From 2ee55cc1520b9a35892035624bd26dfb99625ee2 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 20 Oct 2025 11:25:45 -0700
Subject: [PATCH 01/32] Add loguru logging to LEX

---
 lex/annual_cycle.py     |  3 ++-
 lex/common.py           | 23 ++++++++++++++++++-----
 lex/energy/energy.py    |  5 ++++-
 lex/smb/smb_icecores.py | 11 ++++++++++-
 lex/time_series_plot.py |  4 +++-
 5 files changed, 37 insertions(+), 9 deletions(-)

diff --git a/lex/annual_cycle.py b/lex/annual_cycle.py
index 5a34470..859e7c4 100644
--- a/lex/annual_cycle.py
+++ b/lex/annual_cycle.py
@@ -6,6 +6,7 @@
 import pandas as pd
 import xarray as xr
 from livvkit import elements as el
+from loguru import logger
 
 import lex.common as lxc
 
@@ -16,7 +17,6 @@
 Sign of component based on its contribution to total.
 """
 
-
 def main(args, config):
     model_data = xr.open_mfdataset(
         [config["climo_remap"].format(clim=f"{mon:02d}") for mon in range(1, 13)],
@@ -40,6 +40,7 @@ def main(args, config):
     model_data_out = {}
 
     for idx, data_var in enumerate(config["data_vars"]):
+        logger.info(f"WORKING ON {data_var['title']}")
         _obs_in = {}
 
         aavg_config = data_var.get("aavg", None)
diff --git a/lex/common.py b/lex/common.py
index 3c28c00..8843349 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -19,6 +19,7 @@
 from livvkit import elements as el
 from livvkit.util.LIVVDict import LIVVDict
 from numpy import ma
+from loguru import logger
 
 import lex.utils as lxu
 
@@ -377,6 +378,7 @@ def _fcn_filt(_var):
     return var_files
 
 
+@logger.catch
 def load_timeseries_data(config):
     """Load data for timeseries."""
     files = {}
@@ -389,19 +391,30 @@ def load_timeseries_data(config):
         for _var in config["data_vars"]:
             files[overs].extend(gen_file_list_timeseries(config, _var[overs], overs))
 
-        if len(set(files[overs])) == 1:
+        if  len(set(files[overs]))== 1:
             files[overs] = files[overs][0]
-
+            _nfiles = 1
+        else:
+            _nfiles = len(set(files[overs]))
+        _dsname = config['dataset_names'].get(
+            overs, config['dataset_names'].get('model_native')
+        )
+        logger.info(
+            f"LOAD TIMESERIES DATA FOR {overs}: {_dsname} NFILES: {_nfiles}"
+        )
         try:
-            obs_data[overs] = xr.open_mfdataset(files[overs]).squeeze()
+            obs_data[overs] = xr.open_mfdataset(files[overs]).squeeze().load()
         except (xr.MergeError, ValueError):
             if isinstance(files[overs], Path):
-                obs_data[overs] = xr.open_dataset(files[overs]).squeeze()
+                obs_data[overs] = xr.open_dataset(files[overs]).squeeze().load()
             else:
                 obs_data[overs] = xr.open_mfdataset(
                     files[overs],
                     combine="nested",
-                ).squeeze()
+                ).squeeze().load()
+        logger.info(
+            f"LOAD TIMESERIES DATA FOR {overs}: {_dsname} DONE"
+        )
 
     return obs_data
 
diff --git a/lex/energy/energy.py b/lex/energy/energy.py
index 8dc5cd9..c5af009 100644
--- a/lex/energy/energy.py
+++ b/lex/energy/energy.py
@@ -34,7 +34,7 @@
 import argparse
 import os
 from pathlib import Path
-
+from loguru import logger
 import livvkit
 import pandas as pd
 from livvkit import elements as el
@@ -64,6 +64,7 @@ def run(name, config):
 
     """
     img_dir = Path(livvkit.output_dir, "validation", "imgs", name)
+    logger.info(f"Starting ENERGY BALANCE WITH OUTPUT TO {img_dir}")
     if not img_dir.exists():
         img_dir.mkdir(parents=True)
 
@@ -86,6 +87,7 @@ def run(name, config):
     tables = {}
 
     for season in ["ANN", "DJF", "MAM", "JJA", "SON"]:
+        logger.info(f"PLOTTING COMPARE GRIDDED FOR {config.get('icesheet', '')} {season}")
         _plots, aavgs = compare_gridded.main(args, config, sea=season)
         images[season] = _plots
 
@@ -102,6 +104,7 @@ def run(name, config):
 
     timeseries_img = []
     if "timeseries_dirs" in config:
+        logger.info(f"PLOTTING TIMESERIES FOR {config.get('icesheet', '')}")
         timeseries_img.extend(time_series_plot.main(args, config))
 
     tabs = {}
diff --git a/lex/smb/smb_icecores.py b/lex/smb/smb_icecores.py
index 8cb88ad..87ab8ec 100644
--- a/lex/smb/smb_icecores.py
+++ b/lex/smb/smb_icecores.py
@@ -46,6 +46,8 @@
     import smb.plot_spatial as plt_spatial
     import smb.preproc as preproc
     import smb.utils as utils
+from loguru import logger
+
 
 PAGE_DOCS = {
     "gis": """Validation of the Greenland Ice Sheet (GrIS) surface mass balance by
@@ -84,8 +86,8 @@ def run(name, config):
     Returns:
        A LIVVkit page element containing the LIVVkit elements to display on a webpage
     """
-
     img_dir = os.path.join(livvkit.output_dir, "validation", "imgs", name)
+    logger.info(f"Starting SMB_ICECORES OUTPUT TO {img_dir}")
     fn.mkdir_p(img_dir)
     config_arg_list = []
     for key, val in config.items():
@@ -100,9 +102,11 @@ def run(name, config):
     statistic_img = []
     timeseries_img = []
     if "smb_cf_file" in config and "smb_mo_file" in config and "ib_file" in config:
+        logger.info(f"PLOT SPATIAL METADATA")
         spatial_img.extend(plt_spatial.plot_metadata(args, config))
 
     if "smb_cf_file" in config and "smb_mo_file" in config:
+        logger.info(f"PLOT SPATIAL CORE DATA")
         spatial_img.extend(plt_spatial.plot_core(args, config))
         transects = c_transects.main(args, config)
         statistic_img.extend(transects[3:])
@@ -110,13 +114,16 @@ def run(name, config):
         statistic_img.extend(c_hists.main(args, config))
 
     if "ib_file" in config:
+        logger.info(f"PLOT SPATIAL IB DATA")
         spatial_img.extend(plt_spatial.plot_ib_spatial(args, config))
         statistic_img.extend(IB_hist.main(args, config))
 
     if "smb_cf_file" in config and "smb_mo_file" in config:
+        logger.info(f"PLOT STATSTICAL DATA")
         statistic_img.extend(transects[:3])
 
     if "timeseries_dirs" in config:
+        logger.info(f"PLOT TIMESERIES DATA")
         timeseries_img.extend(time_series_plot.main(args, config))
 
     seasons = ["ANN", "DJF", "MAM", "JJA", "SON"]
@@ -129,11 +136,13 @@ def _format_table(x):
             return pd.Series([f"{xi:.2f}" for xi in x], index=x.index)
 
         for season in seasons:
+            logger.info(f"COMPARE GRIDDED {season} DATA")
             _img, _aavg = compare_gridded.main(args, config, sea=season)
 
             seasonal_components[season] = []
 
             if season == "ANN":
+                logger.info(f"PLOT ANNUAL CYCLE DATA")
                 seasonal_components[season].extend(annual_cycle.main(args, config))
 
             seasonal_components[season].extend(_img)
diff --git a/lex/time_series_plot.py b/lex/time_series_plot.py
index b21e559..5e61132 100644
--- a/lex/time_series_plot.py
+++ b/lex/time_series_plot.py
@@ -15,6 +15,7 @@
 
 import lex.common as lxc
 import lex.utils as lxu
+from loguru import logger
 
 IMG_GROUP = "Timeseries"
 
@@ -39,7 +40,7 @@ def assemble_outdata(args, config, dataset, aavg_data, ts_data, aavg_units):
             else:
                 _aavg = aavg_data.get(data_var["title"])
         else:
-            print(f"DATA NOT FOUND FOR {data_var['title']} in {dataset}")
+            logger.error(f"DATA NOT FOUND FOR {data_var['title']} in {dataset}")
             continue
 
         aavg_out[data_var["title"].replace(" ", "_")] = xr.DataArray(
@@ -79,6 +80,7 @@ def main(args, config):
             config_names[_dset] = _dset
     img_elem = []
     for idx, data_var in enumerate(config["data_vars"]):
+        logger.info(f"   PLOTTING {config.get('icesheet', '')} TS: {data_var['title']}")
         _obs_in = {}
 
         aavg_config = data_var.get("aavg", None)

From af62cd13f0635000dfb8bc61574511b3b1955806 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 20 Oct 2025 11:38:13 -0700
Subject: [PATCH 02/32] Add check for livv exe per @czender

---
 run_livv.sh | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/run_livv.sh b/run_livv.sh
index 32367a6..f44b0bc 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -1,7 +1,18 @@
 #!/bin/bash
 CASE=$1
+if [ $(command -v conda) ]; then
+    conda activate lex_env
+fi
+
+livv_cmd='livv'
+livv_exe=`which ${livv_cmd}`
+if [ -z "${livv_exe}" ]; then
+     echo "ERROR: Unable to find LIVV binary executable for command \"${livv_cmd}\""
+    exit 1
+else
+    echo "Running LIVV from ${livv_exe}"
+fi
 echo "LEX ON ${CASE}"
-
 # Allow for standalone (outside of batch script) by setting WEBDIR if it's not already set
 WEBDIR="${WEBDIR:-/global/cfs/projectdirs/e3sm/www/${USER}}"
 

From a4b662242ec699ece513cf946a0820ca51cae089 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 20 Oct 2025 11:57:49 -0700
Subject: [PATCH 03/32] Add log lines to indicate being finished

---
 lex/annual_cycle.py     | 3 ++-
 lex/common.py           | 2 +-
 lex/energy/energy.py    | 6 ++++++
 lex/smb/smb_icecores.py | 8 ++++++++
 lex/time_series_plot.py | 2 +-
 5 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/lex/annual_cycle.py b/lex/annual_cycle.py
index 859e7c4..c008def 100644
--- a/lex/annual_cycle.py
+++ b/lex/annual_cycle.py
@@ -65,7 +65,7 @@ def main(args, config):
                 / 365
             )
         except KeyError:
-            print(f"MODEL DATA NOT FOUND FOR {data_var['model']}")
+            logger.error(f"MODEL DATA NOT FOUND FOR {data_var['model']}")
             continue
 
         obs_aavg[data_var["title"]] = {}
@@ -126,6 +126,7 @@ def main(args, config):
             marker=".",
             lw=lw,
         )
+        logger.info(f"DONE - WORKING ON {data_var['title']}")
 
     obs_data_out["month"] = np.arange(1, 12 + 1)
     model_data_out["month"] = np.arange(1, 12 + 1)
diff --git a/lex/common.py b/lex/common.py
index 8843349..b66ffcd 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -413,7 +413,7 @@ def load_timeseries_data(config):
                     combine="nested",
                 ).squeeze().load()
         logger.info(
-            f"LOAD TIMESERIES DATA FOR {overs}: {_dsname} DONE"
+            f"DONE - LOAD TIMESERIES DATA FOR {overs}: {_dsname}"
         )
 
     return obs_data
diff --git a/lex/energy/energy.py b/lex/energy/energy.py
index c5af009..17fd478 100644
--- a/lex/energy/energy.py
+++ b/lex/energy/energy.py
@@ -101,11 +101,16 @@ def run(name, config):
             transpose=True,
         )
         tables[season] = table_el
+        logger.info(
+            "FINISHED PLOTTING COMPARE GRIDDED FOR "
+            f"{config.get('icesheet', '')} {season}"
+        )
 
     timeseries_img = []
     if "timeseries_dirs" in config:
         logger.info(f"PLOTTING TIMESERIES FOR {config.get('icesheet', '')}")
         timeseries_img.extend(time_series_plot.main(args, config))
+        logger.info(f"FINISHED PLOTTING TIMESERIES FOR {config.get('icesheet', '')}")
 
     tabs = {}
 
@@ -135,6 +140,7 @@ def run(name, config):
     tabs["References"] = [ref_ele]
     elements = [run_summary, el.Tabs(tabs)]
 
+    logger.info(f"FINISHED ENERGY BALANCE WITH OUTPUT TO {img_dir}")
     return el.Page(name, PAGE_DOCS[config.get("icesheet", "gis")], elements)
 
 
diff --git a/lex/smb/smb_icecores.py b/lex/smb/smb_icecores.py
index 87ab8ec..71b510c 100644
--- a/lex/smb/smb_icecores.py
+++ b/lex/smb/smb_icecores.py
@@ -104,6 +104,7 @@ def run(name, config):
     if "smb_cf_file" in config and "smb_mo_file" in config and "ib_file" in config:
         logger.info(f"PLOT SPATIAL METADATA")
         spatial_img.extend(plt_spatial.plot_metadata(args, config))
+        logger.info(f"DONE - PLOT SPATIAL METADATA")
 
     if "smb_cf_file" in config and "smb_mo_file" in config:
         logger.info(f"PLOT SPATIAL CORE DATA")
@@ -112,19 +113,23 @@ def run(name, config):
         statistic_img.extend(transects[3:])
         statistic_img.extend(IB_scatter.main(args, config))
         statistic_img.extend(c_hists.main(args, config))
+        logger.info(f"DONE - PLOT SPATIAL CORE DATA")
 
     if "ib_file" in config:
         logger.info(f"PLOT SPATIAL IB DATA")
         spatial_img.extend(plt_spatial.plot_ib_spatial(args, config))
         statistic_img.extend(IB_hist.main(args, config))
+        logger.info(f"DONE - PLOT SPATIAL IB DATA")
 
     if "smb_cf_file" in config and "smb_mo_file" in config:
         logger.info(f"PLOT STATSTICAL DATA")
         statistic_img.extend(transects[:3])
+        logger.info(f"DONE - PLOT STATSTICAL DATA")
 
     if "timeseries_dirs" in config:
         logger.info(f"PLOT TIMESERIES DATA")
         timeseries_img.extend(time_series_plot.main(args, config))
+        logger.info(f"DONE - PLOT TIMESERIES DATA")
 
     seasons = ["ANN", "DJF", "MAM", "JJA", "SON"]
     seasonal_components = {}
@@ -138,12 +143,14 @@ def _format_table(x):
         for season in seasons:
             logger.info(f"COMPARE GRIDDED {season} DATA")
             _img, _aavg = compare_gridded.main(args, config, sea=season)
+            logger.info(f"DONE - COMPARE GRIDDED {season} DATA")
 
             seasonal_components[season] = []
 
             if season == "ANN":
                 logger.info(f"PLOT ANNUAL CYCLE DATA")
                 seasonal_components[season].extend(annual_cycle.main(args, config))
+                logger.info(f"DONE - PLOT ANNUAL CYCLE DATA")
 
             seasonal_components[season].extend(_img)
             seasonal_tables[season] = el.Table(
@@ -187,6 +194,7 @@ def _format_table(x):
 
     tabs["References"] = [refs]
 
+    logger.info(f"FINISHED SMB_ICECORES WITH OUTPUT TO {img_dir}")
     return el.Page(
         name,
         PAGE_DOCS[config.get("icesheet", "gis")],
diff --git a/lex/time_series_plot.py b/lex/time_series_plot.py
index 5e61132..d59bf9b 100644
--- a/lex/time_series_plot.py
+++ b/lex/time_series_plot.py
@@ -261,7 +261,7 @@ def main(args, config):
             relative_to="",
         )
         img_elem.append(_img_elem)
-
+        logger.info(f"   DONE - PLOTTING {config.get('icesheet', '')} TS: {data_var['title']}")
     # assemble_outdata(args, config, "model", model_aavg, ts_data, _aavg_units)
     # assemble_outdata(args, config, "dset_a", obs_aavg, ts_data, _aavg_units)
 

From b1e3b44eb31070bedd0c1cbc98266a4f0a03003c Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Tue, 28 Oct 2025 14:23:14 -0700
Subject: [PATCH 04/32] Fix paths, redirect stderr for field check too

---
 lex/postproc/e3sm/postproc.sbatch | 11 ++++++-----
 lex/postproc/e3sm/split_files.sh  |  2 +-
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/lex/postproc/e3sm/postproc.sbatch b/lex/postproc/e3sm/postproc.sbatch
index b4f8fbb..cd65f6c 100644
--- a/lex/postproc/e3sm/postproc.sbatch
+++ b/lex/postproc/e3sm/postproc.sbatch
@@ -8,8 +8,9 @@
 conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
 echo $conda_activate_script
 source $conda_activate_script
-conda activate lex
+conda activate ${HOME}/.conda/envs/lex_env
 
+LEXDIR=$HOME/lex
 INDIR=/global/cfs/projectdirs/e3sm/zender/livvkit
 LIVVPROJ=/global/cfs/cdirs/e3sm/livvkit
 
@@ -86,10 +87,10 @@ ANN_MEAN_FILE=${OUTDIR}/${OUTCASE}.ANN_mean.nc
 ncra $INFILE ${ANN_MEAN_FILE}
 for var in topo landfrac
 do
-    ncks -m -v ${var} ${INFILE} > /dev/null || ncks -A -C -v ${var} ${INFILE_REF} ${ANN_MEAN_FILE}
+    ncks -m -v ${var} ${INFILE} > /dev/null 2>&1 || ncks -A -C -v ${var} ${INFILE_REF} ${ANN_MEAN_FILE}
 done
 
-srun parallel --jobs 12 ./split_files.sh ::: {0..11}
+srun parallel --jobs 12 ${LEXDIR}/lex/postproc/e3sm/split_files.sh ::: {0..11}
 
 ncra \
     ${OUTDIR}/${OUTCASE}.01.nc \
@@ -122,7 +123,7 @@ do
     do
         # Check if the mean output file has ${var} (topography or landfrac) if it
         # doesn't, then get that field from a reference file (set by the resolution)
-        ncks -m -v ${var} ${MEAN_FILE} > /dev/null || ncks -A -C -v ${var} ${INFILE_REF} ${MEAN_FILE}
+        ncks -m -v ${var} ${MEAN_FILE} > /dev/null 2>&1 || ncks -A -C -v ${var} ${INFILE_REF} ${MEAN_FILE}
     done
 
     ncremap \
@@ -163,7 +164,7 @@ echo "#########################"
 echo "POST PROCESSING COMPLETE"
 echo "#########################"
 
-pushd $HOME/lex
+pushd ${LEXDIR}
 if [ ! -d config/${OUTCASE} ]; then
     echo "CREATING CONFIG DIRECTORY FOR ${OUTCASE}"
     cp -R config/template_${RES} config/${OUTCASE}
diff --git a/lex/postproc/e3sm/split_files.sh b/lex/postproc/e3sm/split_files.sh
index 6d70e57..64d1090 100755
--- a/lex/postproc/e3sm/split_files.sh
+++ b/lex/postproc/e3sm/split_files.sh
@@ -14,7 +14,7 @@ ncra ${OUTDIR}/${MONFILE}.nc ${OUTDIR}/${MONFILE}_mean.nc
 
 for var in topo landfrac
 do
-    ncks -m -v ${var} ${OUTDIR}/${MONFILE}_mean.nc > /dev/null || ncks -A -C -v ${var} ${INFILE_REF} ${OUTDIR}/${MONFILE}_mean.nc
+    ncks -m -v ${var} ${OUTDIR}/${MONFILE}_mean.nc > /dev/null 2>&1 || ncks -A -C -v ${var} ${INFILE_REF} ${OUTDIR}/${MONFILE}_mean.nc
 done
 
 ncremap \

From 01586e46c9158e5aef7a306504cd7b1dcafdc5e6 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Tue, 28 Oct 2025 14:24:50 -0700
Subject: [PATCH 05/32] Improve conda env activation

---
 run_livv.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/run_livv.sh b/run_livv.sh
index f44b0bc..370b156 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -1,7 +1,10 @@
 #!/bin/bash
 CASE=$1
 if [ $(command -v conda) ]; then
-    conda activate lex_env
+    conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
+    echo "ACTIVATE: ${conda_activate_script}"
+    source $conda_activate_script
+    conda activate ${HOME}/.conda/envs/lex_env
 fi
 
 livv_cmd='livv'
@@ -12,6 +15,7 @@ if [ -z "${livv_exe}" ]; then
 else
     echo "Running LIVV from ${livv_exe}"
 fi
+
 echo "LEX ON ${CASE}"
 # Allow for standalone (outside of batch script) by setting WEBDIR if it's not already set
 WEBDIR="${WEBDIR:-/global/cfs/projectdirs/e3sm/www/${USER}}"

From 3f64532ab696e6214c0f6c747c82126c19feb219 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Tue, 28 Oct 2025 14:25:28 -0700
Subject: [PATCH 06/32] Update venv instructions

---
 README.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index c20d467..5bec7a9 100644
--- a/README.md
+++ b/README.md
@@ -41,10 +41,12 @@ $ pip install -e .    # Installs the lex module as an editable Python package to
 ### Python virtualenv
 ```bash
 $ git clone https://github.com/LIVVkit/lex.git
-$ cd lex python -m venv .env
-$ source .env/bin/activate
-$ pip install --upgrade pip # Needed if the system pip version < 21.3
-$ pip install -e .
+$ cd lex
+$ module load python/3.13
+$ python -m venv .env --prompt lex_env  # Creates the virtual env in ${HOME}/lex/.env
+$ source .env/bin/activate              # Switch to the new environment
+$ pip install --upgrade pip             # Needed if the system pip version < 21.3
+$ pip install -e .                      # Installs LEX as editable
 ```
 
 This will create a virtual environment at `lex/.env`, and install the

From ae00fcc6818321999c17f85606885153e11ffd89 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 3 Nov 2025 07:41:30 -0800
Subject: [PATCH 07/32] Add overwrite flag to ncra commands

---
 lex/postproc/e3sm/postproc.sbatch | 4 ++++
 lex/postproc/e3sm/split_files.sh  | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/lex/postproc/e3sm/postproc.sbatch b/lex/postproc/e3sm/postproc.sbatch
index cd65f6c..a0cba8b 100644
--- a/lex/postproc/e3sm/postproc.sbatch
+++ b/lex/postproc/e3sm/postproc.sbatch
@@ -93,24 +93,28 @@ done
 srun parallel --jobs 12 ${LEXDIR}/lex/postproc/e3sm/split_files.sh ::: {0..11}
 
 ncra \
+    -O \
     ${OUTDIR}/${OUTCASE}.01.nc \
     ${OUTDIR}/${OUTCASE}.02.nc \
     ${OUTDIR}/${OUTCASE}.12.nc \
     ${OUTDIR}/${OUTCASE}.DJF_mean.nc &
 
 ncra \
+    -O \
     ${OUTDIR}/${OUTCASE}.03.nc \
     ${OUTDIR}/${OUTCASE}.04.nc \
     ${OUTDIR}/${OUTCASE}.05.nc \
     ${OUTDIR}/${OUTCASE}.MAM_mean.nc &
 
 ncra \
+    -O \
     ${OUTDIR}/${OUTCASE}.06.nc \
     ${OUTDIR}/${OUTCASE}.07.nc \
     ${OUTDIR}/${OUTCASE}.08.nc \
     ${OUTDIR}/${OUTCASE}.JJA_mean.nc &
 
 ncra \
+    -O \
     ${OUTDIR}/${OUTCASE}.09.nc \
     ${OUTDIR}/${OUTCASE}.10.nc \
     ${OUTDIR}/${OUTCASE}.11.nc \
diff --git a/lex/postproc/e3sm/split_files.sh b/lex/postproc/e3sm/split_files.sh
index 64d1090..954eb4d 100755
--- a/lex/postproc/e3sm/split_files.sh
+++ b/lex/postproc/e3sm/split_files.sh
@@ -7,7 +7,7 @@ MON=$(printf "%02d" $(($MON_IDX + 1)))
 
 # Monthly split
 MONFILE=${OUTCASE}.${YEAR_STR}${MON}
-ncks -t 16 -d time,$MON_IDX,$MAXTIME,12 $INFILE ${OUTDIR}/$MONFILE.nc
+ncks -O -t 16 -d time,$MON_IDX,$MAXTIME,12 $INFILE ${OUTDIR}/$MONFILE.nc
 
 # echo "MEAN FOR ${MON}: ${MON_IDX}-${MAXTIME}"
 ncra ${OUTDIR}/${MONFILE}.nc ${OUTDIR}/${MONFILE}_mean.nc

From 8bb6002c613e885e9428d2bdf12971f284b54ae1 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 3 Nov 2025 11:23:15 -0800
Subject: [PATCH 08/32] Find the lex_env conda environment a little better

---
 lex/postproc/e3sm/postproc.sbatch | 12 +++++++++++-
 run_livv.sh                       | 11 ++++++++++-
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/lex/postproc/e3sm/postproc.sbatch b/lex/postproc/e3sm/postproc.sbatch
index a0cba8b..903bb2f 100644
--- a/lex/postproc/e3sm/postproc.sbatch
+++ b/lex/postproc/e3sm/postproc.sbatch
@@ -8,7 +8,17 @@
 conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
 echo $conda_activate_script
 source $conda_activate_script
-conda activate ${HOME}/.conda/envs/lex_env
+
+if [ -d ${HOME}/.conda/envs/lex_env ]; then
+    conda activate ${HOME}/.conda/envs/lex_env
+else if [ -d ${HOME}/anaconda/envs/lex_env ]; then
+    conda activate ${HOME}/anaconda/envs/lex_env
+else
+    echo "LEX ENV NOT FOUND AT EITHER $HOME/.conda or $HOME/anaconda "
+    echo "SET LEX_ENV variable to point to \$CONDA_PREFIX for lex_env"
+    exit 1
+fi
+fi
 
 LEXDIR=$HOME/lex
 INDIR=/global/cfs/projectdirs/e3sm/zender/livvkit
diff --git a/run_livv.sh b/run_livv.sh
index 370b156..1bc61ef 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -4,7 +4,16 @@ if [ $(command -v conda) ]; then
     conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
     echo "ACTIVATE: ${conda_activate_script}"
     source $conda_activate_script
-    conda activate ${HOME}/.conda/envs/lex_env
+    if [ -d ${HOME}/.conda/envs/lex_env ]; then
+        conda activate ${HOME}/.conda/envs/lex_env
+    else if [ -d ${HOME}/anaconda/envs/lex_env ]; then
+        conda activate ${HOME}/anaconda/envs/lex_env
+    else
+        echo "LEX ENV NOT FOUND AT EITHER $HOME/.conda or $HOME/anaconda "
+        echo "SET LEX_ENV variable to point to \$CONDA_PREFIX for lex_env"
+        exit 1
+    fi
+    fi
 fi
 
 livv_cmd='livv'

From b59ae664f02f4800f0cdf3a93ac11ed110831729 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 3 Nov 2025 11:38:49 -0800
Subject: [PATCH 09/32] Remove conda activation from batch script

---
 run_lex_pm-cpu.sbatch | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/run_lex_pm-cpu.sbatch b/run_lex_pm-cpu.sbatch
index 0b1054a..18dce3d 100644
--- a/run_lex_pm-cpu.sbatch
+++ b/run_lex_pm-cpu.sbatch
@@ -4,14 +4,9 @@
 #SBATCH --nodes=1
 #SBATCH --constraint=cpu
 
-conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
-echo $conda_activate_script
-source $conda_activate_script
-
 # NERSC Portal project location
 export WEBDIR=/global/cfs/projectdirs/e3sm/www/${USER}
 
-conda activate lex
 CASES=(
     "v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020"
     "v3.LR.piControl-deepfirn_0001_0100"

From 0512c10e2bb59583c9a1d026b3e6c4b626bd5a9a Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Tue, 16 Dec 2025 15:13:49 -0600
Subject: [PATCH 10/32] Use yaml anchor for simple test

---
 tests/simple_test.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/simple_test.yml b/tests/simple_test.yml
index bfd88d0..94336fe 100644
--- a/tests/simple_test.yml
+++ b/tests/simple_test.yml
@@ -1,4 +1,9 @@
 ---
+common:
+    meta: &meta
+        Case ID: TestCaseId
+        Clim Years: 1890-1906
 ExtensionTest:
     module: tests/extension_simple.py
     description: A minimal LIVVkit extensions test.
+    meta: *meta

From 3092dac3955743cfc848002322c8e9f814b5fccc Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Wed, 17 Dec 2025 11:17:34 -0600
Subject: [PATCH 11/32] Add Jinja template and script for generating config

---
 config/template_r05/all.jinja | 747 ++++++++++++++++++++++++++++++++++
 lex/generate_cfg.py           | 101 +++++
 requirements.txt              |   1 +
 3 files changed, 849 insertions(+)
 create mode 100644 config/template_r05/all.jinja
 create mode 100644 lex/generate_cfg.py

diff --git a/config/template_r05/all.jinja b/config/template_r05/all.jinja
new file mode 100644
index 0000000..d2aa3dc
--- /dev/null
+++ b/config/template_r05/all.jinja
@@ -0,0 +1,747 @@
+common: &common
+    meta: &meta
+      Case ID: [{{ case_id }}]
+      Climatology years: [1980-2020]
+      Model: [E3SM-ELM]
+    climo: {{ case_out_dir }}/{{ case_id }}.{clim}_mean.nc
+    latlon: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    elevation: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    lnd_climo: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    topo: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    glc_surf: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    latv: lat
+    lonv: lon
+    topov: topo
+    landfracv: landfrac
+    img_height: 300
+
+common_smb: &common_smb
+    smbv: QICE
+    maskv: gis_mask2
+    smbscale: 31536000
+    core_year_s: 1980
+    core_year_e: 2021
+    ib_year_e: 1987-1976
+    ib_year_s: 2014-2004
+    preprocess: []
+    preproc_dir: {{ livvproj_dir }}/data/smb/processed
+    zwally_file: model_zwally_basins_elm_r05.csv
+    ib_file: IceBridge_modelXY_elm{}_r05.csv
+    smb_cf_file: SMB_CoreFirnEstimates_elm{}_r05.csv
+    smb_mo_file: SMB_Obs_Model_elm{}_r05.csv
+    cmap: BrBG
+    cmap_diff: BrBG
+    clim_even: 1
+    units: mm w. e. yr^-1
+    References:
+      - {{ livvproj_dir }}/data/smb/smb_icecores.bib
+      - {{ livvproj_dir }}/data/livvkit.bib
+    timeseries_dirs:
+      {
+        model: "{{ model_ts_dir }}",
+        dset_a: "{{ racmo_root_dir }}/ts",
+      }
+    ts_file_patterns:
+      {
+        model: "{{ case_id }}.nc",
+        dset_a: "{_var}_{icesheet}_{year_s}01_{year_e}12.nc",
+      }
+
+common_energy: &common_energy
+  desc: Surface energy balance component {component}{comment} from {data_var_names}
+  references:
+    - {{ livvproj_dir }}/data/racmo/Noel2015.bib
+    - {{ livvproj_dir }}/data/cism/glissade/cism-glissade.bib
+    - {{ livvproj_dir }}/data/e3sm/Evans2019.bib
+    - {{ livvproj_dir }}/data/livvkit.bib
+  cmap: plasma
+  cmap_diff: RdBu_r
+
+common_racmo: &common_racmo
+    clim_years:
+      dset_a: { year_s: 1980, year_e: 2020 }
+    dataset_names: { model: ELM, dset_a: RACMO 2.4 }
+    in_dirs: { dset_a: "{{ racmo_root_dir }}/clm/{_var}" }
+    file_patterns:
+      { dset_a: "{_var}_{icesheet}_{season}_{sea_s}_{sea_e}_climo.nc" }
+
+common_era5: &common_era5
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_era5.nc
+  dataset_names: {model_remap: 'ELM [ERA5 Grid]', model_native: ELM, dset_a: ERA5}
+  aavg_sort: [ELM, 'ELM [ERA5 Grid]', ERA5]
+  scales: {model: 1, dset_a: 1}
+  clim_years:
+    dset_a: { year_s: 1979, year_e: 2019}
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/ERA5}
+  file_patterns: {dset_a: 'ERA5_{season}_{sea_s}_{sea_e}_climo.nc'}
+  masks: {
+    dset_a: {{ livvproj_dir }}/grids/msk_gis_rcm_r025_regrid_era5_traave_20250213.nc,
+    model_remap: {{ livvproj_dir }}/grids/msk_gis_rcm_r025_regrid_era5_traave_20250213.nc,
+    model_native: {{ livvproj_dir }}/grids/msk_gis_rcm_r05.nc
+  }
+
+common_merra: &common_merra
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_merra2.nc
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/MERRA2}
+  file_patterns: {dset_a: 'MERRA2_{season}_{sea_s}_{sea_e}_climo.nc'}
+  masks: {dset_a: {{ livvproj_dir }}/grids/msk_gis_r025_remap_merra2.traave.20250124.nc,
+    model_remap: {{ livvproj_dir }}/grids/msk_gis_r025_remap_merra2.traave.20250124.nc,
+    model_native: {{ livvproj_dir }}/grids/msk_gis_rcm_r05.nc}
+  dataset_names: {model_remap: 'ELM [MERRA2 Grid]', model_native: ELM, dset_a: MERRA2}
+  aavg_sort: [ELM, 'ELM [MERRA2 Grid]', MERRA2]
+  scales: {model: 1, dset_a: 1}
+  clim_years:
+    dset_a: { year_s: 1980, year_e: 2016}
+
+common_ceres: &common_ceres
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_cmip6.nc
+  dataset_names:
+    { model_native: ELM, model_remap: "ELM [CERES Grid]", dset_a: CERES }
+  aavg_sort: [ELM, "ELM [CERES Grid]", CERES]
+  scales: { model: 1, dset_a: 1 }
+  clim_years:
+    dset_a: { year_s: 2001, year_e: 2018 }
+  in_dirs:
+    dset_a: {{ e3sm_diags_data_dir }}/climatology/ceres_ebaf_surface_v4.1
+  file_patterns:
+    dset_a: ceres_ebaf_surface_v4.1_{season}_{sea_s}_{sea_e}_climo.nc
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_gis_r025_remap_cmip6.traave.20250124.nc
+    model_native: {{ grid_dir }}/msk_gis_rcm_r05.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_gis_r025_remap_cmip6.traave.20250124.nc
+
+common_racmo_gis: &common_racmo_gis
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_rcmgis.nc
+  icesheet: gis
+  masks:
+    {
+        dset_a: {{ grid_dir }}/msk_gis_r025_rcm.nc,
+        model: {{ grid_dir }}/msk_gis_r025_rcm.nc,
+        model_native: {{ livvproj_dir }}/grids/msk_gis_rcm_r05.nc,
+      }
+
+common_racmo_ais: &common_racmo_ais
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_rcmais.nc
+  icesheet: ais
+  masks:
+    {
+        dset_a: {{ grid_dir }}/msk_ais_r025_rcm.nc,
+        model: {{ grid_dir }}/msk_ais_r025_rcm.nc,
+        model_native: {{ livvproj_dir }}/grids/msk_ais_rcm_r05.nc,
+      }
+common_racmo_smb_vars: &common_racmo_smb_vars
+  # Surface mass balance variables for dset_a: RACMO 2.4, model: ELM
+  # Each field must have:
+  #   - title: Human readable field name
+  #   - dset_a: definition for the field in dset_a dataset (i.e. RACMO)
+  #   - model: definition for the field in model dataset (i.e. ELM)
+  #   - units: Units of this field
+  #   - ac_contrib_sign: For each dataset, multiply the annual cycle by +/- 1 to achieve
+  #                      correct contribution to annual cycle of SMB
+  #   - aavg: parameters for ice sheet-area-averaging
+  #       - scale: Further scale the area-average, (this typically converts mm w.e./yr to GT/yr)
+  #       - units: Units of area average (only applicable if different than units for the field)
+  #       - sum: Perform area-weighted sum if true (area weighted mean if false)
+
+  # Additional parameters which may be defined are:
+  #   - mask_weight: mask variable acts as a weight (e.g. partial mask at edge of the ice sheet)
+  #   - primary_var: True for the primary field of interest for an annual cycle plot
+  #   - cmap: Override for colourmap for the fields
+  #   - cmap_diff: Override for colourmap for the difference plot
+  #   - cmin, cmax, cmin_d, cmax_d: Override for min / max values for fields and differences respectively
+  #   - comment: added to figure caption on output (usually used to indicate signedness of fluxes)
+
+  # Surface mass balance
+  - title: Surface Mass Balance
+    dset_a: smbgl
+    model: QICE
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    mask_weight: true
+    primary_var: true
+
+  # Total precipitation
+  - title: Total precip
+    dset_a: prgl
+    model: [+, SNOW, RAIN]
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+
+  # Snowfall
+  - title: Snowfall
+    dset_a: sf
+    model: SNOW
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Rainfall
+  - title: Rain
+    dset_a: [+, crrate, lsrrate]
+    model: RAIN
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Re-freeze
+  - title: Re-freeze
+    dset_a: rfrzgl
+    model: QSNOFRZ
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    cmin: 0
+    cmap: YlGnBu
+
+  # Runoff
+  - title: Runoff
+    dset_a: totrunoff
+    model: QRUNOFF
+    ac_contrib_sign: { model: -1, dset_a: -1 }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    # cmin: -20.0
+    cmin: 0
+    # cmax: 20.0
+    cmap: YlGnBu
+
+  # Snow & ice melt
+  - title: Snow + ice melt
+    dset_a: mltgl
+    model: ["+", QSNOMELT, QICE_MELT]
+    ac_contrib_sign: { model: -1, dset_a: -1 }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    # cmin: -20.0
+    # cmax: 20.0
+    cmin: 0
+    # cmax: 20.0
+    cmap: YlGnBu
+
+  # Sublimation
+  - title: Sublimation
+    dset_a: sublgl
+    model: QSOIL
+    comment: " (Positive to atmosphere)"
+    ac_contrib_sign: { model: -1, dset_a: 1 }
+    scales: { model: 365 * 24 * 3600, dset_a: -365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+
+common_racmo_cmb_vars: &common_racmo_cmb_vars
+  # Climatic mass balance variables for dset_a: RACMO 2.4, model: ELM
+
+  # Climatic mass balance
+  - title: Climatic Mass Balance
+    dset_a: ["-", "prgl", ["-", "totrunoff", "sublgl"]]
+    model: ["-", ["+", "SNOW", "RAIN"], ["+", "QRUNOFF", "QSOIL"]]
+    ac_contrib_sign: { model: 1, dset_a: 1, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    mask_weight: true
+    primary_var: true
+
+  # Snowfall
+  - title: Snowfall
+    dset_a: sf
+    model: SNOW
+    ac_contrib_sign: { model: 1, dset_a: 1, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Rainfall
+  - title: Rain
+    dset_a: [+, crrate, lsrrate]
+    model: RAIN
+    ac_contrib_sign: { model: 1, dset_a: 1, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Runoff
+  - title: Runoff
+    dset_a: totrunoff
+    model: QRUNOFF
+    ac_contrib_sign: { model: -1, dset_a: -1, }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    cmin: 0
+    cmap: YlGnBu
+
+  # Sublimation
+  - title: Sublimation
+    dset_a: sublgl
+    model: QSOIL
+    comment: " (Positive to atmosphere)"
+    ac_contrib_sign: { model: -1, dset_a: 1, }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: -365 * 24 * 3600,  }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+
+common_racmo_energy_vars: &common_racmo_energy_vars
+  - title: Surface temperature
+    dset_a: tas
+    model: TSA
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: K
+
+  - title: Albedo
+    dset_a: [/, rsusgl, rsds]
+    model:
+    - /
+    - [+, FSRND, FSRVD]
+    - [+, FSDSVD, FSDSND]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: unitless
+    cmin: 0.5
+    cmax: 0.9
+    cmin_d: -0.2
+    cmax_d: 0.2
+
+  - title: Shortwave net
+    dset_a: ['-', rsds, rsusgl]
+    model: FSA
+    comment: ' (Positive to surface)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Shortwave down
+    dset_a: rsds
+    model: FSDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave net
+    dset_a: strgl
+    model: FIRA
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: -1, model: 1}
+    units: W m^-2
+
+  - title: Longwave down
+    dset_a: rlds
+    model: FLDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Sensible heat
+    dset_a: hfssgl
+    model: FSH
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: -1, model: 1}
+    units: W m^-2
+
+  - title: Latent Heat Flux
+    dset_a: hflsgl
+    model: EFLX_LH_TOT
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: -1, model: 1}
+    units: W m^-2
+
+  - title: Net energy balance
+    dset_a:
+    - +
+    - ['-', rsds, rsusgl]
+    - - +
+      - strgl
+      - [+, hfssgl, hflsgl]
+    model:
+    - '-'
+    - FSA
+    - - +
+      - FIRA
+      - [+, FSH, EFLX_LH_TOT]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+    cmin: -10
+    cmax: 10
+    cmap: RdBu_r
+
+common_era_energy_vars: &common_era_energy_vars
+  - title: Surface temperature
+    dset_a: ts
+    model: TSA
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: K
+
+  - title: Albedo
+    dset_a: [/, rsus, rsds]
+    model:
+    - /
+    - [+, FSRND, FSRVD]
+    - [+, FSDSVD, FSDSND]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: unitless
+    cmin: 0.5
+    cmax: 1.0
+    cmin_d: -0.2
+    cmax_d: 0.2
+
+  - title: Shortwave net
+    dset_a: ['-', rsds, rsus]
+    model: FSA
+    comment: ' (Positive to surface)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Shortwave down
+    dset_a: rsds
+    model: FSDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - model: FIRA
+    title: Longwave net
+    dset_a: ['-', rlus, rlds]
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave down
+    dset_a: rlds
+    model: FLDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - model: FSH
+    dset_a: hfss
+    title: Sensible heat
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Latent Heat Flux
+    dset_a: hfls
+    model: EFLX_LH_TOT
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Net energy balance
+    dset_a:
+    - '-'
+    - ['-', rsds, rsus]
+    - - +
+      - ['-', rlus, rlds]
+      - [+, hfss, hfls]
+    model:
+    - '-'
+    - FSA
+    - - +
+      - FIRA
+      - [+, FSH, EFLX_LH_TOT]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+    cmin: -10
+    cmax: 10
+    cmap: RdBu_r
+
+common_merra_energy_vars: &common_merra_energy_vars
+  - title: Surface temperature
+    dset_a: tas
+    model: TSA
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: K
+
+  - title: Albedo
+    dset_a: [/, rsus, rsds]
+    model:
+    - /
+    - [+, FSRND, FSRVD]
+    - [+, FSDSVD, FSDSND]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: unitless
+    cmin: 0.5
+    cmax: 0.83
+    cmin_d: -0.2
+    cmax_d: 0.2
+
+  - title: Shortwave net
+    dset_a: ['-', rsds, rsus]
+    model: FSA
+    comment: ' (Positive to surface)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Shortwave down
+    dset_a: rsds
+    model: FSDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave net
+    dset_a: ['-', rlus, rlds]
+    model: FIRA
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave down
+    dset_a: rlds
+    model: FLDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Sensible heat
+    dset_a: hfss
+    dset_b: FSH
+    model: FSH
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Latent Heat Flux
+    dset_a: hfls
+    dset_b: EFLX_LH_TOT
+    model: EFLX_LH_TOT
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Net energy balance
+    dset_a:
+    - '-'
+    - ['-', rsds, rsus]
+    - - +
+      - ['-', rlus, rlds]
+      - [+, hfss, hfls]
+    model:
+    - '-'
+    - FSA
+    - - +
+      - FIRA
+      - [+, FSH, EFLX_LH_TOT]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+    cmin: -10
+    cmax: 10
+    cmap: RdBu_r
+
+common_ceres_energy_vars: &common_ceres_energy_vars
+    - title: Albedo
+      dset_a: [/, rsus, rsds]
+      model:
+        - /
+        - [+, FSRND, FSRVD]
+        - [+, FSDSVD, FSDSND]
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: unitless
+      cmin: 0.5
+      cmax: 0.83
+      cmin_d: -0.2
+      cmax_d: 0.2
+
+    - title: Shortwave net
+      dset_a: sfc_net_sw_all_mon
+      model: FSA
+      comment: " (Positive to surface)"
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: W m^-2
+
+    - title: Shortwave down
+      dset_a: rsds
+      model: FSDS
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: W m^-2
+
+    - title: Longwave net
+      dset_a: sfc_net_lw_all_mon
+      model: FIRA
+      comment: " (Positive to atmosphere)"
+      sign: 1
+      scales: { dset_a: -1, model: 1 }
+      units: W m^-2
+
+    - title: Longwave down
+      dset_a: rlds
+      model: FLDS
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: W m^-2
+
+{% if run_gis %}
+# Greenland
+{% if set_cmb %}
+Climatic_Mass_Balance_GIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_cmb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_gis]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: Climatic Mass Balance
+  desc: "{component} component of CMB from {data_var_names}"
+{% endif %}
+
+{% if set_smb %}
+Surface_Mass_Balance_GIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_smb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_gis]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: smbgl
+  desc: "{component} component of SMB from {data_var_names}"
+{% endif %}
+
+{% if set_energy_racmo %}
+Energy_Balance_RACMO_GIS:
+  module: lex/energy/energy.py
+  <<: [*common, *common_energy, *common_racmo, *common_racmo_gis]
+  scales: {model: 1, dset_a: 1}
+  data_vars: *common_racmo_energy_vars
+{% endif %}
+
+{% if set_energy_era5 %}
+Energy_Balance_ERA5_GIS:
+  module: lex/energy/energy.py
+  icesheet: gis
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  <<: [*common, *common_energy, *common_era5]
+  data_vars: *common_era_energy_vars
+{% endif %}
+
+{% if set_energy_merra2 %}
+Energy_Balance_MERRA2_GIS:
+  module: lex/energy/energy.py
+  icesheet: gis
+  <<: [*common, *common_energy, *common_merra]
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  data_vars: *common_merra_energy_vars
+{% endif %}
+
+{% if set_energy_ceres %}
+Energy_Balance_CERES_GIS:
+  module: lex/energy/energy.py
+  icesheet: gis
+  <<: [*common, *common_energy, *common_ceres]
+  mask_ocean: { model_native: false, model_remap: true, dset_a: true }
+  data_vars: *common_ceres_energy_vars
+{% endif %}
+{% endif %}
+
+{% if run_ais %}
+# Antarctica
+{% if set_cmb %}
+Climatic_Mass_Balance_AIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_cmb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_ais]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: Climatic Mass Balance
+  desc: "{component} component of CMB from {data_var_names}"
+{% endif %}
+
+{% if set_smb %}
+Surface_Mass_Balance_AIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_smb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_ais]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: smbgl
+  desc: "{component} component of SMB from {data_var_names}"
+{% endif %}
+
+{% if set_energy_racmo %}
+Energy_Balance_RACMO_AIS:
+  module: lex/energy/energy.py
+  <<: [*common, *common_energy, *common_racmo, *common_racmo_ais]
+  scales: {model: 1, dset_a: 1}
+  data_vars: *common_racmo_energy_vars
+{% endif %}
+
+{% if set_energy_era5 %}
+Energy_Balance_ERA5_AIS:
+  module: lex/energy/energy.py
+  icesheet: ais
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  <<: [*common, *common_energy, *common_era5]
+  data_vars: *common_era_energy_vars
+{% endif %}
+
+{% if set_energy_merra2 %}
+Energy_Balance_MERRA2_AIS:
+  module: lex/energy/energy.py
+  icesheet: ais
+  <<: [*common, *common_energy, *common_merra]
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  data_vars: *common_merra_energy_vars
+{% endif %}
+
+{% if set_energy_ceres %}
+Energy_Balance_CERES_AIS:
+  module: lex/energy/energy.py
+  icesheet: ais
+  <<: [*common, *common_energy, *common_ceres]
+  mask_ocean: { model_native: false, model_remap: true, dset_a: true }
+  data_vars: *common_ceres_energy_vars
+{% endif %}
+{% endif %}
\ No newline at end of file
diff --git a/lex/generate_cfg.py b/lex/generate_cfg.py
new file mode 100644
index 0000000..2fd4d1f
--- /dev/null
+++ b/lex/generate_cfg.py
@@ -0,0 +1,101 @@
+"""Generate a LIVVkit Extensions (LEX) config based on template information and defaults.
+"""
+from pathlib import Path
+import jinja2
+import argparse
+
+def args():
+    parser = argparse.ArgumentParser(
+    description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+
+    parser.add_argument(
+        "--template",
+        "-i",
+        type=Path,
+        help="Path to configuration template file.",
+    )
+    parser.add_argument(
+        "--mach",
+        "-m",
+        type=str,
+        default="pm-cpu",
+        help="Name of the machine to be used. [pm-cpu, chrys]"
+    )
+    parser.add_argument(
+        "--case",
+        "-c",
+        type=str,
+        help="Case ID",
+    )
+    parser.add_argument(
+        "--casedir",
+        "-d",
+        type=Path,
+        help="Output directory where climatology files for `case` are stored"
+    )
+    parser.add_argument(
+        "--cfg_out",
+        "-o",
+        type=Path,
+        help="Output directory for config file."
+    )
+    return parser.parse_args()
+
+
+def gen_cfg(cfg_template, params, cfg_out):
+    jenv = jinja2.Environment(loader=jinja2.FileSystemLoader(cfg_template.resolve().parent))
+    template = jenv.get_template(cfg_template.name)
+
+    # Fill in the templated config file with the absolute
+    # path (.resolve()) of the input data directory
+    # Template switches:
+    # Icesheets:
+    #   run_gis
+    #   run_ais
+    # Analyses:
+    #   set_cmb
+    #   set_smb
+    #   set_energy_racmo
+    #   set_energy_era5
+    #   set_energy_merra2
+    #   set_energy_ceres
+
+    cfg = template.render(**params)
+
+    if not Path(cfg_out.parent).exists():
+        print(f"CREATE {cfg_out.parent}")
+        Path(cfg_out.parent).mkdir(parents=True)
+    print(f"WRITE: {cfg_out}")
+    with open(cfg_out, "w", encoding="utf-8") as _cfgout:
+        _cfgout.write(cfg)
+    return cfg_out
+
+
+
+def main():
+    cl_args = args()
+    defaults = {
+        "chrys": {
+            "e3sm_diags_data_dir": Path("/lcrc/group/e3sm/diagnostics/observations/Atm/"),
+            "livvproj_dir": Path("/lcrc/group/e3sm/livvkit"),
+            "ts_dir": Path("/lcrc/group/e3sm/ac.zender/scratch/livvkit"),
+            "grid_dir": Path("/lcrc/group/e3sm/zender/grids"),
+        }
+    }
+    params = {
+        **defaults[cl_args.mach],
+        "case_id": cl_args.case,
+        "case_out_dir": cl_args.casedir,
+        "run_ais": True,
+        "run_gis": True,
+        "set_energy_era5": True,
+        "set_energy_ceres": True,
+        "set_energy_merra2": True
+    }
+    out_cfg = Path(cl_args.cfg_out, cl_args.case, "livvkit.yml")
+    gen_cfg(cl_args.template, params, out_cfg)
+
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 7acf04b..632739a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -7,6 +7,7 @@
   nc-time-axis
   scikit-learn
   ruamel.yaml
+  jinja2
   pylint
   matplotlib
   basemap

From 132041f05bb6ee32bff118dde9e09abfe8e2f6cc Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Wed, 17 Dec 2025 13:52:32 -0600
Subject: [PATCH 12/32] Add initial tests for lex.common

---
 tests/test_common.py | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 tests/test_common.py

diff --git a/tests/test_common.py b/tests/test_common.py
new file mode 100644
index 0000000..076d81e
--- /dev/null
+++ b/tests/test_common.py
@@ -0,0 +1,41 @@
+import numpy as np
+import xarray as xr
+import lex.common as lxc
+
+def test_img_file_prefix():
+    config_1 = {"module": "energy.py"}
+    config_2 = {"EMPTY": "empty.py"}
+
+    assert "energy" == lxc.img_file_prefix(config_1), "PREFIX DOES NOT MATCH"
+    try:
+        _mod = lxc.img_file_prefix(config_2)
+    except KeyError as _err:
+        assert "module" in _err.args, "UN-EXPECTED ERROR"
+
+
+def test_check_longitude():
+    lons = np.arange(-180, 180, 45.)
+    data = {"lon": lons}
+    b_coord = "longitude"
+    data_b = {b_coord: lons}
+    assert lxc.check_longitude(data) == {"lon": lons}
+    assert lxc.check_longitude(data_b, lon_coord=b_coord) == {b_coord: lons}
+
+    lons_2 = np.arange(0, 360, 45.)
+    _shift_lons = np.array([   0.,   45.,   90.,  135., -180., -135.,  -90.,  -45.])
+    _check = lxc.check_longitude({"lon": lons_2})
+    assert np.all(_check["lon"] == _shift_lons), "SHIFTED LONGITUDE DOES NOT MATCH"
+
+    test_data = [0, 1, 2, 3, 4, 5, 6, 7,]
+    test_data_shift = [4, 5, 6, 7, 0, 1, 2, 3]
+    _ds1 = _ds1 = xr.Dataset(data_vars={"x": (["lon"], test_data)}, coords={"lon": lons_2})
+    _check = lxc.check_longitude(_ds1)
+    assert isinstance(_check, xr.Dataset), "CHECK_LON DID NOT RETURN XARRAY.DATASET" 
+    assert (_check["lon"] == lons).all(), "LONGITUDE NOT SHIFTED PROPERLY"
+    assert (_check["x"] == test_data_shift).all(), "DATA NOT ROLLED PROPERLY"
+
+    _da1 = xr.DataArray(test_data, coords={"lon": lons_2}, dims=("lon",))
+    _check = lxc.check_longitude(_da1)
+    assert isinstance(_check, xr.DataArray), "CHECK_LON DID NOT RETURN XARRAY.DATAARRAY" 
+    assert (_check["lon"] == lons).all()
+    assert (_check.values == test_data_shift).all()
\ No newline at end of file

From 704c03424b8458d5f4712ab3ee431c66bc04f5c1 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 08:41:31 -0800
Subject: [PATCH 13/32] Add parsing of sets/icesheets, NERSC defaults

---
 lex/generate_cfg.py | 75 +++++++++++++++++++++++++++++++++------------
 1 file changed, 55 insertions(+), 20 deletions(-)

diff --git a/lex/generate_cfg.py b/lex/generate_cfg.py
index 2fd4d1f..19f8b3f 100644
--- a/lex/generate_cfg.py
+++ b/lex/generate_cfg.py
@@ -3,6 +3,8 @@
 from pathlib import Path
 import jinja2
 import argparse
+ALL_SHEETS="run_gis,run_ais"
+ALL_SETS = "set_cmb,set_smb,set_energy_racmo,set_energy_era5,set_energy_merra2,set_energy_ceres"
 
 def args():
     parser = argparse.ArgumentParser(
@@ -11,7 +13,7 @@ def args():
 
     parser.add_argument(
         "--template",
-        "-i",
+        "-t",
         type=Path,
         help="Path to configuration template file.",
     )
@@ -40,6 +42,29 @@ def args():
         type=Path,
         help="Output directory for config file."
     )
+
+    parser.add_argument(
+        "--sets",
+        "-s",
+        type=str,
+        default="",
+        help=(
+            "Analysis sets to run: set_cmb, set_smb, set_energy_racmo, "
+            "set_energy_era5, set_energy_merra2, set_energy_ceres"
+        )
+    )
+
+    parser.add_argument(
+        "--icesheets",
+        "-i",
+        type=str,
+        default="",
+        help=(
+            "Comma separated icesheets to analyse (run_ais for Antarctica,"
+            " run_gis for Greenland)"
+        )
+    )
+
     return parser.parse_args()
 
 
@@ -47,20 +72,6 @@ def gen_cfg(cfg_template, params, cfg_out):
     jenv = jinja2.Environment(loader=jinja2.FileSystemLoader(cfg_template.resolve().parent))
     template = jenv.get_template(cfg_template.name)
 
-    # Fill in the templated config file with the absolute
-    # path (.resolve()) of the input data directory
-    # Template switches:
-    # Icesheets:
-    #   run_gis
-    #   run_ais
-    # Analyses:
-    #   set_cmb
-    #   set_smb
-    #   set_energy_racmo
-    #   set_energy_era5
-    #   set_energy_merra2
-    #   set_energy_ceres
-
     cfg = template.render(**params)
 
     if not Path(cfg_out.parent).exists():
@@ -72,6 +83,26 @@ def gen_cfg(cfg_template, params, cfg_out):
     return cfg_out
 
 
+def parse_sets(sheets, sets):
+    """Parse comma separated strings of sets / icesheets to analyse.
+    """
+
+    params = {}
+    if sheets.lower() == "run_all":
+        sheets = ALL_SHEETS
+    if sets.lower() == "set_all":
+        sets = ALL_SETS
+
+    _sheets = sheets.lower().split(",")
+    _sets = sets.lower().split(",")
+
+    for _sheet in _sheets:
+        params[_sheet] = True
+
+    for _set in _sets:
+        params[_set] = True
+    return params
+
 
 def main():
     cl_args = args()
@@ -81,17 +112,21 @@ def main():
             "livvproj_dir": Path("/lcrc/group/e3sm/livvkit"),
             "ts_dir": Path("/lcrc/group/e3sm/ac.zender/scratch/livvkit"),
             "grid_dir": Path("/lcrc/group/e3sm/zender/grids"),
+        },
+        "pm-cpu": {
+            "e3sm_diags_data_dir": Path("/global/cfs/cdirs/e3sm/e3sm_diags/obs_for_e3sm_diags"),
+            "livvproj_dir": Path("/global/cfs/cdirs/e3sm/livvkit"),
+            "ts_dir": Path("/global/cfs/projectdirs/e3sm/zender/livvkit"),
+            "grid_dir": Path("/global/cfs/cdirs/e3sm/zender/grids"),
+            "racmo_root_dir": Path("/global/cfs/cdirs/fanssie/racmo/2.4.1")
         }
+        
     }
     params = {
         **defaults[cl_args.mach],
         "case_id": cl_args.case,
         "case_out_dir": cl_args.casedir,
-        "run_ais": True,
-        "run_gis": True,
-        "set_energy_era5": True,
-        "set_energy_ceres": True,
-        "set_energy_merra2": True
+        **parse_sets(cl_args.icesheets, cl_args.sets)
     }
     out_cfg = Path(cl_args.cfg_out, cl_args.case, "livvkit.yml")
     gen_cfg(cl_args.template, params, out_cfg)

From 15c115a995a75d25aa338ebfd8408604e861d2f6 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 09:41:43 -0800
Subject: [PATCH 14/32] Add fields to export / merge list

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 5bec7a9..a5fd401 100644
--- a/README.md
+++ b/README.md
@@ -105,7 +105,7 @@ $ sbatch run_lex_pm-cpu.sbatch
 ## Running new cases on PM-CPU
 
 ### Generate a single timeseries file from ELM h0 outputs
-- `ncrcat -v topo,landfrac,QSNOFRZ,FSRND,FSRVD,FSDSVD,FSDSND,EFLX_LH_TOT,FIRA,FLDS,FSA,FSDS,FSH,QICE,QRUNOFF,QSNOMELT,QSOIL,RAIN,SNOW,TSA elm*h0*.nc -o ${CASE}.nc`
+- `ncrcat -v topo,landfrac,QSNOFRZ,FSRND,FSRVD,FSDSVD,FSDSND,EFLX_LH_TOT,FIRA,FLDS,FSA,FSDS,FSH,QICE,QRUNOFF,QSNOMELT,QSOIL,RAIN,SNOW,TSA,SNOWICE,SNOWLIQ,H2OSNO elm*h0*.nc -o ${CASE}.nc`
 
 ### Perform post-processing on a single time series ELM h0 output
 - Edit the `lex/lex/postproc/e3sm/postproc.sbatch` batch file to mach the new run

From e7a1efc1f9a6b0173079567b9fb4b1c904245e4e Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 09:43:14 -0800
Subject: [PATCH 15/32] Improve conda env checking

---
 lex/postproc/e3sm/postproc.sbatch | 5 ++++-
 run_livv.sh                       | 7 ++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/lex/postproc/e3sm/postproc.sbatch b/lex/postproc/e3sm/postproc.sbatch
index 903bb2f..dc6553d 100644
--- a/lex/postproc/e3sm/postproc.sbatch
+++ b/lex/postproc/e3sm/postproc.sbatch
@@ -9,7 +9,9 @@ conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profil
 echo $conda_activate_script
 source $conda_activate_script
 
-if [ -d ${HOME}/.conda/envs/lex_env ]; then
+if [ -n ${LEX_ENV} ]; then
+    conda activate ${LEX_ENV}
+else if [ -d ${HOME}/.conda/envs/lex_env ]; then
     conda activate ${HOME}/.conda/envs/lex_env
 else if [ -d ${HOME}/anaconda/envs/lex_env ]; then
     conda activate ${HOME}/anaconda/envs/lex_env
@@ -19,6 +21,7 @@ else
     exit 1
 fi
 fi
+fi
 
 LEXDIR=$HOME/lex
 INDIR=/global/cfs/projectdirs/e3sm/zender/livvkit
diff --git a/run_livv.sh b/run_livv.sh
index 1bc61ef..8b8ab8b 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -4,7 +4,9 @@ if [ $(command -v conda) ]; then
     conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
     echo "ACTIVATE: ${conda_activate_script}"
     source $conda_activate_script
-    if [ -d ${HOME}/.conda/envs/lex_env ]; then
+    if [ ! -z ${LEX_ENV+x} ]; then
+        conda activate ${LEX_ENV}
+    else if [ -d ${HOME}/.conda/envs/lex_env ]; then
         conda activate ${HOME}/.conda/envs/lex_env
     else if [ -d ${HOME}/anaconda/envs/lex_env ]; then
         conda activate ${HOME}/anaconda/envs/lex_env
@@ -14,6 +16,7 @@ if [ $(command -v conda) ]; then
         exit 1
     fi
     fi
+    fi
 fi
 
 livv_cmd='livv'
@@ -66,3 +69,5 @@ for htmlfile in validation/*.html
 do
     sed -i "s/\(<\!-- GROUP LINK-->\)/\<a id=\"header-group\" href=\"..\/..\/current_runs.html\">\nCurrent\ runs\n\<\/a\>/g" ${htmlfile}
 done
+echo "LIVVkit results availalble at:"
+echo "https://portal.nersc.gov/project/e3sm/${USER}/${CASE}/index.html"
\ No newline at end of file

From 41c634d4b8c2ecb79a9cf918bf1765b510eddb6b Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 11:26:09 -0800
Subject: [PATCH 16/32] Refactor away from Basemap

---
 lex/compare_gridded.py      |  40 ++++-
 lex/smb/smb/plot_spatial.py | 330 ++++++++++++++++++------------------
 requirements.txt            |   1 -
 3 files changed, 195 insertions(+), 176 deletions(-)

diff --git a/lex/compare_gridded.py b/lex/compare_gridded.py
index c8349fa..e598ec7 100644
--- a/lex/compare_gridded.py
+++ b/lex/compare_gridded.py
@@ -48,6 +48,11 @@ def add_colorbar(color_field, fig, axis, cblabel, cbar_span=False, ndsets=3):
             _ = fig.colorbar(
                 color_field, cax=cbar_ax, orientation="horizontal", label=cblabel
             )
+    elif ndsets == 1:
+        _ = fig.colorbar(
+            color_field, location="right", shrink=0.85, pad=0.01, label=cblabel
+        )
+
     else:
         raise NotImplementedError(
             f"THIS NUMBER OF PLOTS ({ndsets}) NOT IMPLEMENTED (yet)"
@@ -74,11 +79,22 @@ def annotate_plot(
     xlabel=None,
     cblabel=None,
     cnrtxt=None,
+    gridline_args=None,
     icesheet="gis",
 ):
     """Add land / ocean, gridlines, colourbar."""
     axis.coastlines(linewidth=0.1)
-    axis.gridlines(linestyle="--", linewidth=0.1)
+    gridline_args_def = {"linestyle": "--", "linewidth": 0.1}
+
+    if gridline_args is None:
+        gridline_args = gridline_args_def
+    else:
+        for _arg, _value in gridline_args_def.items():
+            if _arg not in gridline_args:
+                gridline_args[_arg] = _value
+
+    axis.gridlines(**gridline_args)
+
     if icesheet.lower() == "gis":
         axis.set_extent([-60, -27, 59, 84], ccrs.PlateCarree())
     elif icesheet.lower() == "ais":
@@ -116,12 +132,22 @@ def annotate_plot(
         )
 
 
-def get_figure(n_dsets, proj, icesheet="gis"):
+def get_figure(n_dsets, proj=None, icesheet="gis"):
     """Set up figure based on number of datasets to be plotted."""
     fig_size = {
-        "gis": {3: (10, 10), 2: (10, 8)},
-        "ais": {3: (10, 10), 2: (16, 7)},
+        "gis": {3: (10, 10), 2: (10, 8), 1: (7, 10)},
+        "ais": {3: (10, 10), 2: (16, 7), 1: (8, 8)},
     }
+    if proj is None:
+        if icesheet == "gis":
+            lon_0 = -45
+            lat_0 = 70
+            proj = ccrs.LambertConformal(
+                central_longitude=lon_0, central_latitude=lat_0
+            )
+        elif icesheet == "ais":
+            proj = ccrs.SouthPolarStereo(central_longitude=0)
+
     fig = plt.figure(figsize=fig_size[icesheet][n_dsets], dpi=90)
 
     if n_dsets == 3:
@@ -131,8 +157,10 @@ def get_figure(n_dsets, proj, icesheet="gis"):
         )
     elif n_dsets == 2:
         axes = [fig.add_subplot(1, 3, i + 1, projection=proj) for i in range(3)]
+    elif n_dsets == 1:
+        axes = [fig.add_subplot(1, 1, 1, projection=proj)]
 
-    return fig, axes
+    return fig, axes, proj
 
 
 def main(args, config, sea="ANN"):
@@ -303,7 +331,7 @@ def main(args, config, sea="ANN"):
         else:
             raise NotImplementedError(f"ICESHEET {icesheet} NOT FOUND USE ais / gis")
 
-        fig, axes = get_figure(n_dsets_to_plot, proj, icesheet=icesheet)
+        fig, axes, _ = get_figure(n_dsets_to_plot, proj, icesheet=icesheet)
 
         for _vers in _plt_data:
             try:
diff --git a/lex/smb/smb/plot_spatial.py b/lex/smb/smb/plot_spatial.py
index 6dca4df..f319c83 100644
--- a/lex/smb/smb/plot_spatial.py
+++ b/lex/smb/smb/plot_spatial.py
@@ -7,6 +7,7 @@
 import os
 from pathlib import Path
 
+import cartopy.crs as ccrs
 import matplotlib.pyplot as plt
 import numpy as np
 import numpy.ma as ma
@@ -14,10 +15,11 @@
 import smb.preproc as preproc
 from livvkit import elements as el
 from matplotlib import colors as c
-from mpl_toolkits.basemap import Basemap
 from netCDF4 import Dataset
 from scipy.interpolate import griddata
 
+import lex.compare_gridded as lxcg
+
 DESCRIBE_CORE = """
 Filled contour of modeled annual surface mass balance of the Greenland ice
 sheet, with firn and core field estimates overlaid as filled circles. Data were
@@ -57,6 +59,13 @@
 
 IMG_GROUP = "Spatial"
 
+GRIDLINE_ARGS = {
+    "draw_labels": ["top", "bottom", "left"],
+    "x_inline": False,
+    "y_inline": False,
+    "linewidth": 1.0,
+}
+
 
 def mali_to_contour(lon_cell, lat_cell, data_cell):
     """Convert MALI unstructured to gridded data."""
@@ -75,27 +84,28 @@ def mali_to_contour(lon_cell, lat_cell, data_cell):
     return x_grid, y_grid, z_grid
 
 
-def load_model_data(args, config, regrid=True):
+def load_model_data(config, regrid=True):
     """Load Model data."""
-    nc1 = Dataset(config["climo"].format(m_s=1, m_e=12, clim="ANN"), mode="r")
-    nc2 = Dataset(args.latlon, mode="r")
-    nc3 = Dataset(args.elevation, mode="r")
+    clim_nc = Dataset(config["climo"].format(m_s=1, m_e=12, clim="ANN"), mode="r")
+    grid_nc = Dataset(config["latlon"], mode="r")
+    elev_nc = Dataset(config["elevation"], mode="r")
 
-    lats_model = nc1.variables[config["latv"]][:]
-    lons_model = nc1.variables[config["lonv"]][:]
-    if nc2.variables[args.lonv].units == "radians":
+    lats_model = clim_nc.variables[config["latv"]][:]
+    lons_model = clim_nc.variables[config["lonv"]][:]
+    if grid_nc.variables[config["lonv"]].units == "radians":
         lats_model = np.degrees(lats_model)
         lons_model = np.degrees(lons_model)
 
-    smb_model = nc1.variables[args.smbv][:]
+    smb_model = clim_nc.variables[config["smbv"]][:]
+
+    thk_model = clim_nc.variables[config["topov"]][:]
+    if config["landfracv"] in clim_nc.variables:
+        smb_model *= clim_nc.variables[config["landfracv"]][:]
+    smb_model *= config["smbscale"]
 
-    thk_model = nc1.variables[args.topov][:]
-    if args.landfracv in nc1.variables:
-        smb_model *= nc1.variables[args.landfracv][:]
-    smb_model *= args.smbscale
-    nc1.close()
-    nc2.close()
-    nc3.close()
+    clim_nc.close()
+    grid_nc.close()
+    elev_nc.close()
 
     mask = thk_model.flatten() < 0.0001
     smb_flat = smb_model.flatten()
@@ -112,110 +122,58 @@ def load_model_data(args, config, regrid=True):
     return lons_model, lats_model, msmb
 
 
-def gen_map(lon_0, lat_0):
-    """
-    Create Basemap on which to plot.
-
-    Parameters
-    ----------
-    lon_0, lat_0 : float
-        Center location of map to be drawn
-
-    Returns
-    -------
-    pmap : basemap.Basemap
-        Lambert conformal conic `Basemap` centered on Greenland
-        (future: do a stereographic for Antarctica)
-
-    """
-    pmap = Basemap(
-        width=2000000,
-        height=3000000,
-        rsphere=(6378137.00, 6356752.3142),
-        resolution="l",
-        projection="lcc",
-        lat_0=lat_0,
-        lon_0=lon_0,
-    )
-    return pmap
-
-
-def annotate_map(pmap, axis=None):
-    """
-    Add common details to basemap.
-
-    Draw grid and coastlines, and fill the continents with colour.
-
-    Parameters
-    ----------
-    pmap : basemap.Basemap
-        Basemap on which to draw annotations
-
-    axis : matplotlib.pyplot.Axis, optional
-        Axis where Basemap is drawn, default is None
-
-    """
-    pmap.drawcoastlines(ax=axis)
-    pmap.drawcountries(ax=axis)
-    pmap.fillcontinents(color="gainsboro", lake_color="aqua", zorder=1)
-    pmap.drawparallels(
-        np.arange(-80.0, 81.0, 5.0),
-        labels=[1, 0, 0, 0],
-        fontsize=10,
-        color="lightgrey",
-        zorder=1,
-        ax=axis,
-    )
-    pmap.drawmeridians(
-        np.arange(-180.0, 181.0, 10.0),
-        labels=[0, 0, 0, 1],
-        fontsize=10,
-        color="lightgrey",
-        zorder=1,
-        ax=axis,
-    )
-
-
 def plot_core(args, config):
     """Plot Ice Core data on map with model data."""
     img_list = []
     _, _, _, core_file = preproc.core_file(config)
     smb_avg = pd.read_csv(core_file)
 
-    plt.figure(figsize=(12, 12))
+    tform = ccrs.PlateCarree()
+    lons_model, lats_model, msmb = load_model_data(config)
+    fig, axes, proj = lxcg.get_figure(1, icesheet="gis")
 
-    # lon_0 = lons_model.mean()
-    # lat_0 = lats_model.mean()
-    lon_0 = -40.591
-    lat_0 = 71.308
-
-    lons_model, lats_model, msmb = load_model_data(args, config)
-    pmap = gen_map(lon_0, lat_0)
-    annotate_map(pmap)
-    xi, yi = pmap(lons_model.squeeze(), lats_model.squeeze())
     vabsmax = 2000
-    # smb = pmap.scatter(xi, yi, c=msmb.squeeze(), vmin=-1500, vmax=1500,
-    #                 cmap='Spectral', zorder=2)
-    smb = pmap.pcolormesh(
-        xi, yi, msmb.squeeze(), vmin=-vabsmax, vmax=vabsmax, cmap="Spectral", zorder=2
+    cf_smb_model = axes[0].pcolormesh(
+        lons_model,
+        lats_model,
+        msmb.squeeze(),
+        vmin=-vabsmax,
+        vmax=vabsmax,
+        cmap="Spectral",
+        zorder=2,
+        transform=tform,
+    )
+
+    lxcg.annotate_plot(
+        axes[0],
+        icesheet="gis",
+        gridline_args=GRIDLINE_ARGS,
+    )
+
+    lxcg.add_colorbar(
+        cf_smb_model,
+        fig,
+        axes[0],
+        "Surface mass balance (kg m$^{-2}$ a$^{-1}$)",
+        cbar_span=False,
+        ndsets=1,
     )
-    cbar = pmap.colorbar(smb, location="bottom", pad="5%")
-    cbar.set_label("Surface mass balance (kg m$^{-2}$ a$^{-1}$)")
 
     lat_obs = smb_avg["Y"].values
     lon_obs = smb_avg["X"].values
-    xobs, yobs = pmap(lon_obs, lat_obs)
     smbobs = smb_avg.b
-    _ = pmap.scatter(
-        xobs,
-        yobs,
+
+    _ = axes[0].scatter(
+        lon_obs,
+        lat_obs,
         c=smbobs,
-        vmin=-1500,
-        vmax=1500,
+        vmin=-vabsmax,
+        vmax=vabsmax,
         marker="o",
         edgecolor="black",
         cmap="Spectral",
         zorder=3,
+        transform=tform,
     )
 
     plt.tight_layout()
@@ -244,34 +202,36 @@ def plot_ib_spatial(args, config):
     img_list = []
     _, _, ib_file = preproc.ib_outfile(config)
     ice_bridge = pd.read_csv(ib_file)
-    # lons_model, lats_model, msmb = load_model_data(args, config)
-    fig = plt.figure(figsize=(12, 12))
-    axis = fig.add_subplot(1, 1, 1)
-
-    # lon_0 = lons_model.mean()
-    # lat_0 = lats_model.mean()
-    lon_0 = -40.591
-    lat_0 = 71.30
 
-    # print(f"LON0: {lon_0} LAT0: {lat_0}")
-    pmap = gen_map(lon_0, lat_0)
-    annotate_map(pmap, axis)
+    # Plot the IceBridge data
+    tform = ccrs.PlateCarree()
+    _, _, ib_file = preproc.ib_outfile(config)
+    ice_bridge = pd.read_csv(ib_file)
+    fig, axes, proj = lxcg.get_figure(1, icesheet="gis")
 
     lat_obs = ice_bridge["Y"].values
     lon_obs = ice_bridge["X"].values
-    xobs, yobs = pmap(lon_obs, lat_obs)
-    # xmod, ymod = m(lons_model, lats_model)
 
     smbobs = ice_bridge["b"].values
-    obs = pmap.scatter(
-        xobs, yobs, c=smbobs, marker="o", cmap="viridis", zorder=3, lw=0, ax=axis
+    cf_obs = axes[0].scatter(
+        lon_obs,
+        lat_obs,
+        c=smbobs,
+        marker="o",
+        cmap="Spectral",
+        zorder=3,
+        lw=0,
+        transform=tform,
+    )
+    lxcg.annotate_plot(axes[0], icesheet="gis", gridline_args=GRIDLINE_ARGS)
+    lxcg.add_colorbar(
+        cf_obs,
+        fig,
+        axes[0],
+        "Surface mass balance (kg m$^{-2}$ a$^{-1}$)",
+        cbar_span=False,
+        ndsets=1,
     )
-    # _map = pmap.contour(xmod, ymod, climo_data[0], colors="k")
-    # _map = pmap.contour(xmod, ymod, climo_data, color="k")
-
-    cbar = pmap.colorbar(obs, location="bottom", pad="5%", ax=axis)
-    cbar.set_label("Surface mass balance (kg m$^-2$ a$^{-1}$)")
-
     plt.tight_layout()
     img_file = os.path.join(args.out, "IB_spatial.png")
     plt.savefig(img_file)
@@ -290,30 +250,33 @@ def plot_ib_spatial(args, config):
     )
     img_list.append(img_elem)
 
-    fig = plt.figure(figsize=(12, 12))
-    axis = fig.add_subplot(1, 1, 1)
-    annotate_map(pmap, axis)
-
-    lat_obs = ice_bridge["Y"].values
-    lon_obs = ice_bridge["X"].values
-    xobs, yobs = pmap(lon_obs, lat_obs)
-    smbobs = ice_bridge["mod_b"].values - ice_bridge["b"].values
-    obs = pmap.scatter(
-        xobs,
-        yobs,
-        c=smbobs,
+    # Plot IB - Model difference
+    fig, axes, proj = lxcg.get_figure(1, icesheet="gis")
+    smbobs_diff = ice_bridge["mod_b"].values - ice_bridge["b"].values
+    cf_diff = axes[0].scatter(
+        lon_obs,
+        lat_obs,
+        c=smbobs_diff,
         marker="o",
         cmap="RdBu",
         zorder=3,
         vmin=-200,
         vmax=200,
         lw=0,
-        ax=axis,
+        transform=tform,
     )
-
-    cbar = pmap.colorbar(obs, location="bottom", pad="5%")
-    cbar.set_label(
-        "Difference in surface mass balance \n (Model - IceBridge) (kg m$^-2$ a$^{-1}$)"
+    lxcg.annotate_plot(
+        axes[0],
+        icesheet="gis",
+        gridline_args=GRIDLINE_ARGS,
+    )
+    lxcg.add_colorbar(
+        cf_diff,
+        fig,
+        axes[0],
+        "Surface mass balance difference (kg m$^{-2}$ a$^{-1}$)",
+        cbar_span=False,
+        ndsets=1,
     )
 
     plt.tight_layout()
@@ -340,6 +303,8 @@ def plot_metadata(args, config):
     """
     Create plot of basin locations, ice bridge transects, and core locations.
     """
+    tform = ccrs.PlateCarree()
+
     img_list = []
     _, _, ib_file = preproc.ib_outfile(config)
     _, _, _, core_file = preproc.core_file(config)
@@ -348,11 +313,11 @@ def plot_metadata(args, config):
     except pd.errors.EmptyDataError:
         print(ib_file)
         raise
+
     smb_avg = pd.read_csv(core_file)
     zwally_data = pd.read_csv(Path(config["preproc_dir"], config["zwally_file"]))
 
-    lons_model, lats_model, smb_model = load_model_data(args, config, regrid=False)
-    plt.figure(figsize=(12, 12))
+    lons_model, lats_model, smb_model = load_model_data(config, regrid=False)
 
     forcolors = c.ListedColormap(
         [
@@ -368,13 +333,7 @@ def plot_metadata(args, config):
         ]
     )
 
-    # This will be the center of our map
-    # lon_0 = lons_model.mean()
-    # lat_0 = lats_model.mean()
-    lon_0 = -40.591
-    lat_0 = 71.308
-    pmap = gen_map(lon_0, lat_0)
-    annotate_map(pmap)
+    fig, axes, proj = lxcg.get_figure(1, icesheet="gis")
 
     # Read in the zwally basins and mask out model cells that are missing a basin designation
     basins = np.floor(zwally_data.zwally_basin.values)
@@ -384,15 +343,15 @@ def plot_metadata(args, config):
     mbasins = ma.masked_invalid(basins)
 
     # Plotting the basins pseudocolor
-    if lons_model.ndim == 1 and lons_model.shape[0] < 1441:
+    if lons_model.ndim == 1 and "elm" in config["meta"]["Model"][0].lower():
         lons_model, lats_model = np.meshgrid(lons_model, lats_model)
-    elif lons_model.shape[0] >= 1441:
+    elif "mali" in config["meta"]["Model"][0].lower():
         lons_model, lats_model, mbasins = mali_to_contour(
             lons_model, lats_model, mbasins
         )
-
-    xi, yi = pmap(lons_model.squeeze(), lats_model.squeeze())
-    _ = pmap.pcolormesh(xi, yi, mbasins, cmap=forcolors, zorder=2)
+    _ = axes[0].pcolormesh(
+        lons_model, lats_model, mbasins, cmap=forcolors, zorder=2, transform=tform
+    )
 
     basin_labels = {
         "1": (-48, 80.5),
@@ -405,43 +364,76 @@ def plot_metadata(args, config):
         "8": (-55, 75),
     }
     for lbl, loc in basin_labels.items():
-        xi, yi = pmap(loc[0], loc[1])
-        plt.text(xi, yi, lbl, fontsize=16, fontweight="bold", color="#FF7900")
+        # xi, yi = pmap(loc[0], loc[1])
+        plt.text(
+            loc[0],
+            loc[1],
+            lbl,
+            fontsize=16,
+            fontweight="bold",
+            color="#FF7900",
+            transform=tform,
+        )
 
     # Adding in firn/core measurement locations. Size by the number of years in the record
     lat_obs = smb_avg["Y"].values
     lon_obs = smb_avg["X"].values
-    xobs, yobs = pmap(lon_obs, lat_obs)
-    smb_avg.loc[smb_avg["nyears"] > 50] = 50
-    smb_avg.loc[smb_avg["nyears"] < 5] = 5
-    _ = pmap.scatter(
-        xobs, yobs, marker="o", edgecolor="black", s=4 * smb_avg["nyears"], zorder=4
+    # xobs, yobs = pmap(lon_obs, lat_obs)
+    smb_avg[smb_avg["nyears"] > 50].loc[:, "nyears"] = 50
+    smb_avg[smb_avg["nyears"] < 5].loc[:, "nyears"] = 5
+
+    _ = axes[0].scatter(
+        lon_obs,
+        lat_obs,
+        marker="o",
+        edgecolor="black",
+        s=4 * smb_avg["nyears"],
+        zorder=4,
+        transform=tform,
     )
 
     # Color the ablation zone (PROMICE) measurements yellow
     smb_promice = smb_avg[smb_avg.source == "promice"].copy()
     lat_obs = smb_promice["Y"].values
     lon_obs = smb_promice["X"].values
-    xobs, yobs = pmap(lon_obs, lat_obs)
-    smb_promice.loc[smb_promice["nyears"] > 50] = 50
-    smb_promice.loc[smb_promice["nyears"] < 5] = 5
-    _ = pmap.scatter(
-        xobs,
-        yobs,
+
+    smb_promice[smb_promice["nyears"] > 50].loc[:, "nyears"] = 50
+    smb_promice[smb_promice["nyears"] < 5].loc[:, "nyears"] = 5
+
+    _ = axes[0].scatter(
+        lon_obs,
+        lat_obs,
         marker="^",
         color="yellow",
         edgecolor="black",
         s=4 * smb_promice["nyears"],
         zorder=4,
+        transform=tform,
     )
 
     # Add IceBridge transects
+    _, _, ib_file = preproc.ib_outfile(config)
+    ice_bridge = pd.read_csv(ib_file)
     lat_obs = ice_bridge["Y"].values
     lon_obs = ice_bridge["X"].values
-    xobs, yobs = pmap(lon_obs, lat_obs)
-    _ = pmap.scatter(xobs, yobs, marker="o", lw=0, zorder=3, s=3, color="white")
+    _ = axes[0].scatter(
+        lon_obs,
+        lat_obs,
+        marker="o",
+        lw=0,
+        zorder=3,
+        s=2,
+        color="white",
+        transform=tform,
+    )
 
+    lxcg.annotate_plot(
+        axes[0],
+        icesheet="gis",
+        gridline_args=GRIDLINE_ARGS,
+    )
     plt.tight_layout()
+
     img_file = os.path.join(args.out, "plot_meta_old.png")
     plt.savefig(img_file)
     plt.close()
diff --git a/requirements.txt b/requirements.txt
index 632739a..517ee0a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -10,7 +10,6 @@
   jinja2
   pylint
   matplotlib
-  basemap
   netcdf4
   pandas
   nco

From ea094bebbdcefae0d504dd15c22b09a073e596b4 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 11:41:47 -0800
Subject: [PATCH 17/32] Fix timeseries directory template

---
 config/template_r05/all.jinja | 23 ++++++++-------
 lex/generate_cfg.py           | 54 +++++++++++++++++++----------------
 2 files changed, 41 insertions(+), 36 deletions(-)

diff --git a/config/template_r05/all.jinja b/config/template_r05/all.jinja
index d2aa3dc..e59c727 100644
--- a/config/template_r05/all.jinja
+++ b/config/template_r05/all.jinja
@@ -36,16 +36,7 @@ common_smb: &common_smb
     References:
       - {{ livvproj_dir }}/data/smb/smb_icecores.bib
       - {{ livvproj_dir }}/data/livvkit.bib
-    timeseries_dirs:
-      {
-        model: "{{ model_ts_dir }}",
-        dset_a: "{{ racmo_root_dir }}/ts",
-      }
-    ts_file_patterns:
-      {
-        model: "{{ case_id }}.nc",
-        dset_a: "{_var}_{icesheet}_{year_s}01_{year_e}12.nc",
-      }
+
 
 common_energy: &common_energy
   desc: Surface energy balance component {component}{comment} from {data_var_names}
@@ -64,6 +55,16 @@ common_racmo: &common_racmo
     in_dirs: { dset_a: "{{ racmo_root_dir }}/clm/{_var}" }
     file_patterns:
       { dset_a: "{_var}_{icesheet}_{season}_{sea_s}_{sea_e}_climo.nc" }
+    timeseries_dirs:
+      {
+        model: "{{ model_ts_dir }}",
+        dset_a: "{{ racmo_root_dir }}/ts",
+      }
+    ts_file_patterns:
+      {
+        model: "{{ case_id }}.nc",
+        dset_a: "{_var}_{icesheet}_{year_s}01_{year_e}12.nc",
+      }
 
 common_era5: &common_era5
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_era5.nc
@@ -744,4 +745,4 @@ Energy_Balance_CERES_AIS:
   mask_ocean: { model_native: false, model_remap: true, dset_a: true }
   data_vars: *common_ceres_energy_vars
 {% endif %}
-{% endif %}
\ No newline at end of file
+{% endif %}
diff --git a/lex/generate_cfg.py b/lex/generate_cfg.py
index 19f8b3f..e98f472 100644
--- a/lex/generate_cfg.py
+++ b/lex/generate_cfg.py
@@ -1,14 +1,17 @@
-"""Generate a LIVVkit Extensions (LEX) config based on template information and defaults.
-"""
+"""Generate a LIVVkit Extensions (LEX) config based on template information and defaults."""
+
+import argparse
 from pathlib import Path
+
 import jinja2
-import argparse
-ALL_SHEETS="run_gis,run_ais"
+
+ALL_SHEETS = "run_gis,run_ais"
 ALL_SETS = "set_cmb,set_smb,set_energy_racmo,set_energy_era5,set_energy_merra2,set_energy_ceres"
 
+
 def args():
     parser = argparse.ArgumentParser(
-    description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter
+        description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter
     )
 
     parser.add_argument(
@@ -22,7 +25,7 @@ def args():
         "-m",
         type=str,
         default="pm-cpu",
-        help="Name of the machine to be used. [pm-cpu, chrys]"
+        help="Name of the machine to be used. [pm-cpu, chrys]",
     )
     parser.add_argument(
         "--case",
@@ -34,13 +37,10 @@ def args():
         "--casedir",
         "-d",
         type=Path,
-        help="Output directory where climatology files for `case` are stored"
+        help="Output directory where climatology files for `case` are stored",
     )
     parser.add_argument(
-        "--cfg_out",
-        "-o",
-        type=Path,
-        help="Output directory for config file."
+        "--cfg_out", "-o", type=Path, help="Output directory for config file."
     )
 
     parser.add_argument(
@@ -51,7 +51,7 @@ def args():
         help=(
             "Analysis sets to run: set_cmb, set_smb, set_energy_racmo, "
             "set_energy_era5, set_energy_merra2, set_energy_ceres"
-        )
+        ),
     )
 
     parser.add_argument(
@@ -62,14 +62,16 @@ def args():
         help=(
             "Comma separated icesheets to analyse (run_ais for Antarctica,"
             " run_gis for Greenland)"
-        )
+        ),
     )
 
     return parser.parse_args()
 
 
 def gen_cfg(cfg_template, params, cfg_out):
-    jenv = jinja2.Environment(loader=jinja2.FileSystemLoader(cfg_template.resolve().parent))
+    jenv = jinja2.Environment(
+        loader=jinja2.FileSystemLoader(cfg_template.resolve().parent)
+    )
     template = jenv.get_template(cfg_template.name)
 
     cfg = template.render(**params)
@@ -84,8 +86,7 @@ def gen_cfg(cfg_template, params, cfg_out):
 
 
 def parse_sets(sheets, sets):
-    """Parse comma separated strings of sets / icesheets to analyse.
-    """
+    """Parse comma separated strings of sets / icesheets to analyse."""
 
     params = {}
     if sheets.lower() == "run_all":
@@ -108,29 +109,32 @@ def main():
     cl_args = args()
     defaults = {
         "chrys": {
-            "e3sm_diags_data_dir": Path("/lcrc/group/e3sm/diagnostics/observations/Atm/"),
+            "e3sm_diags_data_dir": Path(
+                "/lcrc/group/e3sm/diagnostics/observations/Atm/"
+            ),
             "livvproj_dir": Path("/lcrc/group/e3sm/livvkit"),
-            "ts_dir": Path("/lcrc/group/e3sm/ac.zender/scratch/livvkit"),
+            "model_ts_dir": Path("/lcrc/group/e3sm/ac.zender/scratch/livvkit"),
             "grid_dir": Path("/lcrc/group/e3sm/zender/grids"),
         },
         "pm-cpu": {
-            "e3sm_diags_data_dir": Path("/global/cfs/cdirs/e3sm/e3sm_diags/obs_for_e3sm_diags"),
+            "e3sm_diags_data_dir": Path(
+                "/global/cfs/cdirs/e3sm/e3sm_diags/obs_for_e3sm_diags"
+            ),
             "livvproj_dir": Path("/global/cfs/cdirs/e3sm/livvkit"),
-            "ts_dir": Path("/global/cfs/projectdirs/e3sm/zender/livvkit"),
+            "model_ts_dir": Path("/global/cfs/projectdirs/e3sm/zender/livvkit"),
             "grid_dir": Path("/global/cfs/cdirs/e3sm/zender/grids"),
-            "racmo_root_dir": Path("/global/cfs/cdirs/fanssie/racmo/2.4.1")
-        }
-        
+            "racmo_root_dir": Path("/global/cfs/cdirs/fanssie/racmo/2.4.1"),
+        },
     }
     params = {
         **defaults[cl_args.mach],
         "case_id": cl_args.case,
         "case_out_dir": cl_args.casedir,
-        **parse_sets(cl_args.icesheets, cl_args.sets)
+        **parse_sets(cl_args.icesheets, cl_args.sets),
     }
     out_cfg = Path(cl_args.cfg_out, cl_args.case, "livvkit.yml")
     gen_cfg(cl_args.template, params, out_cfg)
 
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()

From 835c525c36d48fde78820e71f04661309ce0846e Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 11:42:53 -0800
Subject: [PATCH 18/32] Fix formatting

---
 lex/annual_cycle.py     |  1 +
 lex/common.py           | 28 ++++++++++++++--------------
 lex/smb/smb_icecores.py | 26 +++++++++++++-------------
 lex/time_series_plot.py |  6 ++++--
 tests/test_common.py    | 29 +++++++++++++++++++++--------
 5 files changed, 53 insertions(+), 37 deletions(-)

diff --git a/lex/annual_cycle.py b/lex/annual_cycle.py
index c008def..d55b160 100644
--- a/lex/annual_cycle.py
+++ b/lex/annual_cycle.py
@@ -17,6 +17,7 @@
 Sign of component based on its contribution to total.
 """
 
+
 def main(args, config):
     model_data = xr.open_mfdataset(
         [config["climo_remap"].format(clim=f"{mon:02d}") for mon in range(1, 13)],
diff --git a/lex/common.py b/lex/common.py
index b66ffcd..6bf86a5 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -18,8 +18,8 @@
 from cartopy import feature as cfeature
 from livvkit import elements as el
 from livvkit.util.LIVVDict import LIVVDict
-from numpy import ma
 from loguru import logger
+from numpy import ma
 
 import lex.utils as lxu
 
@@ -391,30 +391,30 @@ def load_timeseries_data(config):
         for _var in config["data_vars"]:
             files[overs].extend(gen_file_list_timeseries(config, _var[overs], overs))
 
-        if  len(set(files[overs]))== 1:
+        if len(set(files[overs])) == 1:
             files[overs] = files[overs][0]
             _nfiles = 1
         else:
             _nfiles = len(set(files[overs]))
-        _dsname = config['dataset_names'].get(
-            overs, config['dataset_names'].get('model_native')
-        )
-        logger.info(
-            f"LOAD TIMESERIES DATA FOR {overs}: {_dsname} NFILES: {_nfiles}"
+        _dsname = config["dataset_names"].get(
+            overs, config["dataset_names"].get("model_native")
         )
+        logger.info(f"LOAD TIMESERIES DATA FOR {overs}: {_dsname} NFILES: {_nfiles}")
         try:
             obs_data[overs] = xr.open_mfdataset(files[overs]).squeeze().load()
         except (xr.MergeError, ValueError):
             if isinstance(files[overs], Path):
                 obs_data[overs] = xr.open_dataset(files[overs]).squeeze().load()
             else:
-                obs_data[overs] = xr.open_mfdataset(
-                    files[overs],
-                    combine="nested",
-                ).squeeze().load()
-        logger.info(
-            f"DONE - LOAD TIMESERIES DATA FOR {overs}: {_dsname}"
-        )
+                obs_data[overs] = (
+                    xr.open_mfdataset(
+                        files[overs],
+                        combine="nested",
+                    )
+                    .squeeze()
+                    .load()
+                )
+        logger.info(f"DONE - LOAD TIMESERIES DATA FOR {overs}: {_dsname}")
 
     return obs_data
 
diff --git a/lex/smb/smb_icecores.py b/lex/smb/smb_icecores.py
index 71b510c..2c6f801 100644
--- a/lex/smb/smb_icecores.py
+++ b/lex/smb/smb_icecores.py
@@ -46,8 +46,8 @@
     import smb.plot_spatial as plt_spatial
     import smb.preproc as preproc
     import smb.utils as utils
-from loguru import logger
 
+from loguru import logger
 
 PAGE_DOCS = {
     "gis": """Validation of the Greenland Ice Sheet (GrIS) surface mass balance by
@@ -102,34 +102,34 @@ def run(name, config):
     statistic_img = []
     timeseries_img = []
     if "smb_cf_file" in config and "smb_mo_file" in config and "ib_file" in config:
-        logger.info(f"PLOT SPATIAL METADATA")
+        logger.info("PLOT SPATIAL METADATA")
         spatial_img.extend(plt_spatial.plot_metadata(args, config))
-        logger.info(f"DONE - PLOT SPATIAL METADATA")
+        logger.info("DONE - PLOT SPATIAL METADATA")
 
     if "smb_cf_file" in config and "smb_mo_file" in config:
-        logger.info(f"PLOT SPATIAL CORE DATA")
+        logger.info("PLOT SPATIAL CORE DATA")
         spatial_img.extend(plt_spatial.plot_core(args, config))
         transects = c_transects.main(args, config)
         statistic_img.extend(transects[3:])
         statistic_img.extend(IB_scatter.main(args, config))
         statistic_img.extend(c_hists.main(args, config))
-        logger.info(f"DONE - PLOT SPATIAL CORE DATA")
+        logger.info("DONE - PLOT SPATIAL CORE DATA")
 
     if "ib_file" in config:
-        logger.info(f"PLOT SPATIAL IB DATA")
+        logger.info("PLOT SPATIAL IB DATA")
         spatial_img.extend(plt_spatial.plot_ib_spatial(args, config))
         statistic_img.extend(IB_hist.main(args, config))
-        logger.info(f"DONE - PLOT SPATIAL IB DATA")
+        logger.info("DONE - PLOT SPATIAL IB DATA")
 
     if "smb_cf_file" in config and "smb_mo_file" in config:
-        logger.info(f"PLOT STATSTICAL DATA")
+        logger.info("PLOT STATSTICAL DATA")
         statistic_img.extend(transects[:3])
-        logger.info(f"DONE - PLOT STATSTICAL DATA")
+        logger.info("DONE - PLOT STATSTICAL DATA")
 
     if "timeseries_dirs" in config:
-        logger.info(f"PLOT TIMESERIES DATA")
+        logger.info("PLOT TIMESERIES DATA")
         timeseries_img.extend(time_series_plot.main(args, config))
-        logger.info(f"DONE - PLOT TIMESERIES DATA")
+        logger.info("DONE - PLOT TIMESERIES DATA")
 
     seasons = ["ANN", "DJF", "MAM", "JJA", "SON"]
     seasonal_components = {}
@@ -148,9 +148,9 @@ def _format_table(x):
             seasonal_components[season] = []
 
             if season == "ANN":
-                logger.info(f"PLOT ANNUAL CYCLE DATA")
+                logger.info("PLOT ANNUAL CYCLE DATA")
                 seasonal_components[season].extend(annual_cycle.main(args, config))
-                logger.info(f"DONE - PLOT ANNUAL CYCLE DATA")
+                logger.info("DONE - PLOT ANNUAL CYCLE DATA")
 
             seasonal_components[season].extend(_img)
             seasonal_tables[season] = el.Table(
diff --git a/lex/time_series_plot.py b/lex/time_series_plot.py
index d59bf9b..1babcfc 100644
--- a/lex/time_series_plot.py
+++ b/lex/time_series_plot.py
@@ -12,10 +12,10 @@
 import numpy as np
 import xarray as xr
 from livvkit import elements as el
+from loguru import logger
 
 import lex.common as lxc
 import lex.utils as lxu
-from loguru import logger
 
 IMG_GROUP = "Timeseries"
 
@@ -261,7 +261,9 @@ def main(args, config):
             relative_to="",
         )
         img_elem.append(_img_elem)
-        logger.info(f"   DONE - PLOTTING {config.get('icesheet', '')} TS: {data_var['title']}")
+        logger.info(
+            f"   DONE - PLOTTING {config.get('icesheet', '')} TS: {data_var['title']}"
+        )
     # assemble_outdata(args, config, "model", model_aavg, ts_data, _aavg_units)
     # assemble_outdata(args, config, "dset_a", obs_aavg, ts_data, _aavg_units)
 
diff --git a/tests/test_common.py b/tests/test_common.py
index 076d81e..83b56a1 100644
--- a/tests/test_common.py
+++ b/tests/test_common.py
@@ -1,7 +1,9 @@
 import numpy as np
 import xarray as xr
+
 import lex.common as lxc
 
+
 def test_img_file_prefix():
     config_1 = {"module": "energy.py"}
     config_2 = {"EMPTY": "empty.py"}
@@ -14,28 +16,39 @@ def test_img_file_prefix():
 
 
 def test_check_longitude():
-    lons = np.arange(-180, 180, 45.)
+    lons = np.arange(-180, 180, 45.0)
     data = {"lon": lons}
     b_coord = "longitude"
     data_b = {b_coord: lons}
     assert lxc.check_longitude(data) == {"lon": lons}
     assert lxc.check_longitude(data_b, lon_coord=b_coord) == {b_coord: lons}
 
-    lons_2 = np.arange(0, 360, 45.)
-    _shift_lons = np.array([   0.,   45.,   90.,  135., -180., -135.,  -90.,  -45.])
+    lons_2 = np.arange(0, 360, 45.0)
+    _shift_lons = np.array([0.0, 45.0, 90.0, 135.0, -180.0, -135.0, -90.0, -45.0])
     _check = lxc.check_longitude({"lon": lons_2})
     assert np.all(_check["lon"] == _shift_lons), "SHIFTED LONGITUDE DOES NOT MATCH"
 
-    test_data = [0, 1, 2, 3, 4, 5, 6, 7,]
+    test_data = [
+        0,
+        1,
+        2,
+        3,
+        4,
+        5,
+        6,
+        7,
+    ]
     test_data_shift = [4, 5, 6, 7, 0, 1, 2, 3]
-    _ds1 = _ds1 = xr.Dataset(data_vars={"x": (["lon"], test_data)}, coords={"lon": lons_2})
+    _ds1 = _ds1 = xr.Dataset(
+        data_vars={"x": (["lon"], test_data)}, coords={"lon": lons_2}
+    )
     _check = lxc.check_longitude(_ds1)
-    assert isinstance(_check, xr.Dataset), "CHECK_LON DID NOT RETURN XARRAY.DATASET" 
+    assert isinstance(_check, xr.Dataset), "CHECK_LON DID NOT RETURN XARRAY.DATASET"
     assert (_check["lon"] == lons).all(), "LONGITUDE NOT SHIFTED PROPERLY"
     assert (_check["x"] == test_data_shift).all(), "DATA NOT ROLLED PROPERLY"
 
     _da1 = xr.DataArray(test_data, coords={"lon": lons_2}, dims=("lon",))
     _check = lxc.check_longitude(_da1)
-    assert isinstance(_check, xr.DataArray), "CHECK_LON DID NOT RETURN XARRAY.DATAARRAY" 
+    assert isinstance(_check, xr.DataArray), "CHECK_LON DID NOT RETURN XARRAY.DATAARRAY"
     assert (_check["lon"] == lons).all()
-    assert (_check.values == test_data_shift).all()
\ No newline at end of file
+    assert (_check.values == test_data_shift).all()

From ac1fa761db2e177b6117e0481283cb53e95e0889 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 13:04:24 -0800
Subject: [PATCH 19/32] Use correct mask per icesheet

---
 config/template_r05/all.jinja | 87 +++++++++++++++--------------------
 lex/annual_cycle.py           |  4 +-
 lex/common.py                 |  7 ++-
 lex/compare_gridded.py        |  4 +-
 lex/time_series_plot.py       |  4 +-
 5 files changed, 50 insertions(+), 56 deletions(-)

diff --git a/config/template_r05/all.jinja b/config/template_r05/all.jinja
index e59c727..55cc3c6 100644
--- a/config/template_r05/all.jinja
+++ b/config/template_r05/all.jinja
@@ -19,16 +19,6 @@ common_smb: &common_smb
     smbv: QICE
     maskv: gis_mask2
     smbscale: 31536000
-    core_year_s: 1980
-    core_year_e: 2021
-    ib_year_e: 1987-1976
-    ib_year_s: 2014-2004
-    preprocess: []
-    preproc_dir: {{ livvproj_dir }}/data/smb/processed
-    zwally_file: model_zwally_basins_elm_r05.csv
-    ib_file: IceBridge_modelXY_elm{}_r05.csv
-    smb_cf_file: SMB_CoreFirnEstimates_elm{}_r05.csv
-    smb_mo_file: SMB_Obs_Model_elm{}_r05.csv
     cmap: BrBG
     cmap_diff: BrBG
     clim_even: 1
@@ -49,22 +39,22 @@ common_energy: &common_energy
   cmap_diff: RdBu_r
 
 common_racmo: &common_racmo
-    clim_years:
-      dset_a: { year_s: 1980, year_e: 2020 }
-    dataset_names: { model: ELM, dset_a: RACMO 2.4 }
-    in_dirs: { dset_a: "{{ racmo_root_dir }}/clm/{_var}" }
-    file_patterns:
-      { dset_a: "{_var}_{icesheet}_{season}_{sea_s}_{sea_e}_climo.nc" }
-    timeseries_dirs:
-      {
-        model: "{{ model_ts_dir }}",
-        dset_a: "{{ racmo_root_dir }}/ts",
-      }
-    ts_file_patterns:
-      {
-        model: "{{ case_id }}.nc",
-        dset_a: "{_var}_{icesheet}_{year_s}01_{year_e}12.nc",
-      }
+  clim_years:
+    dset_a: { year_s: 1980, year_e: 2020 }
+  dataset_names: { model: ELM, dset_a: RACMO 2.4 }
+  in_dirs: { dset_a: "{{ racmo_root_dir }}/clm/{_var}" }
+  file_patterns:
+    dset_a: "{_var}_{icesheet}_{season}_{sea_s}_{sea_e}_climo.nc"
+  timeseries_dirs:
+    model: "{{ model_ts_dir }}"
+    dset_a: "{{ racmo_root_dir }}/ts"
+  ts_file_patterns:
+    model: "{{ case_id }}.nc"
+    dset_a: "{_var}_{icesheet}_{year_s}01_{year_e}12.nc"
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_rcm.nc
+    model: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_rcm.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r05.nc
 
 common_era5: &common_era5
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_era5.nc
@@ -75,19 +65,19 @@ common_era5: &common_era5
     dset_a: { year_s: 1979, year_e: 2019}
   in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/ERA5}
   file_patterns: {dset_a: 'ERA5_{season}_{sea_s}_{sea_e}_climo.nc'}
-  masks: {
-    dset_a: {{ livvproj_dir }}/grids/msk_gis_rcm_r025_regrid_era5_traave_20250213.nc,
-    model_remap: {{ livvproj_dir }}/grids/msk_gis_rcm_r025_regrid_era5_traave_20250213.nc,
-    model_native: {{ livvproj_dir }}/grids/msk_gis_rcm_r05.nc
-  }
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_era5.traave.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_era5.traave.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r05.nc
 
 common_merra: &common_merra
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_merra2.nc
   in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/MERRA2}
   file_patterns: {dset_a: 'MERRA2_{season}_{sea_s}_{sea_e}_climo.nc'}
-  masks: {dset_a: {{ livvproj_dir }}/grids/msk_gis_r025_remap_merra2.traave.20250124.nc,
-    model_remap: {{ livvproj_dir }}/grids/msk_gis_r025_remap_merra2.traave.20250124.nc,
-    model_native: {{ livvproj_dir }}/grids/msk_gis_rcm_r05.nc}
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_merra2.traave.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_merra2.traave.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r05.nc
   dataset_names: {model_remap: 'ELM [MERRA2 Grid]', model_native: ELM, dset_a: MERRA2}
   aavg_sort: [ELM, 'ELM [MERRA2 Grid]', MERRA2]
   scales: {model: 1, dset_a: 1}
@@ -107,29 +97,28 @@ common_ceres: &common_ceres
   file_patterns:
     dset_a: ceres_ebaf_surface_v4.1_{season}_{sea_s}_{sea_e}_climo.nc
   masks:
-    dset_a: {{ livvproj_dir }}/grids/msk_gis_r025_remap_cmip6.traave.20250124.nc
-    model_native: {{ grid_dir }}/msk_gis_rcm_r05.nc
-    model_remap: {{ livvproj_dir }}/grids/msk_gis_r025_remap_cmip6.traave.20250124.nc
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_cmip6.traave.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_cmip6.traave.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r05.nc
 
 common_racmo_gis: &common_racmo_gis
+  core_year_s: 1980
+  core_year_e: 2021
+  ib_year_e: 1987-1976
+  ib_year_s: 2014-2004
+  preprocess: []
+  preproc_dir: {{ livvproj_dir }}/data/smb/processed
+  zwally_file: model_zwally_basins_elm_r05.csv
+  ib_file: IceBridge_modelXY_elm{}_r05.csv
+  smb_cf_file: SMB_CoreFirnEstimates_elm{}_r05.csv
+  smb_mo_file: SMB_Obs_Model_elm{}_r05.csv
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_rcmgis.nc
   icesheet: gis
-  masks:
-    {
-        dset_a: {{ grid_dir }}/msk_gis_r025_rcm.nc,
-        model: {{ grid_dir }}/msk_gis_r025_rcm.nc,
-        model_native: {{ livvproj_dir }}/grids/msk_gis_rcm_r05.nc,
-      }
 
 common_racmo_ais: &common_racmo_ais
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_rcmais.nc
   icesheet: ais
-  masks:
-    {
-        dset_a: {{ grid_dir }}/msk_ais_r025_rcm.nc,
-        model: {{ grid_dir }}/msk_ais_r025_rcm.nc,
-        model_native: {{ livvproj_dir }}/grids/msk_ais_rcm_r05.nc,
-      }
+
 common_racmo_smb_vars: &common_racmo_smb_vars
   # Surface mass balance variables for dset_a: RACMO 2.4, model: ELM
   # Each field must have:
diff --git a/lex/annual_cycle.py b/lex/annual_cycle.py
index d55b160..b6e6a07 100644
--- a/lex/annual_cycle.py
+++ b/lex/annual_cycle.py
@@ -79,7 +79,7 @@ def main(args, config):
                 lxc.area_avg(
                     _obs_in[_vers],
                     {},
-                    area_file=config["masks"][_vers],
+                    area_file=config["masks"][_vers].format(icesheet=config["icesheet"]),
                     area_var="area",
                     mask_var="Icemask",
                     sum_out=_do_sum,
@@ -88,7 +88,7 @@ def main(args, config):
         model_aavg[data_var["title"]], _, _, _ = lxc.area_avg(
             _model_plt,
             {},
-            area_file=config["masks"]["model"],
+            area_file=config["masks"]["model"].format(icesheet=config["icesheet"]),
             area_var="area",
             mask_var="Icemask",
             sum_out=_do_sum,
diff --git a/lex/common.py b/lex/common.py
index 6bf86a5..f9695f1 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -481,7 +481,12 @@ def area_avg(
         Input `data` masked by `isheet_mask`
 
     """
-    area_data = xr.open_dataset(area_file)
+    try:
+        area_data = xr.open_dataset(area_file)
+    except ValueError as err:
+        logger.error(f"INCOMPATABLE FILE {area_file}")
+        raise
+
     area_data = check_longitude(area_data)
     if mask_file is None:
         mask_data = area_data
diff --git a/lex/compare_gridded.py b/lex/compare_gridded.py
index e598ec7..bfa30fb 100644
--- a/lex/compare_gridded.py
+++ b/lex/compare_gridded.py
@@ -286,7 +286,7 @@ def main(args, config, sea="ANN"):
             all_aavg[_vers], mask_r[_vers], area_r[_vers], _ = lxc.area_avg(
                 _plt_data[_vers],
                 config,
-                area_file=config["masks"][_vers],
+                area_file=config["masks"][_vers].format(icesheet=config["icesheet"]),
                 area_var="area",
                 mask_var="Icemask",
                 sum_out=_do_sum,
@@ -302,7 +302,7 @@ def main(args, config, sea="ANN"):
             diffs_aavg[_diffname], _, _, _ = lxc.area_avg(
                 diffs[_diffname],
                 config,
-                area_file=config["masks"][_ds2],
+                area_file=config["masks"][_ds2].format(icesheet=config["icesheet"]),
                 area_var="area",
                 mask_var="Icemask",
                 sum_out=_do_sum,
diff --git a/lex/time_series_plot.py b/lex/time_series_plot.py
index 1babcfc..bea22e6 100644
--- a/lex/time_series_plot.py
+++ b/lex/time_series_plot.py
@@ -116,7 +116,7 @@ def main(args, config):
                 lxc.area_avg(
                     _obs_in[_vers],
                     {},
-                    area_file=config["masks"][_vers],
+                    area_file=config["masks"][_vers].format(icesheet=config["icesheet"]),
                     area_var="area",
                     mask_var="Icemask",
                     sum_out=_do_sum,
@@ -126,7 +126,7 @@ def main(args, config):
         model_aavg[data_var["title"]], _, _, _ = lxc.area_avg(
             _model_plt,
             {},
-            area_file=config["masks"]["model_native"],
+            area_file=config["masks"]["model_native"].format(icesheet=config["icesheet"]),
             area_var="area",
             mask_var="Icemask",
             sum_out=_do_sum,

From 3494778b36c59433bf484154234947177a2ded83 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 18 Dec 2025 14:05:22 -0800
Subject: [PATCH 20/32] Add high-res template, update run_livv for pm-cpu

---
 config/template_r025/all.jinja | 737 +++++++++++++++++++++++++++++++++
 lex/smb/smb_icecores.py        |   2 +-
 run_livv.sh                    |  37 +-
 3 files changed, 759 insertions(+), 17 deletions(-)
 create mode 100644 config/template_r025/all.jinja

diff --git a/config/template_r025/all.jinja b/config/template_r025/all.jinja
new file mode 100644
index 0000000..0b3bd04
--- /dev/null
+++ b/config/template_r025/all.jinja
@@ -0,0 +1,737 @@
+common: &common
+    meta: &meta
+      Case ID: [{{ case_id }}]
+      Climatology years: [1980-2020]
+      Model: [E3SM-ELM]
+    climo: {{ case_out_dir }}/{{ case_id }}.{clim}_mean.nc
+    latlon: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    elevation: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    lnd_climo: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    topo: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    glc_surf: {{ case_out_dir }}/{{ case_id }}.ANN_mean.nc
+    latv: lat
+    lonv: lon
+    topov: topo
+    landfracv: landfrac
+    img_height: 300
+
+common_smb: &common_smb
+    smbv: QICE
+    maskv: gis_mask2
+    smbscale: 31536000
+    cmap: BrBG
+    cmap_diff: BrBG
+    clim_even: 1
+    units: mm w. e. yr^-1
+    References:
+      - {{ livvproj_dir }}/data/smb/smb_icecores.bib
+      - {{ livvproj_dir }}/data/livvkit.bib
+
+
+common_energy: &common_energy
+  desc: Surface energy balance component {component}{comment} from {data_var_names}
+  references:
+    - {{ livvproj_dir }}/data/racmo/Noel2015.bib
+    - {{ livvproj_dir }}/data/cism/glissade/cism-glissade.bib
+    - {{ livvproj_dir }}/data/e3sm/Evans2019.bib
+    - {{ livvproj_dir }}/data/livvkit.bib
+  cmap: plasma
+  cmap_diff: RdBu_r
+
+common_racmo: &common_racmo
+  clim_years:
+    dset_a: { year_s: 1980, year_e: 2020 }
+  dataset_names: { model: ELM, dset_a: RACMO 2.4 }
+  in_dirs: { dset_a: "{{ racmo_root_dir }}/clm/{_var}" }
+  file_patterns:
+    dset_a: "{_var}_{icesheet}_{season}_{sea_s}_{sea_e}_climo.nc"
+  timeseries_dirs:
+    model: "{{ model_ts_dir }}"
+    dset_a: "{{ racmo_root_dir }}/ts"
+  ts_file_patterns:
+    model: "{{ case_id }}.nc"
+    dset_a: "{_var}_{icesheet}_{year_s}01_{year_e}12.nc"
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_rcm.nc
+    model: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_rcm.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r025.nc
+
+common_era5: &common_era5
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_era5.nc
+  dataset_names: {model_remap: 'ELM [ERA5 Grid]', model_native: ELM, dset_a: ERA5}
+  aavg_sort: [ELM, 'ELM [ERA5 Grid]', ERA5]
+  scales: {model: 1, dset_a: 1}
+  clim_years:
+    dset_a: { year_s: 1979, year_e: 2019}
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/ERA5}
+  file_patterns: {dset_a: 'ERA5_{season}_{sea_s}_{sea_e}_climo.nc'}
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_era5.traave.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_era5.traave.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r025.nc
+
+common_merra: &common_merra
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_merra2.nc
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/MERRA2}
+  file_patterns: {dset_a: 'MERRA2_{season}_{sea_s}_{sea_e}_climo.nc'}
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_merra2.traave.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_merra2.traave.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r025.nc
+  dataset_names: {model_remap: 'ELM [MERRA2 Grid]', model_native: ELM, dset_a: MERRA2}
+  aavg_sort: [ELM, 'ELM [MERRA2 Grid]', MERRA2]
+  scales: {model: 1, dset_a: 1}
+  clim_years:
+    dset_a: { year_s: 1980, year_e: 2016}
+
+common_ceres: &common_ceres
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_cmip6.nc
+  dataset_names:
+    { model_native: ELM, model_remap: "ELM [CERES Grid]", dset_a: CERES }
+  aavg_sort: [ELM, "ELM [CERES Grid]", CERES]
+  scales: { model: 1, dset_a: 1 }
+  clim_years:
+    dset_a: { year_s: 2001, year_e: 2018 }
+  in_dirs:
+    dset_a: {{ e3sm_diags_data_dir }}/climatology/ceres_ebaf_surface_v4.1
+  file_patterns:
+    dset_a: ceres_ebaf_surface_v4.1_{season}_{sea_s}_{sea_e}_climo.nc
+  masks:
+    dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_cmip6.traave.nc
+    model_remap: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_cmip6.traave.nc
+    model_native: {{ livvproj_dir }}/grids/msk_{icesheet}_rcm_r025.nc
+
+common_racmo_gis: &common_racmo_gis
+  core_year_s: 1980
+  core_year_e: 2021
+  ib_year_e: 1987-1976
+  ib_year_s: 2014-2004
+  preprocess: []
+  preproc_dir: {{ livvproj_dir }}/data/smb/processed
+  zwally_file: model_zwally_basins_elm_r025.csv
+  ib_file: IceBridge_modelXY_elm{}_r025.csv
+  smb_cf_file: SMB_CoreFirnEstimates_elm{}_r025.csv
+  smb_mo_file: SMB_Obs_Model_elm{}_r025.csv
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_rcmgis.nc
+  icesheet: gis
+
+common_racmo_ais: &common_racmo_ais
+  climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_rcmais.nc
+  icesheet: ais
+
+common_racmo_smb_vars: &common_racmo_smb_vars
+  # Surface mass balance variables for dset_a: RACMO 2.4, model: ELM
+  # Each field must have:
+  #   - title: Human readable field name
+  #   - dset_a: definition for the field in dset_a dataset (i.e. RACMO)
+  #   - model: definition for the field in model dataset (i.e. ELM)
+  #   - units: Units of this field
+  #   - ac_contrib_sign: For each dataset, multiply the annual cycle by +/- 1 to achieve
+  #                      correct contribution to annual cycle of SMB
+  #   - aavg: parameters for ice sheet-area-averaging
+  #       - scale: Further scale the area-average, (this typically converts mm w.e./yr to GT/yr)
+  #       - units: Units of area average (only applicable if different than units for the field)
+  #       - sum: Perform area-weighted sum if true (area weighted mean if false)
+
+  # Additional parameters which may be defined are:
+  #   - mask_weight: mask variable acts as a weight (e.g. partial mask at edge of the ice sheet)
+  #   - primary_var: True for the primary field of interest for an annual cycle plot
+  #   - cmap: Override for colourmap for the fields
+  #   - cmap_diff: Override for colourmap for the difference plot
+  #   - cmin, cmax, cmin_d, cmax_d: Override for min / max values for fields and differences respectively
+  #   - comment: added to figure caption on output (usually used to indicate signedness of fluxes)
+
+  # Surface mass balance
+  - title: Surface Mass Balance
+    dset_a: smbgl
+    model: QICE
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    mask_weight: true
+    primary_var: true
+
+  # Total precipitation
+  - title: Total precip
+    dset_a: prgl
+    model: [+, SNOW, RAIN]
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+
+  # Snowfall
+  - title: Snowfall
+    dset_a: sf
+    model: SNOW
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Rainfall
+  - title: Rain
+    dset_a: [+, crrate, lsrrate]
+    model: RAIN
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Re-freeze
+  - title: Re-freeze
+    dset_a: rfrzgl
+    model: QSNOFRZ
+    ac_contrib_sign: { model: 1, dset_a: 1 }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    cmin: 0
+    cmap: YlGnBu
+
+  # Runoff
+  - title: Runoff
+    dset_a: totrunoff
+    model: QRUNOFF
+    ac_contrib_sign: { model: -1, dset_a: -1 }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    # cmin: -20.0
+    cmin: 0
+    # cmax: 20.0
+    cmap: YlGnBu
+
+  # Snow & ice melt
+  - title: Snow + ice melt
+    dset_a: mltgl
+    model: ["+", QSNOMELT, QICE_MELT]
+    ac_contrib_sign: { model: -1, dset_a: -1 }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    # cmin: -20.0
+    # cmax: 20.0
+    cmin: 0
+    # cmax: 20.0
+    cmap: YlGnBu
+
+  # Sublimation
+  - title: Sublimation
+    dset_a: sublgl
+    model: QSOIL
+    comment: " (Positive to atmosphere)"
+    ac_contrib_sign: { model: -1, dset_a: 1 }
+    scales: { model: 365 * 24 * 3600, dset_a: -365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+
+common_racmo_cmb_vars: &common_racmo_cmb_vars
+  # Climatic mass balance variables for dset_a: RACMO 2.4, model: ELM
+
+  # Climatic mass balance
+  - title: Climatic Mass Balance
+    dset_a: ["-", "prgl", ["-", "totrunoff", "sublgl"]]
+    model: ["-", ["+", "SNOW", "RAIN"], ["+", "QRUNOFF", "QSOIL"]]
+    ac_contrib_sign: { model: 1, dset_a: 1, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    mask_weight: true
+    primary_var: true
+
+  # Snowfall
+  - title: Snowfall
+    dset_a: sf
+    model: SNOW
+    ac_contrib_sign: { model: 1, dset_a: 1, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Rainfall
+  - title: Rain
+    dset_a: [+, crrate, lsrrate]
+    model: RAIN
+    ac_contrib_sign: { model: 1, dset_a: 1, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    units: mm w. e. yr^-1
+    cmap: YlGnBu
+    cmin: 0
+    mask_weight: true
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+
+  # Runoff
+  - title: Runoff
+    dset_a: totrunoff
+    model: QRUNOFF
+    ac_contrib_sign: { model: -1, dset_a: -1, }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600, }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+    cmin: 0
+    cmap: YlGnBu
+
+  # Sublimation
+  - title: Sublimation
+    dset_a: sublgl
+    model: QSOIL
+    comment: " (Positive to atmosphere)"
+    ac_contrib_sign: { model: -1, dset_a: 1, }
+    scales:
+      { model: 365 * 24 * 3600, dset_a: -365 * 24 * 3600,  }
+    aavg: { scale: 1e-06, units: GT yr^-1, sum: true }
+    mask_weight: true
+    units: mm w. e. yr^-1
+
+common_racmo_energy_vars: &common_racmo_energy_vars
+  - title: Surface temperature
+    dset_a: tas
+    model: TSA
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: K
+
+  - title: Albedo
+    dset_a: [/, rsusgl, rsds]
+    model:
+    - /
+    - [+, FSRND, FSRVD]
+    - [+, FSDSVD, FSDSND]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: unitless
+    cmin: 0.5
+    cmax: 0.9
+    cmin_d: -0.2
+    cmax_d: 0.2
+
+  - title: Shortwave net
+    dset_a: ['-', rsds, rsusgl]
+    model: FSA
+    comment: ' (Positive to surface)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Shortwave down
+    dset_a: rsds
+    model: FSDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave net
+    dset_a: strgl
+    model: FIRA
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: -1, model: 1}
+    units: W m^-2
+
+  - title: Longwave down
+    dset_a: rlds
+    model: FLDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Sensible heat
+    dset_a: hfssgl
+    model: FSH
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: -1, model: 1}
+    units: W m^-2
+
+  - title: Latent Heat Flux
+    dset_a: hflsgl
+    model: EFLX_LH_TOT
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: -1, model: 1}
+    units: W m^-2
+
+  - title: Net energy balance
+    dset_a:
+    - +
+    - ['-', rsds, rsusgl]
+    - - +
+      - strgl
+      - [+, hfssgl, hflsgl]
+    model:
+    - '-'
+    - FSA
+    - - +
+      - FIRA
+      - [+, FSH, EFLX_LH_TOT]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+    cmin: -10
+    cmax: 10
+    cmap: RdBu_r
+
+common_era_energy_vars: &common_era_energy_vars
+  - title: Surface temperature
+    dset_a: ts
+    model: TSA
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: K
+
+  - title: Albedo
+    dset_a: [/, rsus, rsds]
+    model:
+    - /
+    - [+, FSRND, FSRVD]
+    - [+, FSDSVD, FSDSND]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: unitless
+    cmin: 0.5
+    cmax: 1.0
+    cmin_d: -0.2
+    cmax_d: 0.2
+
+  - title: Shortwave net
+    dset_a: ['-', rsds, rsus]
+    model: FSA
+    comment: ' (Positive to surface)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Shortwave down
+    dset_a: rsds
+    model: FSDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - model: FIRA
+    title: Longwave net
+    dset_a: ['-', rlus, rlds]
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave down
+    dset_a: rlds
+    model: FLDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - model: FSH
+    dset_a: hfss
+    title: Sensible heat
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Latent Heat Flux
+    dset_a: hfls
+    model: EFLX_LH_TOT
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Net energy balance
+    dset_a:
+    - '-'
+    - ['-', rsds, rsus]
+    - - +
+      - ['-', rlus, rlds]
+      - [+, hfss, hfls]
+    model:
+    - '-'
+    - FSA
+    - - +
+      - FIRA
+      - [+, FSH, EFLX_LH_TOT]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+    cmin: -10
+    cmax: 10
+    cmap: RdBu_r
+
+common_merra_energy_vars: &common_merra_energy_vars
+  - title: Surface temperature
+    dset_a: tas
+    model: TSA
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: K
+
+  - title: Albedo
+    dset_a: [/, rsus, rsds]
+    model:
+    - /
+    - [+, FSRND, FSRVD]
+    - [+, FSDSVD, FSDSND]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: unitless
+    cmin: 0.5
+    cmax: 0.83
+    cmin_d: -0.2
+    cmax_d: 0.2
+
+  - title: Shortwave net
+    dset_a: ['-', rsds, rsus]
+    model: FSA
+    comment: ' (Positive to surface)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Shortwave down
+    dset_a: rsds
+    model: FSDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave net
+    dset_a: ['-', rlus, rlds]
+    model: FIRA
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Longwave down
+    dset_a: rlds
+    model: FLDS
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Sensible heat
+    dset_a: hfss
+    dset_b: FSH
+    model: FSH
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Latent Heat Flux
+    dset_a: hfls
+    dset_b: EFLX_LH_TOT
+    model: EFLX_LH_TOT
+    comment: ' (Positive to atmosphere)'
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+
+  - title: Net energy balance
+    dset_a:
+    - '-'
+    - ['-', rsds, rsus]
+    - - +
+      - ['-', rlus, rlds]
+      - [+, hfss, hfls]
+    model:
+    - '-'
+    - FSA
+    - - +
+      - FIRA
+      - [+, FSH, EFLX_LH_TOT]
+    sign: 1
+    scales: {dset_a: 1, model: 1}
+    units: W m^-2
+    cmin: -10
+    cmax: 10
+    cmap: RdBu_r
+
+common_ceres_energy_vars: &common_ceres_energy_vars
+    - title: Albedo
+      dset_a: [/, rsus, rsds]
+      model:
+        - /
+        - [+, FSRND, FSRVD]
+        - [+, FSDSVD, FSDSND]
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: unitless
+      cmin: 0.5
+      cmax: 0.83
+      cmin_d: -0.2
+      cmax_d: 0.2
+
+    - title: Shortwave net
+      dset_a: sfc_net_sw_all_mon
+      model: FSA
+      comment: " (Positive to surface)"
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: W m^-2
+
+    - title: Shortwave down
+      dset_a: rsds
+      model: FSDS
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: W m^-2
+
+    - title: Longwave net
+      dset_a: sfc_net_lw_all_mon
+      model: FIRA
+      comment: " (Positive to atmosphere)"
+      sign: 1
+      scales: { dset_a: -1, model: 1 }
+      units: W m^-2
+
+    - title: Longwave down
+      dset_a: rlds
+      model: FLDS
+      sign: 1
+      scales: { dset_a: 1, model: 1 }
+      units: W m^-2
+
+{% if run_gis %}
+# Greenland
+{% if set_cmb %}
+Climatic_Mass_Balance_GIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_cmb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_gis]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: Climatic Mass Balance
+  desc: "{component} component of CMB from {data_var_names}"
+{% endif %}
+
+{% if set_smb %}
+Surface_Mass_Balance_GIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_smb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_gis]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: smbgl
+  desc: "{component} component of SMB from {data_var_names}"
+{% endif %}
+
+{% if set_energy_racmo %}
+Energy_Balance_RACMO_GIS:
+  module: lex/energy/energy.py
+  <<: [*common, *common_energy, *common_racmo, *common_racmo_gis]
+  scales: {model: 1, dset_a: 1}
+  data_vars: *common_racmo_energy_vars
+{% endif %}
+
+{% if set_energy_era5 %}
+Energy_Balance_ERA5_GIS:
+  module: lex/energy/energy.py
+  icesheet: gis
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  <<: [*common, *common_energy, *common_era5]
+  data_vars: *common_era_energy_vars
+{% endif %}
+
+{% if set_energy_merra2 %}
+Energy_Balance_MERRA2_GIS:
+  module: lex/energy/energy.py
+  icesheet: gis
+  <<: [*common, *common_energy, *common_merra]
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  data_vars: *common_merra_energy_vars
+{% endif %}
+
+{% if set_energy_ceres %}
+Energy_Balance_CERES_GIS:
+  module: lex/energy/energy.py
+  icesheet: gis
+  <<: [*common, *common_energy, *common_ceres]
+  mask_ocean: { model_native: false, model_remap: true, dset_a: true }
+  data_vars: *common_ceres_energy_vars
+{% endif %}
+{% endif %}
+
+{% if run_ais %}
+# Antarctica
+{% if set_cmb %}
+Climatic_Mass_Balance_AIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_cmb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_ais]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: Climatic Mass Balance
+  desc: "{component} component of CMB from {data_var_names}"
+{% endif %}
+
+{% if set_smb %}
+Surface_Mass_Balance_AIS:
+  module: lex/smb/smb_icecores.py
+  data_vars: *common_racmo_smb_vars
+  <<: [*common, *common_smb, *common_racmo, *common_racmo_ais]
+  scales:
+    { model: 365 * 24 * 3600, dset_a: 365 * 24 * 3600 }
+  primary_var: smbgl
+  desc: "{component} component of SMB from {data_var_names}"
+{% endif %}
+
+{% if set_energy_racmo %}
+Energy_Balance_RACMO_AIS:
+  module: lex/energy/energy.py
+  <<: [*common, *common_energy, *common_racmo, *common_racmo_ais]
+  scales: {model: 1, dset_a: 1}
+  data_vars: *common_racmo_energy_vars
+{% endif %}
+
+{% if set_energy_era5 %}
+Energy_Balance_ERA5_AIS:
+  module: lex/energy/energy.py
+  icesheet: ais
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  <<: [*common, *common_energy, *common_era5]
+  data_vars: *common_era_energy_vars
+{% endif %}
+
+{% if set_energy_merra2 %}
+Energy_Balance_MERRA2_AIS:
+  module: lex/energy/energy.py
+  icesheet: ais
+  <<: [*common, *common_energy, *common_merra]
+  mask_ocean: {model_native: false, model_remap: true, dset_a: true}
+  data_vars: *common_merra_energy_vars
+{% endif %}
+
+{% if set_energy_ceres %}
+Energy_Balance_CERES_AIS:
+  module: lex/energy/energy.py
+  icesheet: ais
+  <<: [*common, *common_energy, *common_ceres]
+  mask_ocean: { model_native: false, model_remap: true, dset_a: true }
+  data_vars: *common_ceres_energy_vars
+{% endif %}
+{% endif %}
diff --git a/lex/smb/smb_icecores.py b/lex/smb/smb_icecores.py
index 2c6f801..95756d6 100644
--- a/lex/smb/smb_icecores.py
+++ b/lex/smb/smb_icecores.py
@@ -95,7 +95,7 @@ def run(name, config):
 
     config_arg_list.extend(["--out", img_dir])
     args = parse_args(config_arg_list)
-    if config["preprocess"]:
+    if config.get("preprocess", False):
         preproc.main(args, config)
 
     spatial_img = []
diff --git a/run_livv.sh b/run_livv.sh
index 8b8ab8b..4442b8c 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -29,27 +29,32 @@ else
 fi
 
 echo "LEX ON ${CASE}"
+if [[ ${CASE} == *"r05"* || ${CASE} == *".LR."* ]]; then
+    template=config/template_r05/all.jinja
+else if [[ ${CASE} == *"r025"* || ${CASE} == *".HR."* ]]; then
+    template=config/template_r025/all.jinja
+fi
+fi
+
 # Allow for standalone (outside of batch script) by setting WEBDIR if it's not already set
 WEBDIR="${WEBDIR:-/global/cfs/projectdirs/e3sm/www/${USER}}"
 
+# (Re-)generate the config file for this run
+python3 lex/generate_cfg.py \
+    --template ${template} \
+    --mach pm-cpu \
+    --casedir $PSCRATCH/lex/data/e3sm/${CASE} \
+    --case ${CASE} \
+    --cfg_out ./config \
+    --icesheets run_gis,run_ais \
+    --sets set_all
+
 # Run LIVVkit with all the configs we want for this case
 # writes the output website to the user's scratch directory
 mkdir -p ${SCRATCH}/lex
-
-livv -V \
-    config/${CASE}/cmb_gis.yml \
-    config/${CASE}/smb_gis.yml \
-    config/${CASE}/energy_e3sm_racmo_gis.yml \
-    config/${CASE}/energy_e3sm_era5_gis.yml \
-    config/${CASE}/energy_e3sm_merra2_merra_grid_gis.yml \
-    config/${CASE}/energy_e3sm_ceres_gis.yml \
-    config/${CASE}/cmb_ais.yml \
-    config/${CASE}/smb_ais.yml \
-    config/${CASE}/energy_e3sm_racmo_ais.yml \
-    config/${CASE}/energy_e3sm_era5_ais.yml \
-    config/${CASE}/energy_e3sm_merra2_merra_grid_ais.yml \
-    config/${CASE}/energy_e3sm_ceres_ais.yml \
-    -o $SCRATCH/lex/${CASE} &> livv_log_${CASE}.log
+livv \
+    --validate config/${CASE}/livvkit.yml \
+    --out-dir $SCRATCH/lex/${CASE} >> livv_stdoe_${CASE}.log 2>&1
 
 # Backup the existing published version of this analysis
 mv ${WEBDIR}/${CASE} ${WEBDIR}/${CASE}_bkd_$(date +'%Y%m%dT%H%M')
@@ -70,4 +75,4 @@ do
     sed -i "s/\(<\!-- GROUP LINK-->\)/\<a id=\"header-group\" href=\"..\/..\/current_runs.html\">\nCurrent\ runs\n\<\/a\>/g" ${htmlfile}
 done
 echo "LIVVkit results availalble at:"
-echo "https://portal.nersc.gov/project/e3sm/${USER}/${CASE}/index.html"
\ No newline at end of file
+echo "https://portal.nersc.gov/project/e3sm/${USER}/${CASE}/index.html"

From eb9c3a747f441d5ed24d39b4d349b94e217bf6dd Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 22 Dec 2025 12:51:15 -0800
Subject: [PATCH 21/32] Update python version for testing

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 5cea8fb..8f6cbbf 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13",]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4

From 410d9939a6682c9c85ab65a316191d580efb352b Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 22 Dec 2025 12:53:03 -0800
Subject: [PATCH 22/32] Use mache to detect machine and fill in e3sm diags path

---
 config/template_r025/all.jinja |  6 ++---
 config/template_r05/all.jinja  |  6 ++---
 lex/generate_cfg.py            | 43 ++++++++++++++++++++--------------
 requirements.txt               |  1 +
 4 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/config/template_r025/all.jinja b/config/template_r025/all.jinja
index 0b3bd04..93fb066 100644
--- a/config/template_r025/all.jinja
+++ b/config/template_r025/all.jinja
@@ -63,7 +63,7 @@ common_era5: &common_era5
   scales: {model: 1, dset_a: 1}
   clim_years:
     dset_a: { year_s: 1979, year_e: 2019}
-  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/ERA5}
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/observations/Atm/climatology/ERA5}
   file_patterns: {dset_a: 'ERA5_{season}_{sea_s}_{sea_e}_climo.nc'}
   masks:
     dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_era5.traave.nc
@@ -72,7 +72,7 @@ common_era5: &common_era5
 
 common_merra: &common_merra
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_merra2.nc
-  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/MERRA2}
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/observations/Atm/climatology/MERRA2}
   file_patterns: {dset_a: 'MERRA2_{season}_{sea_s}_{sea_e}_climo.nc'}
   masks:
     dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_merra2.traave.nc
@@ -93,7 +93,7 @@ common_ceres: &common_ceres
   clim_years:
     dset_a: { year_s: 2001, year_e: 2018 }
   in_dirs:
-    dset_a: {{ e3sm_diags_data_dir }}/climatology/ceres_ebaf_surface_v4.1
+    dset_a: {{ e3sm_diags_data_dir }}/observations/Atm/climatology/ceres_ebaf_surface_v4.1
   file_patterns:
     dset_a: ceres_ebaf_surface_v4.1_{season}_{sea_s}_{sea_e}_climo.nc
   masks:
diff --git a/config/template_r05/all.jinja b/config/template_r05/all.jinja
index 55cc3c6..06b4a7d 100644
--- a/config/template_r05/all.jinja
+++ b/config/template_r05/all.jinja
@@ -63,7 +63,7 @@ common_era5: &common_era5
   scales: {model: 1, dset_a: 1}
   clim_years:
     dset_a: { year_s: 1979, year_e: 2019}
-  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/ERA5}
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/observations/Atm/climatology/ERA5}
   file_patterns: {dset_a: 'ERA5_{season}_{sea_s}_{sea_e}_climo.nc'}
   masks:
     dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_era5.traave.nc
@@ -72,7 +72,7 @@ common_era5: &common_era5
 
 common_merra: &common_merra
   climo_remap: {{ case_out_dir }}/remap/{{ case_id }}.{clim}_mean_merra2.nc
-  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/climatology/MERRA2}
+  in_dirs: {dset_a: {{ e3sm_diags_data_dir }}/observations/Atm/climatology/MERRA2}
   file_patterns: {dset_a: 'MERRA2_{season}_{sea_s}_{sea_e}_climo.nc'}
   masks:
     dset_a: {{ livvproj_dir }}/grids/msk_{icesheet}_r025_remap_merra2.traave.nc
@@ -93,7 +93,7 @@ common_ceres: &common_ceres
   clim_years:
     dset_a: { year_s: 2001, year_e: 2018 }
   in_dirs:
-    dset_a: {{ e3sm_diags_data_dir }}/climatology/ceres_ebaf_surface_v4.1
+    dset_a: {{ e3sm_diags_data_dir }}/observations/Atm/climatology/ceres_ebaf_surface_v4.1
   file_patterns:
     dset_a: ceres_ebaf_surface_v4.1_{season}_{sea_s}_{sea_e}_climo.nc
   masks:
diff --git a/lex/generate_cfg.py b/lex/generate_cfg.py
index e98f472..2580956 100644
--- a/lex/generate_cfg.py
+++ b/lex/generate_cfg.py
@@ -4,6 +4,7 @@
 from pathlib import Path
 
 import jinja2
+import mache
 
 ALL_SHEETS = "run_gis,run_ais"
 ALL_SETS = "set_cmb,set_smb,set_energy_racmo,set_energy_era5,set_energy_merra2,set_energy_ceres"
@@ -20,27 +21,29 @@ def args():
         type=Path,
         help="Path to configuration template file.",
     )
-    parser.add_argument(
-        "--mach",
-        "-m",
-        type=str,
-        default="pm-cpu",
-        help="Name of the machine to be used. [pm-cpu, chrys]",
-    )
+
     parser.add_argument(
         "--case",
         "-c",
         type=str,
         help="Case ID",
+        required=True,
     )
+
     parser.add_argument(
         "--casedir",
         "-d",
         type=Path,
         help="Output directory where climatology files for `case` are stored",
+        required=True,
     )
+
     parser.add_argument(
-        "--cfg_out", "-o", type=Path, help="Output directory for config file."
+        "--cfg_out",
+        "-o",
+        type=Path,
+        help="Output directory for config file.",
+        default=Path("./").resolve(),
     )
 
     parser.add_argument(
@@ -97,42 +100,46 @@ def parse_sets(sheets, sets):
     _sheets = sheets.lower().split(",")
     _sets = sets.lower().split(",")
 
-    for _sheet in _sheets:
+    sheets = [_sheet.strip() for _sheet in _sheets]
+    sets = [_set.strip() for _set in _sets]
+
+    for _sheet in sheets:
         params[_sheet] = True
 
-    for _set in _sets:
+    for _set in sets:
         params[_set] = True
     return params
 
 
 def main():
     cl_args = args()
+    mach = mache.discover_machine()
+    mach_info = mache.MachineInfo()
+
     defaults = {
         "chrys": {
-            "e3sm_diags_data_dir": Path(
-                "/lcrc/group/e3sm/diagnostics/observations/Atm/"
-            ),
             "livvproj_dir": Path("/lcrc/group/e3sm/livvkit"),
             "model_ts_dir": Path("/lcrc/group/e3sm/ac.zender/scratch/livvkit"),
             "grid_dir": Path("/lcrc/group/e3sm/zender/grids"),
         },
         "pm-cpu": {
-            "e3sm_diags_data_dir": Path(
-                "/global/cfs/cdirs/e3sm/e3sm_diags/obs_for_e3sm_diags"
-            ),
             "livvproj_dir": Path("/global/cfs/cdirs/e3sm/livvkit"),
             "model_ts_dir": Path("/global/cfs/projectdirs/e3sm/zender/livvkit"),
             "grid_dir": Path("/global/cfs/cdirs/e3sm/zender/grids"),
             "racmo_root_dir": Path("/global/cfs/cdirs/fanssie/racmo/2.4.1"),
         },
     }
+    _mach_defaults = defaults[mach]
+    _mach_defaults["e3sm_diags_data_dir"] = Path(
+        mach_info.config.get("diagnostics", "base_path")
+    )
     params = {
-        **defaults[cl_args.mach],
+        **_mach_defaults,
         "case_id": cl_args.case,
         "case_out_dir": cl_args.casedir,
         **parse_sets(cl_args.icesheets, cl_args.sets),
     }
-    out_cfg = Path(cl_args.cfg_out, cl_args.case, "livvkit.yml")
+    out_cfg = Path(cl_args.cfg_out, "livvkit.yml")
     gen_cfg(cl_args.template, params, out_cfg)
 
 
diff --git a/requirements.txt b/requirements.txt
index 517ee0a..374266f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,6 +11,7 @@
   pylint
   matplotlib
   netcdf4
+  mache
   pandas
   nco
   cartopy

From 783323c627e65438690ce21167a1c9b1b9f1f822 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 22 Dec 2025 12:54:16 -0800
Subject: [PATCH 23/32] Make generate_cfg a package script

---
 pyproject.toml | 3 +++
 run_livv.sh    | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 790e972..f664b8c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -73,3 +73,6 @@ dev = { file = ["requirements-dev.txt"] }
 
 [project.urls]
 Homepage = "https://code.ornl.gov/LIVVkit/lex"
+
+[project.scripts]
+lex-cfg = "lex.generate_cfg:main"
diff --git a/run_livv.sh b/run_livv.sh
index 4442b8c..7c05a1f 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -40,7 +40,7 @@ fi
 WEBDIR="${WEBDIR:-/global/cfs/projectdirs/e3sm/www/${USER}}"
 
 # (Re-)generate the config file for this run
-python3 lex/generate_cfg.py \
+lex-cfg \
     --template ${template} \
     --mach pm-cpu \
     --casedir $PSCRATCH/lex/data/e3sm/${CASE} \

From 1c0a53915f510aa74b33c38d6dac8469118dc32f Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 22 Dec 2025 12:54:42 -0800
Subject: [PATCH 24/32] Fix formatting

---
 lex/annual_cycle.py     | 4 +++-
 lex/common.py           | 2 +-
 lex/energy/energy.py    | 7 +++++--
 lex/time_series_plot.py | 8 ++++++--
 4 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/lex/annual_cycle.py b/lex/annual_cycle.py
index b6e6a07..4c12bd1 100644
--- a/lex/annual_cycle.py
+++ b/lex/annual_cycle.py
@@ -79,7 +79,9 @@ def main(args, config):
                 lxc.area_avg(
                     _obs_in[_vers],
                     {},
-                    area_file=config["masks"][_vers].format(icesheet=config["icesheet"]),
+                    area_file=config["masks"][_vers].format(
+                        icesheet=config["icesheet"]
+                    ),
                     area_var="area",
                     mask_var="Icemask",
                     sum_out=_do_sum,
diff --git a/lex/common.py b/lex/common.py
index f9695f1..f4ccdf0 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -483,7 +483,7 @@ def area_avg(
     """
     try:
         area_data = xr.open_dataset(area_file)
-    except ValueError as err:
+    except ValueError:
         logger.error(f"INCOMPATABLE FILE {area_file}")
         raise
 
diff --git a/lex/energy/energy.py b/lex/energy/energy.py
index 17fd478..11ef8e2 100644
--- a/lex/energy/energy.py
+++ b/lex/energy/energy.py
@@ -34,10 +34,11 @@
 import argparse
 import os
 from pathlib import Path
-from loguru import logger
+
 import livvkit
 import pandas as pd
 from livvkit import elements as el
+from loguru import logger
 
 from lex import compare_gridded, time_series_plot, utils
 from lex.common import SEASON_NAME
@@ -87,7 +88,9 @@ def run(name, config):
     tables = {}
 
     for season in ["ANN", "DJF", "MAM", "JJA", "SON"]:
-        logger.info(f"PLOTTING COMPARE GRIDDED FOR {config.get('icesheet', '')} {season}")
+        logger.info(
+            f"PLOTTING COMPARE GRIDDED FOR {config.get('icesheet', '')} {season}"
+        )
         _plots, aavgs = compare_gridded.main(args, config, sea=season)
         images[season] = _plots
 
diff --git a/lex/time_series_plot.py b/lex/time_series_plot.py
index bea22e6..2f85c41 100644
--- a/lex/time_series_plot.py
+++ b/lex/time_series_plot.py
@@ -116,7 +116,9 @@ def main(args, config):
                 lxc.area_avg(
                     _obs_in[_vers],
                     {},
-                    area_file=config["masks"][_vers].format(icesheet=config["icesheet"]),
+                    area_file=config["masks"][_vers].format(
+                        icesheet=config["icesheet"]
+                    ),
                     area_var="area",
                     mask_var="Icemask",
                     sum_out=_do_sum,
@@ -126,7 +128,9 @@ def main(args, config):
         model_aavg[data_var["title"]], _, _, _ = lxc.area_avg(
             _model_plt,
             {},
-            area_file=config["masks"]["model_native"].format(icesheet=config["icesheet"]),
+            area_file=config["masks"]["model_native"].format(
+                icesheet=config["icesheet"]
+            ),
             area_var="area",
             mask_var="Icemask",
             sum_out=_do_sum,

From 7e615abe41f40adcafacdd9916d94f678540d5e0 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 26 Jan 2026 07:34:36 -0800
Subject: [PATCH 25/32] Rework loading files to work with zppy

---
 lex/annual_cycle.py         |  3 ++-
 lex/common.py               | 50 ++++++++++++++++++++++++++++++----
 lex/compare_gridded.py      |  8 +++---
 lex/generate_cfg.py         | 53 ++++++++++++++++++++++++++++---------
 lex/smb/smb/plot_spatial.py | 11 +++++++-
 5 files changed, 102 insertions(+), 23 deletions(-)

diff --git a/lex/annual_cycle.py b/lex/annual_cycle.py
index 4c12bd1..15e8358 100644
--- a/lex/annual_cycle.py
+++ b/lex/annual_cycle.py
@@ -19,8 +19,9 @@
 
 
 def main(args, config):
+    _files = [lxc.proc_climo_file(config, "climo_remap", mon) for mon in range(1, 13)]
     model_data = xr.open_mfdataset(
-        [config["climo_remap"].format(clim=f"{mon:02d}") for mon in range(1, 13)],
+        _files,
         combine="nested",
         concat_dim="time",
     )
diff --git a/lex/common.py b/lex/common.py
index f4ccdf0..998cade 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -82,15 +82,18 @@ def check_longitude(data, lon_coord="lon"):
 
 def get_season_bounds(season, year_s, year_e, sep="_"):
     """Determine season bounds for climatology files."""
-    _seasons = {"DJF": (1, 12), "MAM": (3, 5), "JJA": (6, 8), "SON": (9, 11)}
+    _seasons = {
+        "DJF": (1, 12),
+        "MAM": (3, 5),
+        "JJA": (6, 8),
+        "SON": (9, 11),
+        "ANN": (1, 12),
+    }
     _annual = (1, 12)
     if season in _seasons:
         _lb, _ub = _seasons[season]
         bound_l = f"{year_s:04d}{_lb:02d}"
         bound_u = f"{year_e:04d}{_ub:02d}"
-    elif season.upper() == "ANN":
-        bound_l = f"{year_s:04d}01"
-        bound_u = f"{year_e:04d}12"
     else:
         # Months
         if isinstance(season, str):
@@ -102,6 +105,40 @@ def get_season_bounds(season, year_s, year_e, sep="_"):
     return bound_l, bound_u
 
 
+def proc_climo_file(config, file_tag, sea):
+    """
+    Process the climatology file to maintain backward compatibility with standalone LEX.
+
+    Parameters
+    ----------
+    config : dict
+        LIVVkit /LEX configuration dict
+    file_tag : str
+        Configuration item which points to climatology filename to be formatted, usually
+        `climo` or `climo_remap`
+    sea : str
+        Season identifier
+
+    Returns
+    -------
+    climo_file : str
+        Formatted name of climatology file
+
+    """
+    _filename = config[file_tag]
+    if "sea_s" in _filename:
+        sea_s, sea_e = get_season_bounds(
+            sea, config.get("year_s", None), config.get("year_e", None)
+        )
+        if isinstance(sea, int):
+            sea = f"{sea:02d}"
+        climo_file = _filename.format(clim=sea, sea_s=sea_s, sea_e=sea_e)
+    else:
+        climo_file = _filename.format(clim=sea)
+
+    return climo_file
+
+
 def get_cycle(sea):
     """Get the name of which type of averaging is used (annual, seasonal, monthly)."""
     if sea == "ANN":
@@ -344,7 +381,10 @@ def _fcn_filt(_var):
 
     clim_years = config.get("clim_years", None)
 
-    clim_years_default = {"year_s": None, "year_e": None}
+    clim_years_default = {
+        "year_s": config.get("year_s", None),
+        "year_e": config.get("year_e", None),
+    }
     if clim_years:
         clim_years = clim_years.get(overs, clim_years_default)
     else:
diff --git a/lex/compare_gridded.py b/lex/compare_gridded.py
index bfa30fb..e0640dc 100644
--- a/lex/compare_gridded.py
+++ b/lex/compare_gridded.py
@@ -187,13 +187,15 @@ def main(args, config, sea="ANN"):
 
     if "model_native" in config["dataset_names"]:
         all_data = {
-            "model_remap": xr.open_dataset(config["climo_remap"].format(clim=sea)),
-            "model_native": xr.open_dataset(config["climo"].format(clim=sea)),
+            "model_remap": xr.open_dataset(
+                lxc.proc_climo_file(config, "climo_remap", sea)
+            ),
+            "model_native": xr.open_dataset(lxc.proc_climo_file(config, "climo", sea)),
             **lxc.load_obs(config, sea, mode=mode),
         }
     else:
         all_data = {
-            "model": xr.open_dataset(config["climo_remap"].format(clim=sea)),
+            "model": xr.open_dataset(lxc.proc_climo_file(config, "climo_remap", sea)),
             **lxc.load_obs(config, sea, mode=mode),
         }
     for _vers in all_data:
diff --git a/lex/generate_cfg.py b/lex/generate_cfg.py
index 2580956..921739d 100644
--- a/lex/generate_cfg.py
+++ b/lex/generate_cfg.py
@@ -6,8 +6,10 @@
 import jinja2
 import mache
 
-ALL_SHEETS = "run_gis,run_ais"
-ALL_SETS = "set_cmb,set_smb,set_energy_racmo,set_energy_era5,set_energy_merra2,set_energy_ceres"
+import lex
+
+ALL_SHEETS = "gis,ais"
+ALL_SETS = "cmb,smb,energy_racmo,energy_era5,energy_merra2,energy_ceres"
 
 
 def args():
@@ -33,7 +35,7 @@ def args():
     parser.add_argument(
         "--casedir",
         "-d",
-        type=Path,
+        type=str,
         help="Output directory where climatology files for `case` are stored",
         required=True,
     )
@@ -50,10 +52,9 @@ def args():
         "--sets",
         "-s",
         type=str,
-        default="",
         help=(
-            "Analysis sets to run: set_cmb, set_smb, set_energy_racmo, "
-            "set_energy_era5, set_energy_merra2, set_energy_ceres"
+            "Analysis sets to run: cmb, smb, energy_racmo, energy_era5, "
+            "energy_merra2, energy_ceres, or all to run all available"
         ),
     )
 
@@ -61,13 +62,20 @@ def args():
         "--icesheets",
         "-i",
         type=str,
-        default="",
         help=(
-            "Comma separated icesheets to analyse (run_ais for Antarctica,"
-            " run_gis for Greenland)"
+            "Comma separated icesheets to analyse (ais for Antarctica,"
+            " gis for Greenland), or all to run both"
         ),
     )
 
+    parser.add_argument(
+        "-z",
+        "--from-zppy",
+        action="store_true",
+        default=False,
+        help="Flag to be called from zppy, makes grid parsed",
+    )
+
     return parser.parse_args()
 
 
@@ -76,7 +84,6 @@ def gen_cfg(cfg_template, params, cfg_out):
         loader=jinja2.FileSystemLoader(cfg_template.resolve().parent)
     )
     template = jenv.get_template(cfg_template.name)
-
     cfg = template.render(**params)
 
     if not Path(cfg_out.parent).exists():
@@ -92,9 +99,9 @@ def parse_sets(sheets, sets):
     """Parse comma separated strings of sets / icesheets to analyse."""
 
     params = {}
-    if sheets.lower() == "run_all":
+    if sheets.lower() == "all":
         sheets = ALL_SHEETS
-    if sets.lower() == "set_all":
+    if sets.lower() == "all":
         sets = ALL_SETS
 
     _sheets = sheets.lower().split(",")
@@ -129,6 +136,22 @@ def main():
             "racmo_root_dir": Path("/global/cfs/cdirs/fanssie/racmo/2.4.1"),
         },
     }
+    climo_dirs = {}
+    ts_dirs = {}
+
+    if cl_args.from_zppy:
+        for _grid in ["native", "racmo_ais", "racmo_gis", "era5", "ceres", "merra2"]:
+            if _grid == "ceres":
+                _grid_dir = cl_args.casedir.replace("DATA_GRID", "180x360_traave")
+            else:
+                _grid_dir = cl_args.casedir.replace("DATA_GRID", _grid)
+
+            _ts_dir = _grid_dir.replace("/clim/", "/ts/monthly/")
+            climo_dirs[f"dir_{_grid}"] = Path(_grid_dir)
+            ts_dirs[f"dir_ts_{_grid}"] = Path(_ts_dir)
+
+    case_dir = Path(cl_args.casedir)
+
     _mach_defaults = defaults[mach]
     _mach_defaults["e3sm_diags_data_dir"] = Path(
         mach_info.config.get("diagnostics", "base_path")
@@ -136,11 +159,15 @@ def main():
     params = {
         **_mach_defaults,
         "case_id": cl_args.case,
-        "case_out_dir": cl_args.casedir,
+        "case_out_dir": case_dir,
+        "lex_root": Path(lex.__file__).parent,
         **parse_sets(cl_args.icesheets, cl_args.sets),
+        **climo_dirs,
+        **ts_dirs,
     }
     out_cfg = Path(cl_args.cfg_out, "livvkit.yml")
     gen_cfg(cl_args.template, params, out_cfg)
+    print(f"CONFIGURATION WRITTEN TO: {out_cfg}")
 
 
 if __name__ == "__main__":
diff --git a/lex/smb/smb/plot_spatial.py b/lex/smb/smb/plot_spatial.py
index f319c83..403befb 100644
--- a/lex/smb/smb/plot_spatial.py
+++ b/lex/smb/smb/plot_spatial.py
@@ -14,10 +14,12 @@
 import pandas as pd
 import smb.preproc as preproc
 from livvkit import elements as el
+from loguru import logger
 from matplotlib import colors as c
 from netCDF4 import Dataset
 from scipy.interpolate import griddata
 
+import lex.common as lxc
 import lex.compare_gridded as lxcg
 
 DESCRIBE_CORE = """
@@ -86,7 +88,14 @@ def mali_to_contour(lon_cell, lat_cell, data_cell):
 
 def load_model_data(config, regrid=True):
     """Load Model data."""
-    clim_nc = Dataset(config["climo"].format(m_s=1, m_e=12, clim="ANN"), mode="r")
+    sea_s, sea_e = lxc.get_season_bounds(
+        "ANN", config.get("year_s", None), config.get("year_e", None)
+    )
+    _climfile = config["climo"].format(sea_s=sea_s, sea_e=sea_e, clim="ANN")
+    _elevfile = config["elevation"].format(sea_s=sea_s, sea_e=sea_e, clim="ANN")
+    _gridfile = config["latlon"].format(sea_s=sea_s, sea_e=sea_e, clim="ANN")
+    logger.info(f"LOADING CLIMO FILE: {_climfile}")
+    clim_nc = Dataset(_climfile, mode="r")
     grid_nc = Dataset(config["latlon"], mode="r")
     elev_nc = Dataset(config["elevation"], mode="r")
 

From 5a6de3e53866ddb57eec953548d1f5562ebd3c86 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 2 Feb 2026 12:25:54 -0600
Subject: [PATCH 26/32] Fix for grid path on chrysalis

---
 lex/generate_cfg.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/lex/generate_cfg.py b/lex/generate_cfg.py
index 921739d..9e1fa7d 100644
--- a/lex/generate_cfg.py
+++ b/lex/generate_cfg.py
@@ -124,7 +124,7 @@ def main():
     mach_info = mache.MachineInfo()
 
     defaults = {
-        "chrys": {
+        "chrysalis": {
             "livvproj_dir": Path("/lcrc/group/e3sm/livvkit"),
             "model_ts_dir": Path("/lcrc/group/e3sm/ac.zender/scratch/livvkit"),
             "grid_dir": Path("/lcrc/group/e3sm/zender/grids"),
@@ -142,7 +142,8 @@ def main():
     if cl_args.from_zppy:
         for _grid in ["native", "racmo_ais", "racmo_gis", "era5", "ceres", "merra2"]:
             if _grid == "ceres":
-                _grid_dir = cl_args.casedir.replace("DATA_GRID", "180x360_traave")
+                _ceres_grid = "180x360_traave"
+                _grid_dir = cl_args.casedir.replace("DATA_GRID", _ceres_grid)
             else:
                 _grid_dir = cl_args.casedir.replace("DATA_GRID", _grid)
 

From 878a85f6cf53a0df15734fbb2bf9ece07d3df447 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 2 Feb 2026 11:33:40 -0800
Subject: [PATCH 27/32] Format grid and elevation netCDF links

---
 lex/smb/smb/plot_spatial.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lex/smb/smb/plot_spatial.py b/lex/smb/smb/plot_spatial.py
index 403befb..c6a2e5f 100644
--- a/lex/smb/smb/plot_spatial.py
+++ b/lex/smb/smb/plot_spatial.py
@@ -96,8 +96,8 @@ def load_model_data(config, regrid=True):
     _gridfile = config["latlon"].format(sea_s=sea_s, sea_e=sea_e, clim="ANN")
     logger.info(f"LOADING CLIMO FILE: {_climfile}")
     clim_nc = Dataset(_climfile, mode="r")
-    grid_nc = Dataset(config["latlon"], mode="r")
-    elev_nc = Dataset(config["elevation"], mode="r")
+    grid_nc = Dataset(_gridfile, mode="r")
+    elev_nc = Dataset(_elevfile, mode="r")
 
     lats_model = clim_nc.variables[config["latv"]][:]
     lons_model = clim_nc.variables[config["lonv"]][:]

From 63f3b601a3875250af71e36549d5cf60dea4d5f6 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 2 Feb 2026 11:58:24 -0800
Subject: [PATCH 28/32] Update LIVVkit version requirement

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 374266f..d8e5bf1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -17,4 +17,4 @@
   cartopy
   pybtex
   f90nml
-  livvkit>=3.2.0
+  livvkit>=3.3.0

From cac2a277c431a4d6b8a618c79c8c99e707ac0592 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 2 Feb 2026 13:39:30 -0800
Subject: [PATCH 29/32] Fix issues with standalone LEX

---
 lex/common.py               | 4 +++-
 lex/smb/smb/plot_spatial.py | 2 +-
 run_livv.sh                 | 1 -
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/lex/common.py b/lex/common.py
index 998cade..5d1cc63 100644
--- a/lex/common.py
+++ b/lex/common.py
@@ -126,7 +126,7 @@ def proc_climo_file(config, file_tag, sea):
 
     """
     _filename = config[file_tag]
-    if "sea_s" in _filename:
+    if "{sea_s}" in _filename:
         sea_s, sea_e = get_season_bounds(
             sea, config.get("year_s", None), config.get("year_e", None)
         )
@@ -134,6 +134,8 @@ def proc_climo_file(config, file_tag, sea):
             sea = f"{sea:02d}"
         climo_file = _filename.format(clim=sea, sea_s=sea_s, sea_e=sea_e)
     else:
+        if isinstance(sea, int):
+            sea = f"{sea:02d}"
         climo_file = _filename.format(clim=sea)
 
     return climo_file
diff --git a/lex/smb/smb/plot_spatial.py b/lex/smb/smb/plot_spatial.py
index c6a2e5f..d31a808 100644
--- a/lex/smb/smb/plot_spatial.py
+++ b/lex/smb/smb/plot_spatial.py
@@ -89,7 +89,7 @@ def mali_to_contour(lon_cell, lat_cell, data_cell):
 def load_model_data(config, regrid=True):
     """Load Model data."""
     sea_s, sea_e = lxc.get_season_bounds(
-        "ANN", config.get("year_s", None), config.get("year_e", None)
+        "ANN", config.get("year_s", 0), config.get("year_e", 1)
     )
     _climfile = config["climo"].format(sea_s=sea_s, sea_e=sea_e, clim="ANN")
     _elevfile = config["elevation"].format(sea_s=sea_s, sea_e=sea_e, clim="ANN")
diff --git a/run_livv.sh b/run_livv.sh
index 7c05a1f..82e410d 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -42,7 +42,6 @@ WEBDIR="${WEBDIR:-/global/cfs/projectdirs/e3sm/www/${USER}}"
 # (Re-)generate the config file for this run
 lex-cfg \
     --template ${template} \
-    --mach pm-cpu \
     --casedir $PSCRATCH/lex/data/e3sm/${CASE} \
     --case ${CASE} \
     --cfg_out ./config \

From 646b9c5fda9fddf5d82a04f7df4d046dc98f3915 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Mon, 2 Feb 2026 13:57:33 -0800
Subject: [PATCH 30/32] Update README with new name and supported machines

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index a5fd401..5f8fc6d 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 ![](https://raw.githubusercontent.com/wiki/LIVVkit/LIVVkit/imgs/livvkit.png)
 
-# LIVVkit Extensions (LEX)
+# LIVVkit Extensions (LivvEX)
 
 This repository holds a collection of extensions to
 [LIVVkit](https://livvkit.github.io/Docs/index.html) for validation and
@@ -19,8 +19,8 @@ machines, including Perlmutter at NERSC, and Chrysalis at ANL\'s LCRC.
 The Python package itself is described in `pyproject.toml`, which is used by
 `pip` to install this package
 
-Currently, LEX is designed to run on Perlmutter, but future work is
-planned to support other machines.
+Currently, LEX is designed to run on NERSC's Perlmutter, and ANL-LCRC's Chrysalis, 
+but future work is planned to support other machines where E3SM runs.
 
 ## Environment setup
 

From d54734c8677275b898c2e70f84640c0ad48d0347 Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Wed, 4 Feb 2026 13:29:05 -0800
Subject: [PATCH 31/32] Switch to Pixi for environment management

---
 .pre-commit-config.yaml |  5 +---
 README.md               | 36 +++++++++++---------------
 pyproject.toml          | 57 +++++++++++++++++++++++++++++++++++------
 requirements-dev.txt    |  3 ---
 requirements.txt        | 20 ---------------
 5 files changed, 65 insertions(+), 56 deletions(-)
 delete mode 100644 requirements-dev.txt
 delete mode 100644 requirements.txt

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 528d937..c67f382 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,6 +10,7 @@ repos:
       - id: debug-statements
       - id: destroyed-symlinks
       - id: detect-private-key
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.13.0
@@ -18,7 +19,3 @@ repos:
       - id: ruff-check
       # Run the formatter.
       - id: ruff-format
-  - repo: https://github.com/pycqa/isort
-    rev: 6.0.1
-    hooks:
-      - id: isort
diff --git a/README.md b/README.md
index 5f8fc6d..a900e5d 100644
--- a/README.md
+++ b/README.md
@@ -19,44 +19,38 @@ machines, including Perlmutter at NERSC, and Chrysalis at ANL\'s LCRC.
 The Python package itself is described in `pyproject.toml`, which is used by
 `pip` to install this package
 
-Currently, LEX is designed to run on NERSC's Perlmutter, and ANL-LCRC's Chrysalis, 
+Currently, LEX is designed to run on NERSC's Perlmutter, and ANL-LCRC's Chrysalis,
 but future work is planned to support other machines where E3SM runs.
 
 ## Environment setup
 
 For setting up an environment to which lex and dependencies will be
-installed, conda and Python virtualenv are documented here. **NB** this
-will only currently work on NERSC's Perlmutter, the environment should be
+installed, Pixi and conda are documented here. **NB** this
+will only currently work on Perlmutter and Chrysalis, the environment should be
 created there.
 
-### Conda environment
+### Pixi environment
+[pixi](https://pixi.sh/latest/) is a package management tool, and the primary
+environment management tool for LEX.
+First, it must be [installed](https://pixi.prefix.dev/latest/installation/) locally.
+Then an enviornment for lex development can be created:
 ```bash
 $ git clone https://github.com/LIVVkit/lex.git
 $ cd lex
-$ {conda, mamba} create -n lex_env python --file requirements.txt
-$ {conda, mamba} activate lex_env
-$ pip install -e .    # Installs the lex module as an editable Python package to the lex_env environment.
+$ pixi install --all     # This will install the default and development environments
+$ pixi shell -e default  # To activate the default (runtime) environment
+$ pixi shell -e dev      # To activate the dev environment (for code testing and checks)
 ```
 
-### Python virtualenv
+### Conda environment
 ```bash
 $ git clone https://github.com/LIVVkit/lex.git
 $ cd lex
-$ module load python/3.13
-$ python -m venv .env --prompt lex_env  # Creates the virtual env in ${HOME}/lex/.env
-$ source .env/bin/activate              # Switch to the new environment
-$ pip install --upgrade pip             # Needed if the system pip version < 21.3
-$ pip install -e .                      # Installs LEX as editable
+$ {conda, mamba} create -n lex_env python --file requirements.txt
+$ {conda, mamba} activate lex_env
+$ pip install -e .    # Installs the lex module as an editable Python package to the lex_env environment.
 ```
 
-This will create a virtual environment at `lex/.env`, and install the
-LEX package as editable with all its Python requirements to run.
-
-### Other available environment management solutions
-Not documented here, but also available for environment management
-- [uv](https://docs.astral.sh/uv/)
-- [pixi](https://pixi.sh/latest/)
-
 ## Basic usage
 
 Within the `lex/config` directory there are templates for
diff --git a/pyproject.toml b/pyproject.toml
index f664b8c..04de464 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,6 +42,27 @@ description = "Extensions for the land ice verification and validation toolkit (
 readme = { file = "README.rst", content-type = "text/x-rst" }
 license = { text = "BSD-3-Clause" }
 
+dependencies = [
+    "numpy>=2.4.2",
+    "scipy>=1.17.0",
+    "xarray>=2026.1.0",
+    "dask>=2026.1.2",
+    "seaborn>=0.13.2",
+    "cftime>=1.6.5",
+    "nc-time-axis>=1.4.1",
+    "scikit-learn>=1.8.0",
+    "ruamel.yaml>=0.19.1",
+    "jinja2>=3.1.6",
+    "matplotlib>=3.10.8",
+    "netcdf4>=1.7.4",
+    "pandas>=3.0.0",
+    "cartopy>=0.25.0",
+    "pybtex>=0.25.1",
+    "f90nml>=1.5",
+    "loguru>=0.7.3",
+    "livvkit>=3.3.0",
+]
+
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
@@ -51,28 +72,48 @@ classifiers = [
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
+dynamic = ["version"]
 
-dynamic = ["version", "dependencies", "optional-dependencies"]
+[dependency-groups]
+dev = [
+    "isort",
+    "pytest",
+    "ruff",
+    "pre-commit",
+]
 
 [tool.setuptools]
 packages = ["lex", "lex.smb", "lex.energy"]
 
 [tool.setuptools.dynamic]
-dependencies = { file = ["requirements.txt"] }
 version = { attr = "lex.__version__" }
 
-[tool.setuptools.dynamic.optional-dependencies]
-dev = { file = ["requirements-dev.txt"] }
-
-
 [project.urls]
-Homepage = "https://code.ornl.gov/LIVVkit/lex"
+Homepage = "https://github.com/LIVVkit/lex"
 
 [project.scripts]
 lex-cfg = "lex.generate_cfg:main"
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[tool.pixi.pypi-dependencies]
+lex = { path = ".", editable = true }
+
+[tool.pixi.tasks]
+
+[tool.pixi.dependencies]
+mache = ">=2.1.0"
+nco = ">=5.3.6"
+
+[tool.pixi.feature.dev.dependencies]
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+dev = { features = ["dev"], solve-group = "default" }
diff --git a/requirements-dev.txt b/requirements-dev.txt
deleted file mode 100644
index db616d0..0000000
--- a/requirements-dev.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-isort
-pytest
-ruff
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index d8e5bf1..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-  numpy
-  scipy
-  xarray
-  dask
-  seaborn
-  cftime
-  nc-time-axis
-  scikit-learn
-  ruamel.yaml
-  jinja2
-  pylint
-  matplotlib
-  netcdf4
-  mache
-  pandas
-  nco
-  cartopy
-  pybtex
-  f90nml
-  livvkit>=3.3.0

From 3560a0b3530dc43b353a8de2c4163c50f4312f2a Mon Sep 17 00:00:00 2001
From: Michael Kelleher <kelleher.mike@gmail.com>
Date: Thu, 5 Feb 2026 11:54:02 -0800
Subject: [PATCH 32/32] Switch to Pixi for dev environment

---
 .github/workflows/python-package.yml | 32 +++++++++++-------
 README.md                            | 30 ++++++++++++-----
 env.yml                              | 32 ++++++++++++++++++
 pyproject.toml                       | 49 +++++++++++++++++++---------
 run_livv.sh                          |  6 +++-
 5 files changed, 113 insertions(+), 36 deletions(-)
 create mode 100644 env.yml

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 8f6cbbf..69f53f3 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -16,18 +16,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        include:
+          - python-version: "3.10"
+            pixi-env: py310dev
+          - python-version: "3.11"
+            pixi-env: py311dev
+          - python-version: "3.12"
+            pixi-env: py312dev
+          - python-version: "3.13"
+            pixi-env: py313dev
+          - python-version: "3.14"
+            pixi-env: py314dev
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - uses: actions/checkout@v6
+    - name: Set up Pixi ${{ matrix.python-version }}
+      uses: prefix-dev/setup-pixi@v0.9.4
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+        pixi-version: v0.62.2
+        # Project environment caching uses pixi.lock as the cache key input.
+        # If you don't commit a lockfile, disable caching to avoid ENOENT.
+        # cache: ${{ hashFiles('pixi.lock') != '' }}
+        environments: ${{ matrix.pixi-env }}
+    - name: Run tests
       run: |
-        python3 -m pip install --upgrade pip
-        python3 -m pip install -e .\[dev\]
-    - name: Test with pytest
-      run: |
-        pytest -vvv
+        pixi run -e ${{ matrix.pixi-env }} pytest -vvv
diff --git a/README.md b/README.md
index a900e5d..152030d 100644
--- a/README.md
+++ b/README.md
@@ -37,16 +37,22 @@ Then an enviornment for lex development can be created:
 ```bash
 $ git clone https://github.com/LIVVkit/lex.git
 $ cd lex
-$ pixi install --all     # This will install the default and development environments
-$ pixi shell -e default  # To activate the default (runtime) environment
-$ pixi shell -e dev      # To activate the dev environment (for code testing and checks)
+$ pixi install          # This will install the default environment
+$ pixi shell -e default # To activate the default (runtime) environment
 ```
 
+If development tools are needed (e.g. `pytest`), install and activate the `dev` environment:
+```bash
+$ pixi install -e dev   # Installs the environment
+$ pixi shell -e dev     # Activates the dev environment (for code testing and checks)
+```
+**N.B.** it is not recommended to do `pixi install --all`, as this will install the environment versions used for testing.
+
 ### Conda environment
 ```bash
 $ git clone https://github.com/LIVVkit/lex.git
 $ cd lex
-$ {conda, mamba} create -n lex_env python --file requirements.txt
+$ {conda, mamba} env create -n lex_env python --file env.yml
 $ {conda, mamba} activate lex_env
 $ pip install -e .    # Installs the lex module as an editable Python package to the lex_env environment.
 ```
@@ -68,7 +74,9 @@ website you\'d run this command:
 ```bash
 $ livv -V config/example/example.yml -o vv_test -s
 ```
-This will create a directory in the current directory called `vv_test` (~7.5 MB), and spawn an HTTP server, which should only be used for testing purposes. (This works best if the output is in the current directory)
+This will create a directory in the current directory called `vv_test` (~7.5 MB), and
+spawn an HTTP server, which should only be used for testing purposes.
+(This works best if the output is in the current directory)
 
 *Note:* All the extension configurations files assume you are working
 from the top level `lex` directory. You *can* run any of these
@@ -99,20 +107,24 @@ $ sbatch run_lex_pm-cpu.sbatch
 ## Running new cases on PM-CPU
 
 ### Generate a single timeseries file from ELM h0 outputs
-- `ncrcat -v topo,landfrac,QSNOFRZ,FSRND,FSRVD,FSDSVD,FSDSND,EFLX_LH_TOT,FIRA,FLDS,FSA,FSDS,FSH,QICE,QRUNOFF,QSNOMELT,QSOIL,RAIN,SNOW,TSA,SNOWICE,SNOWLIQ,H2OSNO elm*h0*.nc -o ${CASE}.nc`
+- `CASE="The case name"`
+- `ncrcat -v topo,landfrac,QSNOFRZ,FSRND,FSRVD,FSDSVD,FSDSND,EFLX_LH_TOT,FIRA,FLDS,FSA,FSDS,FSH,QICE,QRUNOFF,QSNOMELT,QSOIL,RAIN,SNOW,TSA,SNOWICE,SNOWLIQ,H2OSNO ${CASE}.elm.h0*.nc -o ${CASE}.nc`
 
 ### Perform post-processing on a single time series ELM h0 output
 - Edit the `lex/lex/postproc/e3sm/postproc.sbatch` batch file to mach the new run
 
     Key variables:
     - `INDIR`: Path which contains single output time series file
-    - `OUTCASE`: Name of the new case which is the name of the netCDF file without extension (e.g. `v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020`)
+    - `OUTCASE`: Name of the new case which is the name of the netCDF file without
+        extension (e.g. `v2.1.r025.IGERA5ELM_MLI-deep_firn_1980_2020`)
     - `RES`: ELM output resolution (currently accepts `R05` and `R025`)
-    - `OUTDIR`: Scratch directory into which climatology files will be written, defaults to `${SCRATCH}/lex/data/e3sm/${OUTCASE}`
+    - `OUTDIR`: Scratch directory into which climatology files will be written,
+        defaults to `${SCRATCH}/lex/data/e3sm/${OUTCASE}`
 - Run the post-processing script:
   - `cd lex/lex/postproc/e3sm; sbatch postproc.sbatch`
 
-**NB**: the `postproc.sbatch` script will create the configuration for your case (based on `OUTCASE` and `OUTDIR`), then run LIVVkit on it with `lex/run_livv.sh`
+**NB**: the `postproc.sbatch` script will create the configuration for your case
+(based on `OUTCASE` and `OUTDIR`), then run LIVVkit on it with `lex/run_livv.sh`
 
 ## Developing a custom extension
 
diff --git a/env.yml b/env.yml
new file mode 100644
index 0000000..93ab51f
--- /dev/null
+++ b/env.yml
@@ -0,0 +1,32 @@
+#
+# This file is autogenerated by pyproject2conda
+# with the following command:
+#
+#     $ pyproject2conda yaml -o env.yml
+#
+# You should not manually edit this file.
+# Instead edit the corresponding pyproject.toml file.
+#
+channels:
+  - conda-forge
+dependencies:
+  - cartopy>=0.25.0
+  - cftime>=1.6.5
+  - dask>=2026.1.2
+  - f90nml>=1.5
+  - jinja2>=3.1.6
+  - livvkit>=3.3.0
+  - loguru>=0.7.3
+  - mache>=2.1.0
+  - matplotlib>=3.10.8
+  - nc-time-axis>=1.4.1
+  - netcdf4>=1.7.4
+  - nco>=5.3.6
+  - numpy>=2.2.6
+  - pandas>=2.2.3
+  - pybtex>=0.25.1
+  - ruamel.yaml>=0.19.1
+  - scikit-learn>=1.7.2
+  - scipy>=1.15.3
+  - seaborn>=0.13.2
+  - xarray>=2025.6.1
diff --git a/pyproject.toml b/pyproject.toml
index 04de464..c12a67b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,25 +37,25 @@ authors = [
     { name = "Joseph H. Kennedy", email = "kennedyjh@ornl.gov" },
 ]
 name = "lex"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 description = "Extensions for the land ice verification and validation toolkit (Livvkit EXtensions)"
 readme = { file = "README.rst", content-type = "text/x-rst" }
 license = { text = "BSD-3-Clause" }
 
 dependencies = [
-    "numpy>=2.4.2",
-    "scipy>=1.17.0",
-    "xarray>=2026.1.0",
+    "numpy>=2.2.6",
+    "scipy>=1.15.3",
+    "xarray>=2025.6.1",
     "dask>=2026.1.2",
     "seaborn>=0.13.2",
     "cftime>=1.6.5",
     "nc-time-axis>=1.4.1",
-    "scikit-learn>=1.8.0",
+    "scikit-learn>=1.7.2",
     "ruamel.yaml>=0.19.1",
     "jinja2>=3.1.6",
     "matplotlib>=3.10.8",
     "netcdf4>=1.7.4",
-    "pandas>=3.0.0",
+    "pandas>=2.2.3",
     "cartopy>=0.25.0",
     "pybtex>=0.25.1",
     "f90nml>=1.5",
@@ -76,17 +76,10 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
 ]
 dynamic = ["version"]
 
-[dependency-groups]
-dev = [
-    "isort",
-    "pytest",
-    "ruff",
-    "pre-commit",
-]
-
 [tool.setuptools]
 packages = ["lex", "lex.smb", "lex.energy"]
 
@@ -112,8 +105,34 @@ lex = { path = ".", editable = true }
 mache = ">=2.1.0"
 nco = ">=5.3.6"
 
+# Development tools
 [tool.pixi.feature.dev.dependencies]
+isort = "*"
+pytest = "*"
+ruff = "*"
+pre-commit = "*"
+
+# Different Python versions for CI testing
+[tool.pixi.feature.py310dev.dependencies]
+python = "3.10.*"
+
+[tool.pixi.feature.py311dev.dependencies]
+python = "3.11.*"
+
+[tool.pixi.feature.py312dev.dependencies]
+python = "3.12.*"
+
+[tool.pixi.feature.py313dev.dependencies]
+python = "3.13.*"
+
+[tool.pixi.feature.py314dev.dependencies]
+python = "3.14.*"
 
 [tool.pixi.environments]
 default = { solve-group = "default" }
-dev = { features = ["dev"], solve-group = "default" }
+dev = ["dev"]
+py310dev = ["py310dev", "dev"]
+py311dev = ["py311dev", "dev"]
+py312dev = ["py312dev", "dev"]
+py313dev = ["py313dev", "dev"]
+py314dev = ["py314dev", "dev"]
diff --git a/run_livv.sh b/run_livv.sh
index 82e410d..5c6f9d9 100755
--- a/run_livv.sh
+++ b/run_livv.sh
@@ -1,6 +1,9 @@
 #!/bin/bash
 CASE=$1
-if [ $(command -v conda) ]; then
+if [ $(command -v pixi) ];then
+    echo "ACTIVATING PIXI SHELL"
+    eval $(pixi shell-hook -e default)
+else if [ $(command -v conda) ]; then
     conda_activate_script=/global/common/software/e3sm/anaconda_envs/base/etc/profile.d/conda.sh
     echo "ACTIVATE: ${conda_activate_script}"
     source $conda_activate_script
@@ -18,6 +21,7 @@ if [ $(command -v conda) ]; then
     fi
     fi
 fi
+fi
 
 livv_cmd='livv'
 livv_exe=`which ${livv_cmd}`