukca,
+        args.netcdf_only,
+    )
+
+
+if __name__ == "__main__":
+    cli_interface()
diff --git a/pyproject.toml b/pyproject.toml
index a0d1632..33b059a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -88,3 +88,4 @@ classifiers = [
 "ancil_create_shapefile.py" = "ants.cli.ancil_create_shapefile:cli_interface"
 "ancil_fill_n_merge.py" = "ants.cli.ancil_fill_n_merge:cli_interface"
 "ancil_general_regrid.py" = "ants.cli.ancil_general_regrid:cli_interface"
+"ancil_vertical_regrid.py" = "ants.cli.ancil_vertical_regrid:cli_interface"

From 250bbfc7c3a40794a15de9c337daf9cdf6bc2f2a Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Tue, 9 Jun 2026 16:07:51 +0100
Subject: [PATCH 02/11] #96 second pass vertical regridder

---
 lib/ants/cli/ancil_vertical_regrid.py | 28 +++++++--------------------
 1 file changed, 7 insertions(+), 21 deletions(-)

diff --git a/lib/ants/cli/ancil_vertical_regrid.py b/lib/ants/cli/ancil_vertical_regrid.py
index acd126c..75cbccf 100644
--- a/lib/ants/cli/ancil_vertical_regrid.py
+++ b/lib/ants/cli/ancil_vertical_regrid.py
@@ -15,13 +15,10 @@
 details.
 """
 import ants
-import ants.decomposition as decomp
 import ants.io.save as save
 import ants.utils
-import iris.cube
 from ants.utils.cube import create_time_constrained_cubes
-import numpy as np
-
+from ants.fileformats._grid_extract import extract_grid
 
 def load_data(
     source,
@@ -33,25 +30,15 @@ def load_data(
     if begin is not None:
         source_cubes = create_time_constrained_cubes(source_cubes, begin, end)
 
-    vertical_grid = ants.io.load.load_grid(target_grid)
-
-    return source_cubes, vertical_grid
-
+    target_cube = ants.io.load.load_grid(target_grid)
 
-def create_target(source_grid, vertical_grid):
-    source = ants.utils.cube.as_cubelist(source_grid)[0]
-    data = np.ones((source.shape[0], source.shape[1], vertical_grid.shape[0]))
-    target_grid = iris.cube.Cube(data)
-    target_grid.add_dim_coord(source.coord("latitude"), 0)
-    target_grid.add_dim_coord(source.coord("longitude"), 1)
-    target_grid.add_dim_coord(vertical_grid.coord("model_level_number"), 2)
-    return target_grid
+    return source_cubes, target_cube
 
 
 def regrid(sources, target):
     sources = ants.utils.cube.as_cubelist(sources)
     results = []
-    scheme = ants.regrid.GeneralRegridScheme(vertical_scheme="Linear")
+    scheme = ants.regrid.GeneralRegridScheme(vertical_scheme='Linear')
     for source in sources:
         results.append(source.regrid(target, scheme))
     return results
@@ -98,20 +85,19 @@ def main(
     A single data cube with the regridded data.
 
     """
-    source_cubes, vertical_grid = load_data(
+    source_cubes, target_cube = load_data(
         source_path,
         target_path,
         begin,
         end,
     )
-    if ants.utils.cube._is_ugrid(vertical_grid):
+    if ants.utils.cube._is_ugrid(target_cube):
         raise ValueError(
             "Target appears to be a UGrid mesh - the regrid to mesh application in "
             "UG-ANTS should be used instead."
         )
 
-    target_cube = create_target(source_cubes, vertical_grid)
-    regridded_cubes = decomp.decompose(regrid, source_cubes, target_cube)
+    regridded_cubes = regrid(source_cubes, target_cube)
 
     if save_ukca:
         save.ukca_netcdf(regridded_cubes, output_path)

From 463430581f47469f5d79fe0b9ea90d4c3e1bba6b Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Tue, 9 Jun 2026 16:22:11 +0100
Subject: [PATCH 03/11] #96 expand possibly axis to altitude

---
 lib/ants/regrid/interpolation.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/lib/ants/regrid/interpolation.py b/lib/ants/regrid/interpolation.py
index 7746486..7f59500 100644
--- a/lib/ants/regrid/interpolation.py
+++ b/lib/ants/regrid/interpolation.py
@@ -178,7 +178,11 @@ def scalar_coord(cube, coord_name):
 
 
 def _guess_axis_interpolation(cube):
-    dims = cube.coord_dims("model_level_number")
+    try:
+        dims = cube.coord_dims("model_level_number")
+    except iris.exceptions.CoordinateNotFoundError:
+        dims = cube.coord_dims("altitude")
+
     if len(dims) != 1:
         raise ValueError(
             "Expecting only a single axis of interpolation, " "got {}".format(len(dims))

From 37717a18444c524ab6e6fee02473810e6126e977 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Tue, 23 Jun 2026 15:45:14 +0100
Subject: [PATCH 04/11] #96 add rose-stem tests

---
 lib/ants/cli/ancil_vertical_regrid.py         |  0
 .../opt/rose-app-ozone_zonal_mean.conf        |  5 ++++
 .../app/ancil_vertical_regrid/rose-app.conf   | 17 ++++++++++++++
 .../opt/rose-app-vertical_regrid.conf         |  3 +++
 rose-stem/flow.cylc                           | 23 +++++++++++++++++++
 5 files changed, 48 insertions(+)
 mode change 100644 => 100755 lib/ants/cli/ancil_vertical_regrid.py
 create mode 100644 rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf
 create mode 100644 rose-stem/app/ancil_vertical_regrid/rose-app.conf
 create mode 100644 rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf

diff --git a/lib/ants/cli/ancil_vertical_regrid.py b/lib/ants/cli/ancil_vertical_regrid.py
old mode 100644
new mode 100755
diff --git a/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf
new file mode 100644
index 0000000..b00a8f0
--- /dev/null
+++ b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf
@@ -0,0 +1,5 @@
+[env]
+output=/data/users/jennifer.hickson/ants_vertical_cli/ozone/$(ROSE_TASK_NAME)
+source=/data/users/jennifer.hickson/ants_vertical_cli/ozone/Ozone_CMIP5_SPARCex_M1994-2005_N36L85_li-ch_G.nc
+target=/data/users/jennifer.hickson/ants_vertical_cli/vertlevs_L70_50t_20s_80km
+target_type=grid
diff --git a/rose-stem/app/ancil_vertical_regrid/rose-app.conf b/rose-stem/app/ancil_vertical_regrid/rose-app.conf
new file mode 100644
index 0000000..1e7c219
--- /dev/null
+++ b/rose-stem/app/ancil_vertical_regrid/rose-app.conf
@@ -0,0 +1,17 @@
+[ants_logging]
+enabled=True
+
+[ants_metadata]
+history=${CYLC_WORKFLOW_ID}@${ROSE_SUITE_REVISION}:${ROSE_TASK_NAME}
+
+[ants_regridding_vertical]
+scheme=Linear
+
+
+[command]
+default=ants-launch ancil_vertical_regrid.py \
+       =${source} -o ${output} --ants-config ${ANTS_CONFIG} --target-${target_type} ${target} \
+       =${begin} ${end}
+
+[env]
+ANTS_CONFIG=rose-app-run.conf
diff --git a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
new file mode 100644
index 0000000..5a01859
--- /dev/null
+++ b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
@@ -0,0 +1,3 @@
+[env]
+filelist=ancil_vertical_regrid_ozone_zonal_mean
+
diff --git a/rose-stem/flow.cylc b/rose-stem/flow.cylc
index 48941eb..fbfadab 100644
--- a/rose-stem/flow.cylc
+++ b/rose-stem/flow.cylc
@@ -5,6 +5,7 @@
 {% set fill_n_merge_source = ['land_cover', 'invert_mask'] %}
 {% set grid_source = ['grid_to_grid', 'grid_to_variable_resolution_grid', 'grid_to_n48e_namelist', 'grid_to_n48_namelist', '3d_to_3d', '3d_to_3d_with_extrapolation', 'invert_mask'] %}
 {% set target_lsm_grid_sources = ['grid_to_grid', 'invert_mask'] %}
+{% set vertical_regrid_source = ['ozone_zonal_mean'] %}
 
 
 # This links a name specified on the command in rose-stem with a
@@ -26,6 +27,7 @@
         install_cold => ancil_general_regrid_invert_mask_latitude_weighted_kdtree<split> => rose_ana_general_regrid_latitude_weighted_kdtree:fail? => plot_comparisons_general_regrid_latitude_weighted_kdtree",
     "general_regrid_time_constrained": "install_cold => ancil_general_regrid_with_time_constraint<fill,split> => rose_ana_general_regrid<fill>:fail? => plot_comparisons_general_regrid<fill>
         install_cold => ancil_general_regrid_with_time_constraint_latitude_weighted_kdtree<split> => rose_ana_general_regrid_latitude_weighted_kdtree:fail? => plot_comparisons_general_regrid_latitude_weighted_kdtree",
+    "vertical_regrid_ozone": "install_cold => ancil_vertical_regrid_ozone_zonal_mean => rose_ana_vertical_regrid:fail? => plot_comparisons_general_regrid",
     "build_documentation_graph": "install_cold => build_docs => linkcheck",
     "unittests_graph": "install_cold => unittests",
     "black_graph": "install_cold => black",
@@ -55,6 +57,7 @@
     "core" : ["ancil_2anc_graph", "fill_n_merge", "general_regrid"],
     "fill_n_merge": ["fill_n_merge_land_cover_graph", "fill_n_merge_invert_mask_graph"],
     "general_regrid": ["general_regrid_grid_to_grid_graph", "general_regrid_grid_to_variable_graph", "general_regrid_grid_to_n48e_namelist_graph", "general_regrid_grid_to_n48_namelist_graph", "general_regrid_3d_to_3d_graph", "general_regrid_3d_to_3d_with_extrapolation", "general_regrid_time_constrained", "general_regrid_invert_mask_graph"],
+    "vertical_regrid": ["vertical_regrid_ozone"],
     "documentation": ["build_documentation_graph"],
     "unittests": ["unittests_graph", "black_graph", "flake8_graph", "isort_graph"],
 }
@@ -272,6 +275,26 @@ fi
             ROSE_TASK_APP = rose_ana
             ROSE_APP_OPT_CONF_KEYS = general_regrid_latitude_weighted_kdtree
 
+
+    {% for source in vertical_regrid_source %}
+    [[ANCIL_VERTICAL_REGRID_{{ source }}]]
+        inherit=ANTS_CORE, LARGE
+
+    [[ancil_vertical_regrid_{{ source }}]]
+        inherit = ANCIL_VERTICAL_REGRID_{{ source }}
+        script = rose task-run --app-key=ancil_vertical_regrid -O {{ source }}
+
+    [[rose_ana_vertical_regrid]]
+        inherit = ROSE_ANA
+        [[[environment]]]
+            ROSE_TASK_APP = rose_ana
+            ROSE_APP_OPT_CONF_KEYS = vertical_regrid
+            ANTS_KGO_DIRECTORY_OVERRIDE = /data/users/jennifer.hickson/ants_vertical_cli/
+
+
+    {% endfor %}
+
+
     # ##################################
     # Build Documentation
     # ##################################

From 56b4e7e42afa513fa1119a0523a7c301718aa7d8 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Tue, 25 Aug 2026 15:19:16 +0100
Subject: [PATCH 05/11] KGO test setup - INCLUDES temporary filepaths

---
 .../ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf  | 4 ++--
 rose-stem/app/ancil_vertical_regrid/rose-app.conf             | 2 +-
 rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf      | 2 +-
 rose-stem/flow.cylc                                           | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf
index b00a8f0..e5b6a92 100644
--- a/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf
+++ b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-ozone_zonal_mean.conf
@@ -1,5 +1,5 @@
 [env]
-output=/data/users/jennifer.hickson/ants_vertical_cli/ozone/$(ROSE_TASK_NAME)
-source=/data/users/jennifer.hickson/ants_vertical_cli/ozone/Ozone_CMIP5_SPARCex_M1994-2005_N36L85_li-ch_G.nc
+output=${ROSE_DATA}/${ROSE_TASK_NAME}
+source=/data/users/jennifer.hickson/ants_vertical_cli/ancil_vertical_regrid_ozone_zonal_mean/Ozone_CMIP5_SPARCex_M1994-2005_N36L85_li-ch_G.nc
 target=/data/users/jennifer.hickson/ants_vertical_cli/vertlevs_L70_50t_20s_80km
 target_type=grid
diff --git a/rose-stem/app/ancil_vertical_regrid/rose-app.conf b/rose-stem/app/ancil_vertical_regrid/rose-app.conf
index 1e7c219..23ff639 100644
--- a/rose-stem/app/ancil_vertical_regrid/rose-app.conf
+++ b/rose-stem/app/ancil_vertical_regrid/rose-app.conf
@@ -11,7 +11,7 @@ scheme=Linear
 [command]
 default=ants-launch ancil_vertical_regrid.py \
        =${source} -o ${output} --ants-config ${ANTS_CONFIG} --target-${target_type} ${target} \
-       =${begin} ${end}
+       =${begin} ${end} --netcdf-only
 
 [env]
 ANTS_CONFIG=rose-app-run.conf
diff --git a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
index 5a01859..492f0d5 100644
--- a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
+++ b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
@@ -1,3 +1,3 @@
 [env]
-filelist=ancil_vertical_regrid_ozone_zonal_mean
+filelist=ancil_vertical_regrid_ozone_zonal_mean.nc
 
diff --git a/rose-stem/flow.cylc b/rose-stem/flow.cylc
index fbfadab..2d14bf9 100644
--- a/rose-stem/flow.cylc
+++ b/rose-stem/flow.cylc
@@ -289,7 +289,7 @@ fi
         [[[environment]]]
             ROSE_TASK_APP = rose_ana
             ROSE_APP_OPT_CONF_KEYS = vertical_regrid
-            ANTS_KGO_DIRECTORY_OVERRIDE = /data/users/jennifer.hickson/ants_vertical_cli/
+            ANTS_KGO_DIRECTORY_OVERRIDE = /data/users/jennifer.hickson/ants_vertical_cli/kgo
 
 
     {% endfor %}

From cc2008b36fc22f232e3d13214db30b3c618900b0 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Tue, 25 Aug 2026 16:10:18 +0100
Subject: [PATCH 06/11] #96 KGO test setup for aerosols - INCLUDES temporary
 filepaths

---
 .../app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf | 5 +++++
 rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf   | 1 +
 rose-stem/flow.cylc                                        | 7 ++++---
 3 files changed, 10 insertions(+), 3 deletions(-)
 create mode 100644 rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf

diff --git a/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf
new file mode 100644
index 0000000..1c2a5bf
--- /dev/null
+++ b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf
@@ -0,0 +1,5 @@
+[env]
+output=${ROSE_DATA}/${ROSE_TASK_NAME}
+source=/data/users/jennifer.hickson/ants_vertical_cli/ancil_vertical_regrid_aerosol_3d/qrclim.aerosols.nc
+target=/data/users/jennifer.hickson/ants_vertical_cli/vertlevs_L70_50t_20s_80km
+target_type=grid
diff --git a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
index 492f0d5..d825a5f 100644
--- a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
+++ b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
@@ -1,3 +1,4 @@
 [env]
 filelist=ancil_vertical_regrid_ozone_zonal_mean.nc
+         ancil_vertical_regrid_aerosol_3d.nc
 
diff --git a/rose-stem/flow.cylc b/rose-stem/flow.cylc
index 2d14bf9..b9545cd 100644
--- a/rose-stem/flow.cylc
+++ b/rose-stem/flow.cylc
@@ -5,7 +5,7 @@
 {% set fill_n_merge_source = ['land_cover', 'invert_mask'] %}
 {% set grid_source = ['grid_to_grid', 'grid_to_variable_resolution_grid', 'grid_to_n48e_namelist', 'grid_to_n48_namelist', '3d_to_3d', '3d_to_3d_with_extrapolation', 'invert_mask'] %}
 {% set target_lsm_grid_sources = ['grid_to_grid', 'invert_mask'] %}
-{% set vertical_regrid_source = ['ozone_zonal_mean'] %}
+{% set vertical_regrid_source = ['ozone_zonal_mean', 'aerosol_3d'] %}
 
 
 # This links a name specified on the command in rose-stem with a
@@ -27,7 +27,8 @@
         install_cold => ancil_general_regrid_invert_mask_latitude_weighted_kdtree<split> => rose_ana_general_regrid_latitude_weighted_kdtree:fail? => plot_comparisons_general_regrid_latitude_weighted_kdtree",
     "general_regrid_time_constrained": "install_cold => ancil_general_regrid_with_time_constraint<fill,split> => rose_ana_general_regrid<fill>:fail? => plot_comparisons_general_regrid<fill>
         install_cold => ancil_general_regrid_with_time_constraint_latitude_weighted_kdtree<split> => rose_ana_general_regrid_latitude_weighted_kdtree:fail? => plot_comparisons_general_regrid_latitude_weighted_kdtree",
-    "vertical_regrid_ozone": "install_cold => ancil_vertical_regrid_ozone_zonal_mean => rose_ana_vertical_regrid:fail? => plot_comparisons_general_regrid",
+    "vertical_regrid_zonal_mean": "install_cold => ancil_vertical_regrid_ozone_zonal_mean => rose_ana_vertical_regrid:fail? => plot_comparisons_general_regrid",
+    "vertical_regrid_3d": "install_cold => ancil_vertical_regrid_aerosol_3d => rose_ana_vertical_regrid:fail? => plot_comparisons_general_regrid",
     "build_documentation_graph": "install_cold => build_docs => linkcheck",
     "unittests_graph": "install_cold => unittests",
     "black_graph": "install_cold => black",
@@ -57,7 +58,7 @@
     "core" : ["ancil_2anc_graph", "fill_n_merge", "general_regrid"],
     "fill_n_merge": ["fill_n_merge_land_cover_graph", "fill_n_merge_invert_mask_graph"],
     "general_regrid": ["general_regrid_grid_to_grid_graph", "general_regrid_grid_to_variable_graph", "general_regrid_grid_to_n48e_namelist_graph", "general_regrid_grid_to_n48_namelist_graph", "general_regrid_3d_to_3d_graph", "general_regrid_3d_to_3d_with_extrapolation", "general_regrid_time_constrained", "general_regrid_invert_mask_graph"],
-    "vertical_regrid": ["vertical_regrid_ozone"],
+    "vertical_regrid": ["vertical_regrid_zonal_mean", "vertical_regrid_3d"],
     "documentation": ["build_documentation_graph"],
     "unittests": ["unittests_graph", "black_graph", "flake8_graph", "isort_graph"],
 }

From ec00ac7fb1efc4b3828a41ce51f98d505c94731e Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Fri, 28 Aug 2026 13:27:41 +0100
Subject: [PATCH 07/11] #96 add check for vertical only and docs

---
 docs/source/ancil_vertica;_regrid.rst | 16 ++++++++++++
 lib/ants/cli/ancil_vertical_regrid.py | 37 ++++++++++++++++++++++-----
 2 files changed, 46 insertions(+), 7 deletions(-)
 create mode 100644 docs/source/ancil_vertica;_regrid.rst

diff --git a/docs/source/ancil_vertica;_regrid.rst b/docs/source/ancil_vertica;_regrid.rst
new file mode 100644
index 0000000..d8ddae7
--- /dev/null
+++ b/docs/source/ancil_vertica;_regrid.rst
@@ -0,0 +1,16 @@
+.. meta::
+   :description lang=en: ancil_vertical_regrid.py
+   :keywords: ANTS, utils
+   :property=og:locale: en_GB
+
+=======================
+ancil_vertical_regrid.py
+=======================
+
+For a full description see :mod:`ants.cli.ancil_vertical_regrid`.
+
+.. argparse::
+    :module: ants.cli.ancil_vertical_regrid
+    :func: _get_parser
+    :prog: ancil_vertical_regrid
+    :nodescription:
diff --git a/lib/ants/cli/ancil_vertical_regrid.py b/lib/ants/cli/ancil_vertical_regrid.py
index 75cbccf..98e9b53 100755
--- a/lib/ants/cli/ancil_vertical_regrid.py
+++ b/lib/ants/cli/ancil_vertical_regrid.py
@@ -32,13 +32,41 @@ def load_data(
 
     target_cube = ants.io.load.load_grid(target_grid)
 
+    check_target(target_cube, source_cubes)
+
     return source_cubes, target_cube
 
+def check_target(
+        target_cube,
+        source_cubes,
+):
+    """
+    Check the target cube against common pitfalls. This application is for
+    structured mesh and vertical regridding only.
+    """
+    if ants.utils.cube._is_ugrid(target_cube):
+        raise ValueError(
+            "Target appears to be a UGrid mesh - the regrid to mesh application in "
+            "UG-ANTS should be used instead."
+        )
+
+    target_coords = [coord.name() for coord in target_cube.coords()]
+
+    if 'latitude' in target_coords:
+        for cube in source_cubes:
+            if cube.coord('latitude') != target_cube.coord('latitude'):
+                raise ValueError('Target grid latitude coordinates do not match source grid latitude coordinates')
+
+    if 'longitude' in target_coords:
+        for cube in source_cubes:
+            if cube.coord('longitude') != target_cube.coord('longitude'):
+                raise ValueError('Target grid longitude coordinates do not match source grid longitude coordinates')
+
 
 def regrid(sources, target):
     sources = ants.utils.cube.as_cubelist(sources)
     results = []
-    scheme = ants.regrid.GeneralRegridScheme(vertical_scheme='Linear')
+    scheme = ants.regrid.GeneralRegridScheme()
     for source in sources:
         results.append(source.regrid(target, scheme))
     return results
@@ -54,7 +82,7 @@ def main(
     netcdf_only,
 ):
     """
-    General regrid application top level call function.
+    Vertical regrid application top level call function.
 
     Loads source data cubes, regrids them to match target data cube
     co-ordinates, and saves result to output.  In addition to writing the
@@ -91,11 +119,6 @@ def main(
         begin,
         end,
     )
-    if ants.utils.cube._is_ugrid(target_cube):
-        raise ValueError(
-            "Target appears to be a UGrid mesh - the regrid to mesh application in "
-            "UG-ANTS should be used instead."
-        )
 
     regridded_cubes = regrid(source_cubes, target_cube)
 

From 0142f7bc0f644ad1445c50c5aab54807ac2d5973 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Wed, 2 Sep 2026 14:27:34 +0100
Subject: [PATCH 08/11] #96 linting

---
 ...;_regrid.rst => ancil_vertical_regrid.rst} |  0
 lib/ants/cli/ancil_vertical_regrid.py         | 25 ++++++++++++-------
 2 files changed, 16 insertions(+), 9 deletions(-)
 rename docs/source/{ancil_vertica;_regrid.rst => ancil_vertical_regrid.rst} (100%)

diff --git a/docs/source/ancil_vertica;_regrid.rst b/docs/source/ancil_vertical_regrid.rst
similarity index 100%
rename from docs/source/ancil_vertica;_regrid.rst
rename to docs/source/ancil_vertical_regrid.rst
diff --git a/lib/ants/cli/ancil_vertical_regrid.py b/lib/ants/cli/ancil_vertical_regrid.py
index 98e9b53..83a982c 100755
--- a/lib/ants/cli/ancil_vertical_regrid.py
+++ b/lib/ants/cli/ancil_vertical_regrid.py
@@ -18,7 +18,7 @@
 import ants.io.save as save
 import ants.utils
 from ants.utils.cube import create_time_constrained_cubes
-from ants.fileformats._grid_extract import extract_grid
+
 
 def load_data(
     source,
@@ -36,9 +36,10 @@ def load_data(
 
     return source_cubes, target_cube
 
+
 def check_target(
-        target_cube,
-        source_cubes,
+    target_cube,
+    source_cubes,
 ):
     """
     Check the target cube against common pitfalls. This application is for
@@ -52,15 +53,21 @@ def check_target(
 
     target_coords = [coord.name() for coord in target_cube.coords()]
 
-    if 'latitude' in target_coords:
+    if "latitude" in target_coords:
         for cube in source_cubes:
-            if cube.coord('latitude') != target_cube.coord('latitude'):
-                raise ValueError('Target grid latitude coordinates do not match source grid latitude coordinates')
+            if cube.coord("latitude") != target_cube.coord("latitude"):
+                raise ValueError(
+                    "Target grid latitude coordinates do not match source grid "
+                    "latitude coordinates"
+                )
 
-    if 'longitude' in target_coords:
+    if "longitude" in target_coords:
         for cube in source_cubes:
-            if cube.coord('longitude') != target_cube.coord('longitude'):
-                raise ValueError('Target grid longitude coordinates do not match source grid longitude coordinates')
+            if cube.coord("longitude") != target_cube.coord("longitude"):
+                raise ValueError(
+                    "Target grid longitude coordinates do not match source grid "
+                    "longitude coordinates"
+                )
 
 
 def regrid(sources, target):

From 712db4b35a72c458560afd0673bdcd1c8cb9b89f Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Thu, 3 Sep 2026 07:59:03 +0100
Subject: [PATCH 09/11] #96 tidy docs, including fixing linkcheck error

---
 docs/source/ancil_vertical_regrid.rst | 4 ++--
 docs/source/core_capabilities.rst     | 7 +++++++
 docs/source/release_notes/3.0.rst     | 2 +-
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/docs/source/ancil_vertical_regrid.rst b/docs/source/ancil_vertical_regrid.rst
index d8ddae7..6d43392 100644
--- a/docs/source/ancil_vertical_regrid.rst
+++ b/docs/source/ancil_vertical_regrid.rst
@@ -3,9 +3,9 @@
    :keywords: ANTS, utils
    :property=og:locale: en_GB
 
-=======================
+========================
 ancil_vertical_regrid.py
-=======================
+========================
 
 For a full description see :mod:`ants.cli.ancil_vertical_regrid`.
 
diff --git a/docs/source/core_capabilities.rst b/docs/source/core_capabilities.rst
index 3138870..7d9df5a 100644
--- a/docs/source/core_capabilities.rst
+++ b/docs/source/core_capabilities.rst
@@ -37,6 +37,12 @@ ancil_general_regrid.py
 The :doc:`ancil_general_regrid` application regrids a source file onto a
 specified target grid.
 
+ancil_vertical_regrid.py
+------------------------
+
+The :doc:`ancil_vertical_regrid` application vertically interpolates a source
+file onto a specified target grid.
+
 .. toctree::
    :maxdepth: 2
 
@@ -44,3 +50,4 @@ specified target grid.
    ancil_create_shapefile.rst
    ancil_fill_n_merge.rst
    ancil_general_regrid.rst
+   ancil_vertical_regrid.rst
diff --git a/docs/source/release_notes/3.0.rst b/docs/source/release_notes/3.0.rst
index aa718cc..71357e4 100644
--- a/docs/source/release_notes/3.0.rst
+++ b/docs/source/release_notes/3.0.rst
@@ -35,7 +35,7 @@ Infrastructure
   integration (CI).
 - :pr:`86`: `pre-commit <https://pre-commit.com/>`_ hooks are now supported in
   ANTS.
-- :pr:`90`: `setuptools-scm <https://setuptools-scm.readthedocs.io/en/latest/>`_
+- :pr:`90`: `setuptools-scm <https://setuptools-scm.readthedocs.io/latest/>`_
   is now used to set the version number automatically from git metadata.
 
 Documentation

From 371f882e0c5c879912fc0f7fabb679b29b526942 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Thu, 10 Sep 2026 09:41:46 +0100
Subject: [PATCH 10/11] #96 add some KGO words

---
 docs/source/tutorial_KGO.rst | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/docs/source/tutorial_KGO.rst b/docs/source/tutorial_KGO.rst
index 553c6ac..e075517 100644
--- a/docs/source/tutorial_KGO.rst
+++ b/docs/source/tutorial_KGO.rst
@@ -84,10 +84,12 @@ should:
 
 1. Add newly generated KGO changes to a local directory.  This only needs to
    be the KGO files needed for any rose stem tests affected by the change,
-   rather than the full set of KGOs.
-2. Add an ``ANTS_KGO_DIRECTORY_OVERRIDE`` or ``CONTRIB_KGO_DIRECTORY_OVERRIDE``
+   rather than the full set of KGOs or directory structure.
+2. KGO filenames should match the expected task output name and be listed in the
+   rose-ana optional configs.
+3. Add an ``ANTS_KGO_DIRECTORY_OVERRIDE`` or ``CONTRIB_KGO_DIRECTORY_OVERRIDE``
    variable (that points to the local directory) to the ``[[[environment]]]``
    section of each affected task's runtime entry within the ``flow.cylc``.
-3. Seek science owner approval for KGO changes.
-4. When the ticket is complete, please include a summary of the KGO changes on
+4. Seek science owner approval for KGO changes.
+5. When the ticket is complete, please include a summary of the KGO changes on
    the ticket template.

From e2790624d0d160a53da299c177bc08ae8b15f922 Mon Sep 17 00:00:00 2001
From: jennyhickson <61183013+jennyhickson@users.noreply.github.com>
Date: Wed, 16 Sep 2026 13:01:59 +0100
Subject: [PATCH 11/11] #96 adjust rose-stem testing with smaller input and
 UM-file output

---
 .../ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf   | 2 +-
 rose-stem/app/ancil_vertical_regrid/rose-app.conf        | 2 +-
 rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf | 4 +++-
 rose-stem/flow.cylc                                      | 9 +++++++--
 4 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf
index 1c2a5bf..1ce4f57 100644
--- a/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf
+++ b/rose-stem/app/ancil_vertical_regrid/opt/rose-app-aerosol_3d.conf
@@ -1,5 +1,5 @@
 [env]
 output=${ROSE_DATA}/${ROSE_TASK_NAME}
-source=/data/users/jennifer.hickson/ants_vertical_cli/ancil_vertical_regrid_aerosol_3d/qrclim.aerosols.nc
+source=/data/users/jennifer.hickson/ants_vertical_cli/ancil_vertical_regrid_aerosol_3d/seasalt_n48.nc
 target=/data/users/jennifer.hickson/ants_vertical_cli/vertlevs_L70_50t_20s_80km
 target_type=grid
diff --git a/rose-stem/app/ancil_vertical_regrid/rose-app.conf b/rose-stem/app/ancil_vertical_regrid/rose-app.conf
index 23ff639..1e7c219 100644
--- a/rose-stem/app/ancil_vertical_regrid/rose-app.conf
+++ b/rose-stem/app/ancil_vertical_regrid/rose-app.conf
@@ -11,7 +11,7 @@ scheme=Linear
 [command]
 default=ants-launch ancil_vertical_regrid.py \
        =${source} -o ${output} --ants-config ${ANTS_CONFIG} --target-${target_type} ${target} \
-       =${begin} ${end} --netcdf-only
+       =${begin} ${end}
 
 [env]
 ANTS_CONFIG=rose-app-run.conf
diff --git a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
index d825a5f..486fdc4 100644
--- a/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
+++ b/rose-stem/app/rose_ana/opt/rose-app-vertical_regrid.conf
@@ -1,4 +1,6 @@
 [env]
-filelist=ancil_vertical_regrid_ozone_zonal_mean.nc
+filelist=ancil_vertical_regrid_ozone_zonal_mean
+         ancil_vertical_regrid_ozone_zonal_mean.nc
+         ancil_vertical_regrid_aerosol_3d
          ancil_vertical_regrid_aerosol_3d.nc
 
diff --git a/rose-stem/flow.cylc b/rose-stem/flow.cylc
index b9545cd..67cce14 100644
--- a/rose-stem/flow.cylc
+++ b/rose-stem/flow.cylc
@@ -27,8 +27,8 @@
         install_cold => ancil_general_regrid_invert_mask_latitude_weighted_kdtree<split> => rose_ana_general_regrid_latitude_weighted_kdtree:fail? => plot_comparisons_general_regrid_latitude_weighted_kdtree",
     "general_regrid_time_constrained": "install_cold => ancil_general_regrid_with_time_constraint<fill,split> => rose_ana_general_regrid<fill>:fail? => plot_comparisons_general_regrid<fill>
         install_cold => ancil_general_regrid_with_time_constraint_latitude_weighted_kdtree<split> => rose_ana_general_regrid_latitude_weighted_kdtree:fail? => plot_comparisons_general_regrid_latitude_weighted_kdtree",
-    "vertical_regrid_zonal_mean": "install_cold => ancil_vertical_regrid_ozone_zonal_mean => rose_ana_vertical_regrid:fail? => plot_comparisons_general_regrid",
-    "vertical_regrid_3d": "install_cold => ancil_vertical_regrid_aerosol_3d => rose_ana_vertical_regrid:fail? => plot_comparisons_general_regrid",
+    "vertical_regrid_zonal_mean": "install_cold => ancil_vertical_regrid_ozone_zonal_mean => rose_ana_vertical_regrid:fail? => plot_comparisons_vertical_regrid",
+    "vertical_regrid_3d": "install_cold => ancil_vertical_regrid_aerosol_3d => rose_ana_vertical_regrid:fail? => plot_comparisons_vertical_regrid",
     "build_documentation_graph": "install_cold => build_docs => linkcheck",
     "unittests_graph": "install_cold => unittests",
     "black_graph": "install_cold => black",
@@ -362,3 +362,8 @@ fi
         inherit = PLOT_COMPARISONS
         [[[environment]]]
             TARGET_ANA_TASK_WORK_DIR=${CYLC_WORKFLOW_WORK_DIR}/${CYLC_TASK_CYCLE_POINT}/rose_ana_general_regrid_${CYLC_TASK_PARAM_fill}
+
+    [[plot_comparisons_vertical_regrid]]
+        inherit = PLOT_COMPARISONS
+        [[[environment]]]
+            TARGET_ANA_TASK_WORK_DIR=${CYLC_WORKFLOW_WORK_DIR}/${CYLC_TASK_CYCLE_POINT}/rose_ana_vertical_regrid