From d95896aa50419e6bc4bca5af8b3be13cdc7f271a Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Thu, 27 Feb 2025 15:02:30 -0500
Subject: [PATCH 01/29] config.py now object oriented and contains
 update_config() function

---
 pygem/setup/config.py | 121 ++++++++++++++++++++++++++++++------------
 1 file changed, 86 insertions(+), 35 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 4645af90..791d4bfd 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -7,42 +7,93 @@
 """
 import os
 import shutil
-import sys
 import yaml
+import argparse
+from ruamel.yaml import YAML
 
-# pygem_params file name
-config_fn = 'config.yaml'
-
-# Define the base directory and the path to the configuration file
-basedir = os.path.join(os.path.expanduser('~'), 'PyGEM')
-config_file = os.path.join(basedir, config_fn)  # Path where you want the config file
-
-# Get the source configuration file path from your package
-package_dir = os.path.dirname(__file__)  # Get the directory of the current script
-source_config_file = os.path.join(package_dir, config_fn)  # Path to params.py
-
-def ensure_config(overwrite=False):
-    isfile = os.path.isfile(config_file)
-    if isfile and overwrite:
-        overwrite = None
-        while overwrite is None:
-            # Ask the user for a y/n response
-            response = input(f"PyGEM configuration.yaml file already exist ({config_file}), do you wish to overwrite (y/n):").strip().lower()
-            # Check if the response is valid
-            if response == 'y' or response == 'yes':
-                overwrite = True
-            elif response == 'n' or response == 'no':
-                overwrite = False
-            else:
-                print("Invalid input. Please enter 'y' or 'n'.")
+class ConfigManager:
+    def __init__(self, config_filename='config.yaml', base_dir=None):
+        """initialize the ConfigManager class"""
+        self.config_filename = config_filename
+        self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
+        self.config_path = os.path.join(self.base_dir, self.config_filename)
+        self.package_dir = os.path.dirname(__file__)
+        self.source_config_path = os.path.join(self.package_dir, self.config_filename)
     
-    if (not isfile) or (overwrite):
-        os.makedirs(basedir, exist_ok=True)  # Ensure the base directory exists
-        shutil.copy(source_config_file, config_file)  # Copy the file
-        print(f"Copied default configuration to {config_file}")
+    def ensure_config(self, overwrite=False):
+        """Ensure the configuration file exists"""
+        if os.path.isfile(self.config_path) and not overwrite:
+            return
+        
+        if os.path.isfile(self.config_path) and overwrite:
+            overwrite = self._prompt_overwrite()
+        
+        if not os.path.isfile(self.config_path) or overwrite:
+            os.makedirs(self.base_dir, exist_ok=True)
+            shutil.copy(self.source_config_path, self.config_path)
+            print(f"Copied default configuration to {self.config_path}")
     
-def read_config():
-    """Read the configuration file and return its contents as a dictionary."""
-    with open(config_file, 'r') as f:
-        config = yaml.safe_load(f)  # Use safe_load to avoid arbitrary code execution
-    return config
\ No newline at end of file
+    def read_config(self):
+        """Read the configuration file and return its contents as a dictionary."""
+        with open(self.config_path, 'r') as f:
+            return yaml.safe_load(f)
+    
+    def update_config(self, updates):
+        """Update multiple keys in the YAML configuration file while preserving quotes and original types."""
+        yaml = YAML()
+        yaml.preserve_quotes = True  # Preserve quotes around string values
+
+        try:
+            with open(self.config_path, 'r') as file:
+                config = yaml.load(file)
+
+            for key, value in updates.items():
+                keys = key.split('.')
+                d = config
+                for k in keys[:-1]:
+                    if k not in d:
+                        print(f"Key '{key}' not found in the config. Skipping update.")
+                        break
+                    d = d[k]
+                else:
+                    # Reparse value with YAML to infer correct type
+                    if keys[-1] in d:
+                        d[keys[-1]] = yaml.load(value)
+                    else:
+                        print(f"Key '{key}' not found in the config. Skipping update.")
+
+            with open(self.config_path, 'w') as file:
+                yaml.dump(config, file)
+
+        except Exception as e:
+            print(f"Error updating config: {e}")
+
+    
+    def _prompt_overwrite(self):
+        """Prompt the user for confirmation before overwriting the config file."""
+        while True:
+            response = input(f"Configuration file already exists ({self.config_path}). Overwrite? (y/n): ").strip().lower()
+            if response in ['y', 'yes']:
+                return True
+            elif response in ['n', 'no']:
+                return False
+            print("Invalid input. Please enter 'y' or 'n'.")
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--config', default='config.yaml', help='Path to the config file')
+    parser.add_argument('updates', nargs='*', help='Key-value pairs to update in the config file')
+    
+    args = parser.parse_args()
+    
+    # Parse the updates into a dictionary
+    updates = {}
+    for update in args.updates:
+        key, value = update.split('=')
+        updates[key] = value
+    
+    config_manager = ConfigManager(config_filename=args.config)
+    config_manager.update_config(updates)
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 0b8209cc884e275458caa8589a8464e942857aa2 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Thu, 27 Feb 2025 15:04:10 -0500
Subject: [PATCH 02/29] all prior calls to config updated for compatability
 with new config.ConfigManager class

---
 pygem/bin/op/duplicate_gdirs.py               |  8 ++++--
 pygem/bin/op/initialize.py                    | 28 ++++++-------------
 pygem/bin/op/list_failed_simulations.py       |  8 ++++--
 .../postproc/postproc_binned_monthly_mass.py  | 10 +++++--
 .../postproc/postproc_compile_simulations.py  |  8 ++++--
 pygem/bin/postproc/postproc_distribute_ice.py | 10 +++++--
 pygem/bin/postproc/postproc_monthly_mass.py   | 10 +++++--
 pygem/bin/preproc/preproc_fetch_mbdata.py     |  8 ++++--
 pygem/bin/preproc/preproc_wgms_estimate_kp.py |  8 ++++--
 pygem/bin/run/run_calibration.py              |  8 ++++--
 .../run/run_calibration_frontalablation.py    |  8 ++++--
 pygem/bin/run/run_calibration_reg_glena.py    | 12 ++++----
 pygem/bin/run/run_mcmc_priors.py              |  8 ++++--
 pygem/bin/run/run_simulation.py               |  8 ++++--
 pygem/class_climate.py                        |  9 +++---
 pygem/gcmbiasadj.py                           |  9 +++---
 pygem/glacierdynamics.py                      |  9 +++---
 pygem/massbalance.py                          |  9 +++---
 pygem/mcmc.py                                 |  9 +++---
 pygem/oggm_compat.py                          |  9 +++---
 pygem/output.py                               |  8 ++++--
 pygem/pygem_modelsetup.py                     | 10 ++++---
 pygem/shop/debris.py                          | 10 ++++---
 pygem/shop/icethickness.py                    | 10 ++++---
 pygem/shop/mbdata.py                          |  8 +++---
 pygem/shop/oib.py                             |  9 +++---
 pygem/utils/_funcs.py                         |  9 +++---
 27 files changed, 148 insertions(+), 112 deletions(-)

diff --git a/pygem/bin/op/duplicate_gdirs.py b/pygem/bin/op/duplicate_gdirs.py
index 016f8c29..823d7f7a 100644
--- a/pygem/bin/op/duplicate_gdirs.py
+++ b/pygem/bin/op/duplicate_gdirs.py
@@ -11,11 +11,13 @@
 import os
 import shutil
 # pygem imports
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 
 def main():
     parser = argparse.ArgumentParser(description="Script to make duplicate oggm glacier directories - primarily to avoid corruption if parellelizing runs on a single glacier")
diff --git a/pygem/bin/op/initialize.py b/pygem/bin/op/initialize.py
index 21685a20..0a0822e8 100644
--- a/pygem/bin/op/initialize.py
+++ b/pygem/bin/op/initialize.py
@@ -11,25 +11,13 @@
 import zipfile
 import os,sys
 import shutil
-from ruamel.yaml import YAML
-# set up config.yaml
-import pygem.setup.config as config
-config.ensure_config(overwrite=True)
-
-def update_config_root(conf_path, datapath):
-    yaml = YAML()
-    yaml.preserve_quotes = True  # Preserve quotes around string values
-    
-    # Read the YAML file
-    with open(conf_path, 'r') as file:
-        config = yaml.load(file)
-
-    # Update the key with the new value
-    config['root'] = datapath
-
-    # Save the updated configuration back to the file
-    with open(conf_path, 'w') as file:
-        yaml.dump(config, file)
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# check for config
+config_manager.ensure_config(overwrite=True)
+# read the config
+pygem_prms = config_manager.read_config()
 
 def print_file_tree(start_path, indent=""):
     # Loop through all files and directories in the current directory
@@ -136,7 +124,7 @@ def main():
 
     # update root path in config.yaml
     try:
-        update_config_root(config.config_file, out+'/sample_data/')
+        config_manager.update_config(updates={'root':f'{out}/sample_data'})
     except:
         pass
     
diff --git a/pygem/bin/op/list_failed_simulations.py b/pygem/bin/op/list_failed_simulations.py
index 66f83c15..fa2c1363 100644
--- a/pygem/bin/op/list_failed_simulations.py
+++ b/pygem/bin/op/list_failed_simulations.py
@@ -15,11 +15,13 @@
 import argparse
 import numpy as np
 # pygem imports
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 def run(reg, simpath, gcm, scenario, calib_opt, bias_adj, gcm_startyear, gcm_endyear):
diff --git a/pygem/bin/postproc/postproc_binned_monthly_mass.py b/pygem/bin/postproc/postproc_binned_monthly_mass.py
index 3fea6ba1..a9888d7a 100644
--- a/pygem/bin/postproc/postproc_binned_monthly_mass.py
+++ b/pygem/bin/postproc/postproc_binned_monthly_mass.py
@@ -21,9 +21,13 @@
 import numpy as np
 import xarray as xr
 # pygem imports
-import pygem.setup.config as config
-# read config
-pygem_prms = config.read_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# check for config
+config_manager.ensure_config()
+# read the config
+pygem_prms = config_manager.read_config()
 
 # ----- FUNCTIONS -----
 def getparser():
diff --git a/pygem/bin/postproc/postproc_compile_simulations.py b/pygem/bin/postproc/postproc_compile_simulations.py
index 2f097dca..f399b73f 100644
--- a/pygem/bin/postproc/postproc_compile_simulations.py
+++ b/pygem/bin/postproc/postproc_compile_simulations.py
@@ -21,11 +21,13 @@
 
 # pygem imports
 import pygem
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 rgi_reg_dict = {'all':'Global',
diff --git a/pygem/bin/postproc/postproc_distribute_ice.py b/pygem/bin/postproc/postproc_distribute_ice.py
index 892c335a..3832470f 100644
--- a/pygem/bin/postproc/postproc_distribute_ice.py
+++ b/pygem/bin/postproc/postproc_distribute_ice.py
@@ -24,9 +24,13 @@
 from oggm import workflow, tasks, cfg
 from oggm.sandbox import distribute_2d
 # pygem imports
-import pygem.setup.config as config
-# read config
-pygem_prms = config.read_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# check for config
+config_manager.ensure_config()
+# read the config
+pygem_prms = config_manager.read_config()
 import pygem
 import pygem.pygem_modelsetup as modelsetup
 from pygem.oggm_compat import single_flowline_glacier_directory
diff --git a/pygem/bin/postproc/postproc_monthly_mass.py b/pygem/bin/postproc/postproc_monthly_mass.py
index ea18f641..dff1d66f 100644
--- a/pygem/bin/postproc/postproc_monthly_mass.py
+++ b/pygem/bin/postproc/postproc_monthly_mass.py
@@ -25,9 +25,13 @@
 import xarray as xr
 # pygem imports
 import pygem
-import pygem.setup.config as config
-# read config
-pygem_prms = config.read_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# check for config
+config_manager.ensure_config()
+# read the config
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 
diff --git a/pygem/bin/preproc/preproc_fetch_mbdata.py b/pygem/bin/preproc/preproc_fetch_mbdata.py
index d25cf9ef..b7e381e7 100644
--- a/pygem/bin/preproc/preproc_fetch_mbdata.py
+++ b/pygem/bin/preproc/preproc_fetch_mbdata.py
@@ -19,11 +19,13 @@
 # oggm
 from oggm import utils
 # pygem imports
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 
diff --git a/pygem/bin/preproc/preproc_wgms_estimate_kp.py b/pygem/bin/preproc/preproc_wgms_estimate_kp.py
index 684258a7..e08ab8a6 100644
--- a/pygem/bin/preproc/preproc_wgms_estimate_kp.py
+++ b/pygem/bin/preproc/preproc_wgms_estimate_kp.py
@@ -22,11 +22,13 @@
 from scipy.stats import median_abs_deviation
 # pygem imports
 from pygem import class_climate
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 
diff --git a/pygem/bin/run/run_calibration.py b/pygem/bin/run/run_calibration.py
index 424780ad..da2f3ae0 100755
--- a/pygem/bin/run/run_calibration.py
+++ b/pygem/bin/run/run_calibration.py
@@ -31,11 +31,13 @@
 import sklearn.model_selection
 
 # pygem imports
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 from pygem import mcmc
 from pygem import class_climate
 from pygem.massbalance import PyGEMMassBalance
diff --git a/pygem/bin/run/run_calibration_frontalablation.py b/pygem/bin/run/run_calibration_frontalablation.py
index cd8b0c3d..7d114d9e 100644
--- a/pygem/bin/run/run_calibration_frontalablation.py
+++ b/pygem/bin/run/run_calibration_frontalablation.py
@@ -24,11 +24,13 @@
 from scipy.stats import linregress
 import xarray as xr
 # pygem imports
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 from pygem.massbalance import PyGEMMassBalance
 from pygem.glacierdynamics import MassRedistributionCurveModel
diff --git a/pygem/bin/run/run_calibration_reg_glena.py b/pygem/bin/run/run_calibration_reg_glena.py
index fb0d1bb5..acc4aaa6 100644
--- a/pygem/bin/run/run_calibration_reg_glena.py
+++ b/pygem/bin/run/run_calibration_reg_glena.py
@@ -22,11 +22,13 @@
 from scipy.optimize import brentq
 # pygem imports
 import pygem
-import pygem.setup.config as config
-# Check for config
-config.ensure_config()  # This will ensure the config file is created
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# check for config
+config_manager.ensure_config()
+# read the config
+pygem_prms = config_manager.read_config()
 from pygem import class_climate
 from pygem.massbalance import PyGEMMassBalance
 from pygem.oggm_compat import single_flowline_glacier_directory
diff --git a/pygem/bin/run/run_mcmc_priors.py b/pygem/bin/run/run_mcmc_priors.py
index b196a7f1..be3ebcce 100644
--- a/pygem/bin/run/run_mcmc_priors.py
+++ b/pygem/bin/run/run_mcmc_priors.py
@@ -13,11 +13,13 @@
 from scipy import stats
 
 # pygem imports
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 # Region dictionary for titles
diff --git a/pygem/bin/run/run_simulation.py b/pygem/bin/run/run_simulation.py
index fb6069c7..33922f2f 100755
--- a/pygem/bin/run/run_simulation.py
+++ b/pygem/bin/run/run_simulation.py
@@ -35,11 +35,13 @@
 
 # pygem imports
 import pygem
-import pygem.setup.config as config
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # check for config
-config.ensure_config()
+config_manager.ensure_config()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.gcmbiasadj as gcmbiasadj
 import pygem.pygem_modelsetup as modelsetup
 from pygem.massbalance import PyGEMMassBalance
diff --git a/pygem/class_climate.py b/pygem/class_climate.py
index 10c28935..bd701d39 100755
--- a/pygem/class_climate.py
+++ b/pygem/class_climate.py
@@ -12,10 +12,11 @@ class of climate data and functions associated with manipulating the dataset to
 import pandas as pd
 import numpy as np
 import xarray as xr
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 class GCM():
     """
diff --git a/pygem/gcmbiasadj.py b/pygem/gcmbiasadj.py
index 52ebce0f..e3cc8e81 100755
--- a/pygem/gcmbiasadj.py
+++ b/pygem/gcmbiasadj.py
@@ -16,10 +16,11 @@
 import numpy as np
 from scipy.ndimage import uniform_filter
 from scipy.stats import percentileofscore
-# load pygem config
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 #%% FUNCTIONS
 def annual_avg_2darray(x):
diff --git a/pygem/glacierdynamics.py b/pygem/glacierdynamics.py
index 6b6b024f..03c22a26 100755
--- a/pygem/glacierdynamics.py
+++ b/pygem/glacierdynamics.py
@@ -17,10 +17,11 @@
 from oggm.core.flowline import FlowlineModel
 from oggm.exceptions import InvalidParamsError
 from oggm import __version__
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 cfg.initialize()
 
diff --git a/pygem/massbalance.py b/pygem/massbalance.py
index 15532c2a..2b143162 100644
--- a/pygem/massbalance.py
+++ b/pygem/massbalance.py
@@ -10,10 +10,11 @@
 # Local libraries
 from oggm.core.massbalance import MassBalanceModel
 from pygem.utils._funcs import annualweightedmean_array
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 #%%
 class PyGEMMassBalance(MassBalanceModel):
diff --git a/pygem/mcmc.py b/pygem/mcmc.py
index 98420d0f..1f41c27c 100644
--- a/pygem/mcmc.py
+++ b/pygem/mcmc.py
@@ -14,10 +14,11 @@
 from tqdm import tqdm
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 torch.set_default_dtype(torch.float64)
 plt.rcParams["font.family"] = "arial"
diff --git a/pygem/oggm_compat.py b/pygem/oggm_compat.py
index b3bebdb4..7a98e844 100755
--- a/pygem/oggm_compat.py
+++ b/pygem/oggm_compat.py
@@ -20,10 +20,11 @@
 from oggm.core.massbalance import MassBalanceModel
 #from oggm.shop import rgitopo
 from pygem.shop import debris, mbdata, icethickness
-# Local libraries
-import pygem.setup.config as config
-# read config
-pygem_prms = config.read_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 
 class CompatGlacDir:
diff --git a/pygem/output.py b/pygem/output.py
index a04e7ec9..e01bc6cd 100644
--- a/pygem/output.py
+++ b/pygem/output.py
@@ -18,9 +18,11 @@
 import pandas as pd
 import xarray as xr
 import os, types, json, cftime, collections
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 ### single glacier output parent class ###
 @dataclass
diff --git a/pygem/pygem_modelsetup.py b/pygem/pygem_modelsetup.py
index a602decc..3182669e 100755
--- a/pygem/pygem_modelsetup.py
+++ b/pygem/pygem_modelsetup.py
@@ -13,10 +13,12 @@
 import pandas as pd
 import numpy as np
 from datetime import datetime
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
+
 
 def datesmodelrun(startyear=pygem_prms['climate']['ref_startyear'], endyear=pygem_prms['climate']['ref_endyear'], 
                   spinupyears=pygem_prms['climate']['ref_spinupyears'], option_wateryear=pygem_prms['climate']['ref_wateryear']):
diff --git a/pygem/shop/debris.py b/pygem/shop/debris.py
index 191f256a..13b3f933 100755
--- a/pygem/shop/debris.py
+++ b/pygem/shop/debris.py
@@ -16,10 +16,12 @@
 from oggm.utils import entity_task
 from oggm.core.gis import rasterio_to_gdir
 from oggm.utils import ncDataset
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+# pygem imports
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 """
 To-do list:
diff --git a/pygem/shop/icethickness.py b/pygem/shop/icethickness.py
index dcdc4656..6d7660d3 100755
--- a/pygem/shop/icethickness.py
+++ b/pygem/shop/icethickness.py
@@ -18,10 +18,12 @@
 from oggm.utils import entity_task
 from oggm.core.gis import rasterio_to_gdir
 from oggm.utils import ncDataset
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+# pygem imports
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 if not 'consensus_mass' in cfg.BASENAMES:
     cfg.BASENAMES['consensus_mass'] = ('consensus_mass.pkl', 'Glacier mass from consensus ice thickness data')
diff --git a/pygem/shop/mbdata.py b/pygem/shop/mbdata.py
index f73ebdc2..ba87ffcd 100755
--- a/pygem/shop/mbdata.py
+++ b/pygem/shop/mbdata.py
@@ -23,11 +23,11 @@
 #from oggm.core.gis import rasterio_to_gdir
 #from oggm.utils import ncDataset
 # pygem imports
-import pygem.setup.config as config
-# check for config
-config.ensure_config()
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
 # read the config
-pygem_prms = config.read_config()
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 
diff --git a/pygem/shop/oib.py b/pygem/shop/oib.py
index cbc79edc..70f1f9fc 100644
--- a/pygem/shop/oib.py
+++ b/pygem/shop/oib.py
@@ -12,10 +12,11 @@
 import pandas as pd
 from scipy import signal, stats
 import matplotlib.pyplot as plt
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 class oib:
     def __init__(self, rgi6id='', rgi7id=''):
diff --git a/pygem/utils/_funcs.py b/pygem/utils/_funcs.py
index 2ecb9b5d..11172bad 100755
--- a/pygem/utils/_funcs.py
+++ b/pygem/utils/_funcs.py
@@ -9,10 +9,11 @@
 """
 import numpy as np
 import json
-# Local libraries
-import pygem.setup.config as config
-# Read the config
-pygem_prms = config.read_config()  # This reads the configuration file
+from pygem.setup.config import ConfigManager
+# instantiate ConfigManager
+config_manager = ConfigManager()
+# read the config
+pygem_prms = config_manager.read_config()
 
 def annualweightedmean_array(var, dates_table):
     """

From f8f6eb03bb2804d535c42e41931e64a6ecdcd3ed Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Thu, 27 Feb 2025 18:13:37 -0500
Subject: [PATCH 03/29] raise errors, and ensure that dictionary keys are not
 overwritten

---
 pygem/setup/config.py | 44 ++++++++++++++++++++++---------------------
 1 file changed, 23 insertions(+), 21 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 791d4bfd..7d65fd25 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -43,31 +43,33 @@ def update_config(self, updates):
         yaml = YAML()
         yaml.preserve_quotes = True  # Preserve quotes around string values
 
-        try:
-            with open(self.config_path, 'r') as file:
-                config = yaml.load(file)
+        with open(self.config_path, 'r') as file:
+            config = yaml.load(file)
 
-            for key, value in updates.items():
-                keys = key.split('.')
-                d = config
-                for k in keys[:-1]:
-                    if k not in d:
-                        print(f"Key '{key}' not found in the config. Skipping update.")
-                        break
-                    d = d[k]
-                else:
-                    # Reparse value with YAML to infer correct type
-                    if keys[-1] in d:
-                        d[keys[-1]] = yaml.load(value)
-                    else:
-                        print(f"Key '{key}' not found in the config. Skipping update.")
+        for key, value in updates.items():
+            keys = key.split('.')
+            d = config
+            # Traverse the keys up to the second-to-last
+            for i, k in enumerate(keys[:-1]):
+                if k not in d:
+                    raise KeyError(f"No matching `{'.'.join(keys[:i+1])}` key found in the configuration file at path: {self.config_path}")
+                d = d[k]
 
-            with open(self.config_path, 'w') as file:
-                yaml.dump(config, file)
+            final_key = keys[-1]
 
-        except Exception as e:
-            print(f"Error updating config: {e}")
+            # Ensure the final key exists before updating its value
+            if final_key not in d:
+                raise KeyError(f"No matching `{key}` key found in the configuration file at path: {self.config_path}")
 
+            # Prevent replacing a dictionary with a non-dictionary value
+            if isinstance(d[final_key], dict):
+                raise ValueError(f"Cannot directly overwrite key `{key}` because it contains a dictionary.")
+            
+            d[final_key] = yaml.load(value)
+
+        # Save the updated config back to the file
+        with open(self.config_path, 'w') as file:
+            yaml.dump(config, file)
     
     def _prompt_overwrite(self):
         """Prompt the user for confirmation before overwriting the config file."""

From 16f85d4d1a9499faec780d28256e5db7aa489d7b Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Thu, 27 Feb 2025 18:23:34 -0500
Subject: [PATCH 04/29] create_config() function created and
 _prompt_overwrite() function removed to clean up the class and remove
 redundancy

---
 pygem/setup/config.py | 31 +++++++++++--------------------
 1 file changed, 11 insertions(+), 20 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 7d65fd25..926e2123 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -21,17 +21,18 @@ def __init__(self, config_filename='config.yaml', base_dir=None):
         self.source_config_path = os.path.join(self.package_dir, self.config_filename)
     
     def ensure_config(self, overwrite=False):
-        """Ensure the configuration file exists"""
-        if os.path.isfile(self.config_path) and not overwrite:
-            return
-        
-        if os.path.isfile(self.config_path) and overwrite:
-            overwrite = self._prompt_overwrite()
-        
+        """Ensure the configuration file exists, creating or overwriting it if necessary"""
         if not os.path.isfile(self.config_path) or overwrite:
-            os.makedirs(self.base_dir, exist_ok=True)
-            shutil.copy(self.source_config_path, self.config_path)
-            print(f"Copied default configuration to {self.config_path}")
+            self.create_config()
+
+    def create_config(self):
+        """Copy the default configuration file to the expected location"""
+        if not os.path.exists(self.source_config_path):
+            raise FileNotFoundError(f"Default config file not found at {self.source_config_path}, there may have been an installation issue")
+        
+        os.makedirs(self.base_dir, exist_ok=True)
+        shutil.copy(self.source_config_path, self.config_path)
+        print(f"Copied default configuration to {self.config_path}")
     
     def read_config(self):
         """Read the configuration file and return its contents as a dictionary."""
@@ -70,16 +71,6 @@ def update_config(self, updates):
         # Save the updated config back to the file
         with open(self.config_path, 'w') as file:
             yaml.dump(config, file)
-    
-    def _prompt_overwrite(self):
-        """Prompt the user for confirmation before overwriting the config file."""
-        while True:
-            response = input(f"Configuration file already exists ({self.config_path}). Overwrite? (y/n): ").strip().lower()
-            if response in ['y', 'yes']:
-                return True
-            elif response in ['n', 'no']:
-                return False
-            print("Invalid input. Please enter 'y' or 'n'.")
 
 def main():
     parser = argparse.ArgumentParser()

From 81531bea64ff90b3b0897f535f4a989667fef24c Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Thu, 27 Feb 2025 19:22:46 -0500
Subject: [PATCH 05/29] config test created

---
 pygem/tests/test_config.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 pygem/tests/test_config.py

diff --git a/pygem/tests/test_config.py b/pygem/tests/test_config.py
new file mode 100644
index 00000000..1f4fa601
--- /dev/null
+++ b/pygem/tests/test_config.py
@@ -0,0 +1,24 @@
+"""
+Python Glacier Evolution Model (PyGEM)
+
+copyright © 2018 David Rounce <drounce@cmu.edu>
+
+Distrubted under the MIT lisence
+"""
+from pygem.setup.config import ConfigManager
+
+def test_update_config():
+    updates = {
+        "sim.nsims": "5",
+        "user.email": "updated@example.com",
+        "constants.density_ice": "850"
+    }
+    
+    config_manager = ConfigManager()
+    config_manager.ensure_config(overwrite=True)
+    config_manager.update_config(updates)
+    config = config_manager.read_config()
+    
+    assert config["sim"]["nsims"] == 5
+    assert config["user"]["email"] == "updated@example.com"
+    assert config["constants"]["density_ice"] == 850
\ No newline at end of file

From b6db8d8aad4ed484665ebafef75e57db17af33b9 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 09:28:22 -0500
Subject: [PATCH 06/29] update source_config_path

Co-authored-by: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
---
 pygem/setup/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 926e2123..4a093f71 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -18,7 +18,7 @@ def __init__(self, config_filename='config.yaml', base_dir=None):
         self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
         self.config_path = os.path.join(self.base_dir, self.config_filename)
         self.package_dir = os.path.dirname(__file__)
-        self.source_config_path = os.path.join(self.package_dir, self.config_filename)
+        self.source_config_path = os.path.join(os.path.abspath(__file__), "config.yaml")
     
     def ensure_config(self, overwrite=False):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""

From b981c1dd32c6e813c47f99a37fe8ae533385ebe0 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 09:29:40 -0500
Subject: [PATCH 07/29] remove self.package_dir definition

---
 pygem/setup/config.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 4a093f71..71a1ac8a 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -17,7 +17,6 @@ def __init__(self, config_filename='config.yaml', base_dir=None):
         self.config_filename = config_filename
         self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
         self.config_path = os.path.join(self.base_dir, self.config_filename)
-        self.package_dir = os.path.dirname(__file__)
         self.source_config_path = os.path.join(os.path.abspath(__file__), "config.yaml")
     
     def ensure_config(self, overwrite=False):

From 4314f85541ffde75f13dce8eba7bda882dce3bd0 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 09:58:16 -0500
Subject: [PATCH 08/29] update source path

Co-authored-by: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
---
 pygem/setup/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 71a1ac8a..7118140e 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -17,7 +17,7 @@ def __init__(self, config_filename='config.yaml', base_dir=None):
         self.config_filename = config_filename
         self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
         self.config_path = os.path.join(self.base_dir, self.config_filename)
-        self.source_config_path = os.path.join(os.path.abspath(__file__), "config.yaml")
+        self.source_config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "config.yaml")
     
     def ensure_config(self, overwrite=False):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""

From 4fd5493f1a9ef26b97e2bcf952a1e5f37c788ec1 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 10:14:00 -0500
Subject: [PATCH 09/29] rename ruamel.yaml.YAML() as ryaml

---
 pygem/setup/config.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 7118140e..8af85da5 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -39,9 +39,13 @@ def read_config(self):
             return yaml.safe_load(f)
     
     def update_config(self, updates):
-        """Update multiple keys in the YAML configuration file while preserving quotes and original types."""
-        yaml = YAML()
-        yaml.preserve_quotes = True  # Preserve quotes around string values
+        """Update multiple keys in the YAML configuration file while preserving quotes and original types.
+
+        Args:
+            updates (dict): Dictionary with key-value pairs to be updated
+        """
+        ryaml = YAML()
+        ryaml.preserve_quotes = True  # Preserve quotes around string values
 
         with open(self.config_path, 'r') as file:
             config = yaml.load(file)
@@ -65,11 +69,11 @@ def update_config(self, updates):
             if isinstance(d[final_key], dict):
                 raise ValueError(f"Cannot directly overwrite key `{key}` because it contains a dictionary.")
             
-            d[final_key] = yaml.load(value)
+            d[final_key] = ryaml.load(value)
 
         # Save the updated config back to the file
         with open(self.config_path, 'w') as file:
-            yaml.dump(config, file)
+            ryaml.dump(config, file)
 
 def main():
     parser = argparse.ArgumentParser()

From 4308e79597ff9a9d68c4ec54867a643c1c94c94d Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 10:14:29 -0500
Subject: [PATCH 10/29] call ensure_config() upon __init__

---
 pygem/setup/config.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 8af85da5..bce651e6 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -18,7 +18,8 @@ def __init__(self, config_filename='config.yaml', base_dir=None):
         self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
         self.config_path = os.path.join(self.base_dir, self.config_filename)
         self.source_config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "config.yaml")
-    
+        self.ensure_config()
+        
     def ensure_config(self, overwrite=False):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""
         if not os.path.isfile(self.config_path) or overwrite:

From 2922e6d75c2a168d69119333afaddcd2ef53e9f0 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 10:17:44 -0500
Subject: [PATCH 11/29] user config validation, make sure necessary keys exist

---
 pygem/setup/config.py | 51 ++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 46 insertions(+), 5 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index bce651e6..c09c97b7 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -19,7 +19,7 @@ def __init__(self, config_filename='config.yaml', base_dir=None):
         self.config_path = os.path.join(self.base_dir, self.config_filename)
         self.source_config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "config.yaml")
         self.ensure_config()
-        
+    
     def ensure_config(self, overwrite=False):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""
         if not os.path.isfile(self.config_path) or overwrite:
@@ -33,11 +33,20 @@ def create_config(self):
         os.makedirs(self.base_dir, exist_ok=True)
         shutil.copy(self.source_config_path, self.config_path)
         print(f"Copied default configuration to {self.config_path}")
-    
-    def read_config(self):
-        """Read the configuration file and return its contents as a dictionary."""
+        
+    def read_config(self, validate=True):
+        """Read the configuration file and return its contents as a dictionary.
+        
+        Args:
+            validate (bool): Whether to compare with the default config
+        """
         with open(self.config_path, 'r') as f:
-            return yaml.safe_load(f)
+            user_config = yaml.safe_load(f)
+
+        if validate:
+            self.compare_with_source()
+
+        return user_config
     
     def update_config(self, updates):
         """Update multiple keys in the YAML configuration file while preserving quotes and original types.
@@ -76,6 +85,38 @@ def update_config(self, updates):
         with open(self.config_path, 'w') as file:
             ryaml.dump(config, file)
 
+    def compare_with_source(self):
+        """Compare the user's config with the default and raise errors for missing keys or type mismatches."""
+        with open(self.source_config_path, 'r') as f:
+            default_config = yaml.safe_load(f)
+        with open(self.config_path, 'r') as f:
+            user_config = yaml.safe_load(f)
+
+        def _check(ref, test, path=""):
+            if not isinstance(ref, dict) or not isinstance(test, dict):
+                return
+            
+            for key in ref:
+                current_path = f"{path}.{key}" if path else key
+                if key not in test:
+                    raise ValueError(f"Missing key in user config: {current_path}")
+
+                ref_val, test_val = ref[key], test[key]
+
+                # Allow any type if ref[key] is None
+                if ref_val is not None:
+                    # Ignore type mismatches if the source was a list but now a single value
+                    if isinstance(ref_val, list) and not isinstance(test_val, list):
+                        pass  # Ignore type mismatch
+                    elif type(ref_val) != type(test_val):
+                        raise TypeError(f"Type mismatch at {current_path}: "
+                                        f"expected {type(ref_val)}, got {type(test_val)}")
+
+                if isinstance(ref_val, dict):
+                    _check(ref_val, test_val, current_path)
+
+        _check(default_config, user_config)
+
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('--config', default='config.yaml', help='Path to the config file')

From 4cc29aca510c91571ae711656f384441bd17aa80 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 10:26:08 -0500
Subject: [PATCH 12/29] ConfigManager.ensure_config() calls removed, now
 handled on __init__

---
 pygem/bin/op/duplicate_gdirs.py                    | 2 --
 pygem/bin/op/initialize.py                         | 4 +---
 pygem/bin/op/list_failed_simulations.py            | 2 --
 pygem/bin/postproc/postproc_binned_monthly_mass.py | 2 --
 pygem/bin/postproc/postproc_compile_simulations.py | 2 --
 pygem/bin/postproc/postproc_distribute_ice.py      | 2 --
 pygem/bin/postproc/postproc_monthly_mass.py        | 2 --
 pygem/bin/preproc/preproc_fetch_mbdata.py          | 2 --
 pygem/bin/preproc/preproc_wgms_estimate_kp.py      | 2 --
 pygem/bin/run/run_calibration.py                   | 2 --
 pygem/bin/run/run_calibration_frontalablation.py   | 2 --
 pygem/bin/run/run_calibration_reg_glena.py         | 2 --
 pygem/bin/run/run_mcmc_priors.py                   | 2 --
 pygem/bin/run/run_simulation.py                    | 2 --
 pygem/setup/config.py                              | 7 ++++---
 pygem/tests/test_config.py                         | 3 +--
 16 files changed, 6 insertions(+), 34 deletions(-)

diff --git a/pygem/bin/op/duplicate_gdirs.py b/pygem/bin/op/duplicate_gdirs.py
index 823d7f7a..a84a2f4b 100644
--- a/pygem/bin/op/duplicate_gdirs.py
+++ b/pygem/bin/op/duplicate_gdirs.py
@@ -14,8 +14,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 
diff --git a/pygem/bin/op/initialize.py b/pygem/bin/op/initialize.py
index 0a0822e8..ead82679 100644
--- a/pygem/bin/op/initialize.py
+++ b/pygem/bin/op/initialize.py
@@ -13,9 +13,7 @@
 import shutil
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
-config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config(overwrite=True)
+config_manager = ConfigManager(overwrite=True)
 # read the config
 pygem_prms = config_manager.read_config()
 
diff --git a/pygem/bin/op/list_failed_simulations.py b/pygem/bin/op/list_failed_simulations.py
index fa2c1363..707b1f12 100644
--- a/pygem/bin/op/list_failed_simulations.py
+++ b/pygem/bin/op/list_failed_simulations.py
@@ -18,8 +18,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/postproc/postproc_binned_monthly_mass.py b/pygem/bin/postproc/postproc_binned_monthly_mass.py
index a9888d7a..c72961ff 100644
--- a/pygem/bin/postproc/postproc_binned_monthly_mass.py
+++ b/pygem/bin/postproc/postproc_binned_monthly_mass.py
@@ -24,8 +24,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 
diff --git a/pygem/bin/postproc/postproc_compile_simulations.py b/pygem/bin/postproc/postproc_compile_simulations.py
index f399b73f..8b998626 100644
--- a/pygem/bin/postproc/postproc_compile_simulations.py
+++ b/pygem/bin/postproc/postproc_compile_simulations.py
@@ -24,8 +24,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/postproc/postproc_distribute_ice.py b/pygem/bin/postproc/postproc_distribute_ice.py
index 3832470f..cf350f8f 100644
--- a/pygem/bin/postproc/postproc_distribute_ice.py
+++ b/pygem/bin/postproc/postproc_distribute_ice.py
@@ -27,8 +27,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem
diff --git a/pygem/bin/postproc/postproc_monthly_mass.py b/pygem/bin/postproc/postproc_monthly_mass.py
index dff1d66f..972bb570 100644
--- a/pygem/bin/postproc/postproc_monthly_mass.py
+++ b/pygem/bin/postproc/postproc_monthly_mass.py
@@ -28,8 +28,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/preproc/preproc_fetch_mbdata.py b/pygem/bin/preproc/preproc_fetch_mbdata.py
index b7e381e7..c2282c22 100644
--- a/pygem/bin/preproc/preproc_fetch_mbdata.py
+++ b/pygem/bin/preproc/preproc_fetch_mbdata.py
@@ -22,8 +22,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/preproc/preproc_wgms_estimate_kp.py b/pygem/bin/preproc/preproc_wgms_estimate_kp.py
index e08ab8a6..0cabd84c 100644
--- a/pygem/bin/preproc/preproc_wgms_estimate_kp.py
+++ b/pygem/bin/preproc/preproc_wgms_estimate_kp.py
@@ -25,8 +25,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/run/run_calibration.py b/pygem/bin/run/run_calibration.py
index da2f3ae0..d78378bb 100755
--- a/pygem/bin/run/run_calibration.py
+++ b/pygem/bin/run/run_calibration.py
@@ -34,8 +34,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 from pygem import mcmc
diff --git a/pygem/bin/run/run_calibration_frontalablation.py b/pygem/bin/run/run_calibration_frontalablation.py
index 7d114d9e..6b3a5fb3 100644
--- a/pygem/bin/run/run_calibration_frontalablation.py
+++ b/pygem/bin/run/run_calibration_frontalablation.py
@@ -27,8 +27,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/run/run_calibration_reg_glena.py b/pygem/bin/run/run_calibration_reg_glena.py
index acc4aaa6..18e5ca16 100644
--- a/pygem/bin/run/run_calibration_reg_glena.py
+++ b/pygem/bin/run/run_calibration_reg_glena.py
@@ -25,8 +25,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 from pygem import class_climate
diff --git a/pygem/bin/run/run_mcmc_priors.py b/pygem/bin/run/run_mcmc_priors.py
index be3ebcce..04fc088f 100644
--- a/pygem/bin/run/run_mcmc_priors.py
+++ b/pygem/bin/run/run_mcmc_priors.py
@@ -16,8 +16,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
diff --git a/pygem/bin/run/run_simulation.py b/pygem/bin/run/run_simulation.py
index 33922f2f..e1492e6c 100755
--- a/pygem/bin/run/run_simulation.py
+++ b/pygem/bin/run/run_simulation.py
@@ -38,8 +38,6 @@
 from pygem.setup.config import ConfigManager
 # instantiate ConfigManager
 config_manager = ConfigManager()
-# check for config
-config_manager.ensure_config()
 # read the config
 pygem_prms = config_manager.read_config()
 import pygem.gcmbiasadj as gcmbiasadj
diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index c09c97b7..dcf10228 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -12,17 +12,18 @@
 from ruamel.yaml import YAML
 
 class ConfigManager:
-    def __init__(self, config_filename='config.yaml', base_dir=None):
+    def __init__(self, config_filename='config.yaml', base_dir=None, overwrite=False):
         """initialize the ConfigManager class"""
         self.config_filename = config_filename
         self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
         self.config_path = os.path.join(self.base_dir, self.config_filename)
         self.source_config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "config.yaml")
+        self.overwrite = overwrite
         self.ensure_config()
     
-    def ensure_config(self, overwrite=False):
+    def ensure_config(self):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""
-        if not os.path.isfile(self.config_path) or overwrite:
+        if not os.path.isfile(self.config_path) or self.overwrite:
             self.create_config()
 
     def create_config(self):
diff --git a/pygem/tests/test_config.py b/pygem/tests/test_config.py
index 1f4fa601..c00240b7 100644
--- a/pygem/tests/test_config.py
+++ b/pygem/tests/test_config.py
@@ -14,8 +14,7 @@ def test_update_config():
         "constants.density_ice": "850"
     }
     
-    config_manager = ConfigManager()
-    config_manager.ensure_config(overwrite=True)
+    config_manager = ConfigManager(overwrite=True)
     config_manager.update_config(updates)
     config = config_manager.read_config()
     

From d3d20920109bed306a928dc5e1e84e6c470af8b6 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 10:36:02 -0500
Subject: [PATCH 13/29] bug fix with commit:4fd5493

---
 pygem/setup/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index dcf10228..653a1b16 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -59,7 +59,7 @@ def update_config(self, updates):
         ryaml.preserve_quotes = True  # Preserve quotes around string values
 
         with open(self.config_path, 'r') as file:
-            config = yaml.load(file)
+            config = ryaml.load(file)
 
         for key, value in updates.items():
             keys = key.split('.')

From 197ea6d41f377ce88b040d03d7ef155caf5c9da0 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 11:12:50 -0500
Subject: [PATCH 14/29] more tests added to test_config

---
 pygem/tests/test_config.py | 97 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 96 insertions(+), 1 deletion(-)

diff --git a/pygem/tests/test_config.py b/pygem/tests/test_config.py
index c00240b7..6dec1772 100644
--- a/pygem/tests/test_config.py
+++ b/pygem/tests/test_config.py
@@ -5,8 +5,32 @@
 
 Distrubted under the MIT lisence
 """
+import os, yaml
 from pygem.setup.config import ConfigManager
 
+# Test case to check if the configuration is created or overwritten correctly
+def test_ensure_config():
+    config_manager = ConfigManager(overwrite=True)
+    config_manager.ensure_config()
+
+    # Check if the config file is created
+    assert os.path.isfile(config_manager.config_path)
+    
+    # Check if the default config file was copied correctly
+    with open(config_manager.config_path, 'r') as f:
+        config = f.read()
+    assert "sim" in config  # Check if a known key exists in the config
+
+    # Test without overwriting
+    config_manager_no_overwrite = ConfigManager(overwrite=False)
+    config_manager_no_overwrite.ensure_config()
+
+    # The config should not be overwritten if it already exists
+    with open(config_manager_no_overwrite.config_path, 'r') as f:
+        config_no_overwrite = f.read()
+    assert config_no_overwrite == config  # No change should happen
+
+# Test case to verify updating the config
 def test_update_config():
     updates = {
         "sim.nsims": "5",
@@ -20,4 +44,75 @@ def test_update_config():
     
     assert config["sim"]["nsims"] == 5
     assert config["user"]["email"] == "updated@example.com"
-    assert config["constants"]["density_ice"] == 850
\ No newline at end of file
+    assert config["constants"]["density_ice"] == 850
+
+# Test case to check if the `read_config` function works
+def test_read_config():
+    config_manager = ConfigManager(overwrite=True)
+    config_manager.ensure_config()
+    config = config_manager.read_config()
+
+    # Check that the config reads a known key correctly
+    assert "sim" in config
+    assert isinstance(config["sim"], dict)
+
+# Test case to check if the `compare_with_source` function works
+def test_compare_with_source():
+    config_manager = ConfigManager(overwrite=True)
+    config_manager.ensure_config()
+    
+    # Modify the config file to simulate an error (e.g., remove a required key)
+    config = config_manager.read_config()
+    config["sim"].pop("nsims", None)  # Remove a required key
+    
+    # Write the modified config back to the file
+    with open(config_manager.config_path, 'w') as f:
+        yaml.dump(config, f)
+    
+    # Test if it raises a ValueError when comparing with the source config
+    try:
+        config_manager.compare_with_source()
+        assert False, "Expected ValueError due to missing key"
+    except ValueError:
+        pass  # Expected error, test passes
+
+# Test case for wrong type key-value overwrite
+def test_update_config_wrong_type():
+    # Test for overwriting a dict with a non-dict value
+    updates = {
+        "sim": "invalid_value"  # Trying to overwrite a dict with a non-dict value
+    }
+    
+    config_manager = ConfigManager(overwrite=True)
+    
+    try:
+        config_manager.update_config(updates)
+        assert False, "Expected ValueError due to non-dict overwrite"
+    except ValueError:
+        pass  # Expected error, test passes
+
+    # Test for attempting to overwrite the 'root' key (top-level structure) with a non-dict value
+    updates_root = {
+        "root": "invalid_root_value"  # Trying to overwrite the root of the config with a non-dict value
+    }
+
+    try:
+        config_manager.update_config(updates_root)
+        assert False, "Expected ValueError due to overwriting the root with a non-dict value"
+    except ValueError:
+        pass  # Expected error, test passes
+
+# Test the `create_config` function when the source config doesn't exist
+def test_create_config_missing_source():
+    # Simulate the absence of the source config by removing it if it exists
+    source_config_path = ConfigManager().source_config_path
+    if os.path.exists(source_config_path):
+        os.remove(source_config_path)
+    
+    config_manager = ConfigManager(overwrite=True)
+    
+    try:
+        config_manager.create_config()
+        assert False, "Expected FileNotFoundError due to missing source config"
+    except FileNotFoundError:
+        pass  # Expected error, test passes
\ No newline at end of file

From 441da219f8639736001bb7e094770bde672e17a2 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 11:42:34 -0500
Subject: [PATCH 15/29] more tests and TypeError checks in update_config

---
 pygem/setup/config.py      |  11 ++-
 pygem/tests/test_config.py | 155 +++++++++++++++----------------------
 2 files changed, 70 insertions(+), 96 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 653a1b16..04f81349 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -75,11 +75,16 @@ def update_config(self, updates):
             # Ensure the final key exists before updating its value
             if final_key not in d:
                 raise KeyError(f"No matching `{key}` key found in the configuration file at path: {self.config_path}")
-
             # Prevent replacing a dictionary with a non-dictionary value
             if isinstance(d[final_key], dict):
-                raise ValueError(f"Cannot directly overwrite key `{key}` because it contains a dictionary.")
-            
+                raise TypeError(f"Cannot directly overwrite key `{key}` because it contains a dictionary.")
+            # Check if the original value is a string, and raise an error if a non-string type is passed
+            if isinstance(d[final_key], str) and not isinstance(value, str):
+                raise TypeError(f"Cannot update `{key}` with a non-string value: expected a string.")
+            # Check if the original value is a string, and raise an error if a non-string type is passed
+            if isinstance(d[final_key], bool) and not isinstance(value, bool):
+                raise TypeError(f"Cannot update `{key}` with a non-bool value: expected a bool.")
+
             d[final_key] = ryaml.load(value)
 
         # Save the updated config back to the file
diff --git a/pygem/tests/test_config.py b/pygem/tests/test_config.py
index 6dec1772..f49a5009 100644
--- a/pygem/tests/test_config.py
+++ b/pygem/tests/test_config.py
@@ -1,118 +1,87 @@
-"""
-Python Glacier Evolution Model (PyGEM)
-
-copyright © 2018 David Rounce <drounce@cmu.edu>
-
-Distrubted under the MIT lisence
-"""
-import os, yaml
+import os
+import shutil
 from pygem.setup.config import ConfigManager
 
-# Test case to check if the configuration is created or overwritten correctly
-def test_ensure_config():
-    config_manager = ConfigManager(overwrite=True)
-    config_manager.ensure_config()
-
-    # Check if the config file is created
-    assert os.path.isfile(config_manager.config_path)
+def test_create_config():
+    """Test that create_config creates the config file."""
+    test_dir = os.path.join(os.getcwd(), "test_config")
+    os.makedirs(test_dir, exist_ok=True)
+    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
     
-    # Check if the default config file was copied correctly
-    with open(config_manager.config_path, 'r') as f:
-        config = f.read()
-    assert "sim" in config  # Check if a known key exists in the config
-
-    # Test without overwriting
-    config_manager_no_overwrite = ConfigManager(overwrite=False)
-    config_manager_no_overwrite.ensure_config()
-
-    # The config should not be overwritten if it already exists
-    with open(config_manager_no_overwrite.config_path, 'r') as f:
-        config_no_overwrite = f.read()
-    assert config_no_overwrite == config  # No change should happen
+    config_manager.create_config()
+    assert os.path.isfile(config_manager.config_path), "Config file was not created"
+    
+    # Clean up
+    shutil.rmtree(test_dir)
 
-# Test case to verify updating the config
 def test_update_config():
+    """Test updating keys in the config file."""
+    test_dir = os.path.join(os.getcwd(), "test_config")
+    os.makedirs(test_dir, exist_ok=True)
+    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
+
     updates = {
         "sim.nsims": "5",
         "user.email": "updated@example.com",
         "constants.density_ice": "850"
     }
     
-    config_manager = ConfigManager(overwrite=True)
     config_manager.update_config(updates)
     config = config_manager.read_config()
-    
+
+    # Assert the updates were made correctly
     assert config["sim"]["nsims"] == 5
     assert config["user"]["email"] == "updated@example.com"
     assert config["constants"]["density_ice"] == 850
-
-# Test case to check if the `read_config` function works
-def test_read_config():
-    config_manager = ConfigManager(overwrite=True)
-    config_manager.ensure_config()
-    config = config_manager.read_config()
-
-    # Check that the config reads a known key correctly
-    assert "sim" in config
-    assert isinstance(config["sim"], dict)
-
-# Test case to check if the `compare_with_source` function works
-def test_compare_with_source():
-    config_manager = ConfigManager(overwrite=True)
-    config_manager.ensure_config()
     
-    # Modify the config file to simulate an error (e.g., remove a required key)
-    config = config_manager.read_config()
-    config["sim"].pop("nsims", None)  # Remove a required key
-    
-    # Write the modified config back to the file
-    with open(config_manager.config_path, 'w') as f:
-        yaml.dump(config, f)
-    
-    # Test if it raises a ValueError when comparing with the source config
-    try:
-        config_manager.compare_with_source()
-        assert False, "Expected ValueError due to missing key"
-    except ValueError:
-        pass  # Expected error, test passes
+    # Clean up
+    shutil.rmtree(test_dir)
 
-# Test case for wrong type key-value overwrite
-def test_update_config_wrong_type():
-    # Test for overwriting a dict with a non-dict value
-    updates = {
-        "sim": "invalid_value"  # Trying to overwrite a dict with a non-dict value
-    }
-    
-    config_manager = ConfigManager(overwrite=True)
+def test_update_config_key_error():
+    """Test that update_config raises an error if a key doesn't exist."""
+    test_dir = os.path.join(os.getcwd(), "test_config")
+    os.makedirs(test_dir, exist_ok=True)
+    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
     
     try:
-        config_manager.update_config(updates)
-        assert False, "Expected ValueError due to non-dict overwrite"
-    except ValueError:
-        pass  # Expected error, test passes
-
-    # Test for attempting to overwrite the 'root' key (top-level structure) with a non-dict value
-    updates_root = {
-        "root": "invalid_root_value"  # Trying to overwrite the root of the config with a non-dict value
-    }
+        config_manager.update_config({"nonexistent.key": "value"})
+    except KeyError:
+        pass  # Expected error
+    else:
+        assert False, "KeyError not raised"
+    
+    # Clean up
+    shutil.rmtree(test_dir)
 
+def test_update_config_type_error():
+    """Test that update_config raises an error if there is a type mismatch."""
+    test_dir = os.path.join(os.getcwd(), "test_config")
+    os.makedirs(test_dir, exist_ok=True)
+    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
+    
+    # try setting a dictionary key-value with an value that is not a dictionary
     try:
-        config_manager.update_config(updates_root)
-        assert False, "Expected ValueError due to overwriting the root with a non-dict value"
-    except ValueError:
-        pass  # Expected error, test passes
-
-# Test the `create_config` function when the source config doesn't exist
-def test_create_config_missing_source():
-    # Simulate the absence of the source config by removing it if it exists
-    source_config_path = ConfigManager().source_config_path
-    if os.path.exists(source_config_path):
-        os.remove(source_config_path)
+        config_manager.update_config({"sim": "not a dict"})
+    except TypeError:
+        pass  # Expected error
+    else:
+        assert False, "TypeError not raised"
     
-    config_manager = ConfigManager(overwrite=True)
+    # try setting a bool key-value type with a non-bool value type
+    try:
+        config_manager.update_config({"setup.include_tidewater": -999})
+    except TypeError:
+        pass  # Expected error
+    else:
+        assert False, "TypeError not raised"
     
+    # try setting a string key-value type with a non-string value type
     try:
-        config_manager.create_config()
-        assert False, "Expected FileNotFoundError due to missing source config"
-    except FileNotFoundError:
-        pass  # Expected error, test passes
\ No newline at end of file
+        config_manager.update_config({"root": -999})
+    except TypeError:
+        pass  # Expected error
+    else:
+        assert False, "TypeError not raised"
+    
+    # Clean up
+    shutil.rmtree(test_dir)
\ No newline at end of file

From ceb00c0e8027252cd0e3218f6069e61bafcc705d Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 12:24:15 -0500
Subject: [PATCH 16/29] test ensure config, no overwrite

---
 pygem/tests/test_config.py | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/pygem/tests/test_config.py b/pygem/tests/test_config.py
index f49a5009..6aa19080 100644
--- a/pygem/tests/test_config.py
+++ b/pygem/tests/test_config.py
@@ -14,6 +14,34 @@ def test_create_config():
     # Clean up
     shutil.rmtree(test_dir)
 
+def test_ensure_config_no_overwrite():
+    """Test that create_config does not overwrite the existing config file when overwrite=False."""
+    test_dir = os.path.join(os.getcwd(), "test_config")
+    os.makedirs(test_dir, exist_ok=True)
+    
+    # First, create the config file with overwrite=True
+    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
+    config_manager.create_config()  # This will create the file
+    
+    # Now, try initializing ConfigManager without overwrite=True
+    config_manager_no_overwrite = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=False)
+    
+    # Try to ensure the config - it should not overwrite the existing file
+    try:
+        config_manager_no_overwrite.ensure_config()
+        # If it doesn't raise any exceptions, check that the file exists and is not modified
+        assert os.path.isfile(config_manager_no_overwrite.config_path), "Config file should exist"
+        original_mtime = os.path.getmtime(config_manager.config_path)
+        
+        # Trigger ensure_config again to confirm it does not modify the existing file
+        config_manager_no_overwrite.ensure_config()
+        assert os.path.getmtime(config_manager_no_overwrite.config_path) == original_mtime, "Config file should not be modified"
+    except Exception as e:
+        assert False, f"Unexpected error: {e}"
+    
+    # Clean up
+    shutil.rmtree(test_dir)
+
 def test_update_config():
     """Test updating keys in the config file."""
     test_dir = os.path.join(os.getcwd(), "test_config")

From 0b4b1624dbbb671cb83e5bd9f27efb699749a9d6 Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Fri, 28 Feb 2025 14:42:57 -0500
Subject: [PATCH 17/29] remove CLI update_config funcitonality

---
 pygem/setup/config.py | 21 +--------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 04f81349..03f1f604 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -121,23 +121,4 @@ def _check(ref, test, path=""):
                 if isinstance(ref_val, dict):
                     _check(ref_val, test_val, current_path)
 
-        _check(default_config, user_config)
-
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--config', default='config.yaml', help='Path to the config file')
-    parser.add_argument('updates', nargs='*', help='Key-value pairs to update in the config file')
-    
-    args = parser.parse_args()
-    
-    # Parse the updates into a dictionary
-    updates = {}
-    for update in args.updates:
-        key, value = update.split('=')
-        updates[key] = value
-    
-    config_manager = ConfigManager(config_filename=args.config)
-    config_manager.update_config(updates)
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file
+        _check(default_config, user_config)
\ No newline at end of file

From 9b9dce2ec157ed30e7ccdca4e7f4ad251823d4ea Mon Sep 17 00:00:00 2001
From: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
Date: Sun, 2 Mar 2025 19:27:57 +0000
Subject: [PATCH 18/29] Handle datatypes in `config.yaml` and expand tests
 (#79)

---
 .github/workflows/test_suite.yml |  59 +++++
 pygem/setup/config.py            | 372 ++++++++++++++++++++++++-------
 pygem/tests/test_config.py       | 224 ++++++++++---------
 pygem/tests/test_notebooks.py    |  20 ++
 pygem/tests/test_oggm_compat.py  |  78 -------
 pyproject.toml                   |  10 +-
 6 files changed, 502 insertions(+), 261 deletions(-)
 create mode 100644 .github/workflows/test_suite.yml
 create mode 100644 pygem/tests/test_notebooks.py
 delete mode 100755 pygem/tests/test_oggm_compat.py

diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
new file mode 100644
index 00000000..a0692c85
--- /dev/null
+++ b/.github/workflows/test_suite.yml
@@ -0,0 +1,59 @@
+name: 'Install PyGEM and Run Test Suite'
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+    paths:
+      - '**.py'
+      - '.github/workflows/test_suite.yml'
+      - 'pyproject.toml'
+
+  pull_request:
+    paths:
+      - '**.py'
+      - '.github/workflows/test_suite.yml'
+      - 'pyproject.toml'
+
+  # Run test suite every Saturday at 1AM GMT (1 hour after the Docker image is updated)
+  schedule:
+    - cron: '0 1 * * 6'
+
+# Stop the workflow if a new one is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test_suite:
+    name: 'Test suite'
+    runs-on: ubuntu-latest
+    container:
+      # Use pygem:latest for master branch and pygem:dev otherwise
+      image: ghcr.io/pygem-community/pygem:${{ github.ref == 'refs/heads/master' && 'latest' || 'dev' }}
+      options: --user root
+    env:
+      # Since we are root we need to set PYTHONPATH to be able to find the installed packages
+      PYTHONPATH: /home/ubuntu/.local/lib/python3.12/site-packages
+
+    steps:
+      - name: 'Checkout the PyGEM repo'
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: 'Reinstall PyGEM'
+        run: pip install --break-system-packages -e .
+
+      - name: 'Initialize PyGEM'
+        run: initialize
+
+      - name: 'Clone the PyGEM-notebooks repo'
+        run: |
+          git clone -b 11_config_update --depth 1 https://github.com/pygem-community/PyGEM-notebooks.git
+          echo "PYGEM_NOTEBOOKS_DIRPATH=$(pwd)/PyGEM-notebooks" >> $GITHUB_ENV
+
+      - name: 'Run tests'
+        run: |
+          python3 -m coverage erase
+          python3 -m pytest --cov=pygem -v --durations=20 pygem/tests
diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 03f1f604..1e793ab3 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -9,7 +9,7 @@
 import shutil
 import yaml
 import argparse
-from ruamel.yaml import YAML
+import ruamel.yaml
 
 class ConfigManager:
     def __init__(self, config_filename='config.yaml', base_dir=None, overwrite=False):
@@ -24,101 +24,319 @@ def __init__(self, config_filename='config.yaml', base_dir=None, overwrite=False
     def ensure_config(self):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""
         if not os.path.isfile(self.config_path) or self.overwrite:
-            self.create_config()
+            self.copy_source_config()
 
-    def create_config(self):
+    def copy_source_config(self):
         """Copy the default configuration file to the expected location"""
-        if not os.path.exists(self.source_config_path):
-            raise FileNotFoundError(f"Default config file not found at {self.source_config_path}, there may have been an installation issue")
-        
+
         os.makedirs(self.base_dir, exist_ok=True)
         shutil.copy(self.source_config_path, self.config_path)
         print(f"Copied default configuration to {self.config_path}")
         
     def read_config(self, validate=True):
-        """Read the configuration file and return its contents as a dictionary.
-        
-        Args:
-            validate (bool): Whether to compare with the default config
-        """
+        """Read the configuration file and return its contents as a dictionary while preserving formatting."""
+        ryaml = ruamel.yaml.YAML()
         with open(self.config_path, 'r') as f:
-            user_config = yaml.safe_load(f)
+            user_config = ryaml.load(f)  # Using ruamel.yaml for preservation
 
         if validate:
-            self.compare_with_source()
+            self.validate_config(user_config)
 
         return user_config
+
+    def write_config(self, config):
+        """Write the configuration dictionary to the file while preserving quotes."""
+        ryaml = ruamel.yaml.YAML()
+        ryaml.preserve_quotes = True
+        with open(self.config_path, 'w') as file:
+            ryaml.dump(config, file)  # This will preserve quotes
     
     def update_config(self, updates):
-        """Update multiple keys in the YAML configuration file while preserving quotes and original types.
-
-        Args:
-            updates (dict): Dictionary with key-value pairs to be updated
-        """
-        ryaml = YAML()
-        ryaml.preserve_quotes = True  # Preserve quotes around string values
-
-        with open(self.config_path, 'r') as file:
-            config = ryaml.load(file)
-
+        """Update multiple keys in the YAML configuration file while preserving quotes and original types."""
+        config = self.read_config(validate=False)  # Read existing config
+        
         for key, value in updates.items():
+            if key not in self.EXPECTED_TYPES:
+                raise KeyError(f"Unrecognized configuration key: {key}")
             keys = key.split('.')
             d = config
-            # Traverse the keys up to the second-to-last
-            for i, k in enumerate(keys[:-1]):
-                if k not in d:
-                    raise KeyError(f"No matching `{'.'.join(keys[:i+1])}` key found in the configuration file at path: {self.config_path}")
-                d = d[k]
-
-            final_key = keys[-1]
+            for sub_key in keys[:-1]:
+                d = d[sub_key]
 
-            # Ensure the final key exists before updating its value
-            if final_key not in d:
-                raise KeyError(f"No matching `{key}` key found in the configuration file at path: {self.config_path}")
-            # Prevent replacing a dictionary with a non-dictionary value
-            if isinstance(d[final_key], dict):
-                raise TypeError(f"Cannot directly overwrite key `{key}` because it contains a dictionary.")
-            # Check if the original value is a string, and raise an error if a non-string type is passed
-            if isinstance(d[final_key], str) and not isinstance(value, str):
-                raise TypeError(f"Cannot update `{key}` with a non-string value: expected a string.")
-            # Check if the original value is a string, and raise an error if a non-string type is passed
-            if isinstance(d[final_key], bool) and not isinstance(value, bool):
-                raise TypeError(f"Cannot update `{key}` with a non-bool value: expected a bool.")
-
-            d[final_key] = ryaml.load(value)
-
-        # Save the updated config back to the file
-        with open(self.config_path, 'w') as file:
-            ryaml.dump(config, file)
-
-    def compare_with_source(self):
-        """Compare the user's config with the default and raise errors for missing keys or type mismatches."""
-        with open(self.source_config_path, 'r') as f:
-            default_config = yaml.safe_load(f)
-        with open(self.config_path, 'r') as f:
-            user_config = yaml.safe_load(f)
-
-        def _check(ref, test, path=""):
-            if not isinstance(ref, dict) or not isinstance(test, dict):
-                return
-            
-            for key in ref:
-                current_path = f"{path}.{key}" if path else key
-                if key not in test:
-                    raise ValueError(f"Missing key in user config: {current_path}")
+            d[keys[-1]] = value
+        
+        self.validate_config(config)
+        self.write_config(config)
+    
+    def validate_config(self, data):
+        """Validate the configuration file against expected types and required keys"""
+        for key, expected_type in self.EXPECTED_TYPES.items():
+            keys = key.split(".")
+            sub_data = data
+            for sub_key in keys:
+                if isinstance(sub_data, dict) and sub_key in sub_data:
+                    sub_data = sub_data[sub_key]
+                else:
+                    raise KeyError(f"Missing required key in configuration: {key}")
 
-                ref_val, test_val = ref[key], test[key]
+            if not isinstance(sub_data, expected_type):
+                raise TypeError(f"Invalid type for '{key}': expected {expected_type}, not {type(sub_data)}")
 
-                # Allow any type if ref[key] is None
-                if ref_val is not None:
-                    # Ignore type mismatches if the source was a list but now a single value
-                    if isinstance(ref_val, list) and not isinstance(test_val, list):
-                        pass  # Ignore type mismatch
-                    elif type(ref_val) != type(test_val):
-                        raise TypeError(f"Type mismatch at {current_path}: "
-                                        f"expected {type(ref_val)}, got {type(test_val)}")
+            # Check elements inside lists (if defined)
+            if key in self.LIST_ELEMENT_TYPES and isinstance(sub_data, list):
+                elem_type = self.LIST_ELEMENT_TYPES[key]
+                if not all(isinstance(item, elem_type) for item in sub_data):
+                    raise TypeError(f"Invalid type for elements in '{key}': expected all elements to be {elem_type}, but got {sub_data}")
+    
 
-                if isinstance(ref_val, dict):
-                    _check(ref_val, test_val, current_path)
+    # expected config types
+    EXPECTED_TYPES = {
+        "root": str,
+        "user": dict,
+        "user.name":  (str, type(None)),
+        "user.institution":  (str, type(None)),
+        "user.email":  (str, type(None)),
+        "setup": dict,
+        "setup.rgi_region01": list,
+        "setup.rgi_region02": str,
+        "setup.glac_no_skip": (list, type(None)),
+        "setup.glac_no": (list, type(None)),
+        "setup.min_glac_area_km2": int,
+        "setup.include_landterm": bool,
+        "setup.include_laketerm": bool,
+        "setup.include_tidewater": bool,
+        "setup.include_frontalablation": bool,
+        "oggm": dict,
+        "oggm.base_url": str,
+        "oggm.logging_level": str,
+        "oggm.border": int,
+        "oggm.oggm_gdir_relpath": str,
+        "oggm.overwrite_gdirs": bool,
+        "oggm.has_internet": bool,
+        "climate": dict,
+        "climate.ref_gcm_name": str,
+        "climate.ref_startyear": int,
+        "climate.ref_endyear": int,
+        "climate.ref_wateryear": str,
+        "climate.ref_spinupyears": int,
+        "climate.gcm_name": str,
+        "climate.scenario": (str, type(None)),
+        "climate.gcm_startyear": int,
+        "climate.gcm_endyear": int,
+        "climate.gcm_wateryear": str,
+        "climate.constantarea_years": int,
+        "climate.gcm_spinupyears": int,
+        "climate.hindcast": bool,
+        "climate.paths": dict,
+        "climate.paths.era5_relpath": str,
+        "climate.paths.era5_temp_fn": str,
+        "climate.paths.era5_tempstd_fn": str,
+        "climate.paths.era5_prec_fn": str,
+        "climate.paths.era5_elev_fn": str,
+        "climate.paths.era5_pressureleveltemp_fn": str,
+        "climate.paths.era5_lr_fn": str,
+        "climate.paths.cmip5_relpath": str,
+        "climate.paths.cmip5_fp_var_ending": str,
+        "climate.paths.cmip5_fp_fx_ending": str,
+        "climate.paths.cmip6_relpath": str,
+        "climate.paths.cesm2_relpath": str,
+        "climate.paths.cesm2_fp_var_ending": str,
+        "climate.paths.cesm2_fp_fx_ending": str,
+        "climate.paths.gfdl_relpath": str,
+        "climate.paths.gfdl_fp_var_ending": str,
+        "climate.paths.gfdl_fp_fx_ending": str,
+        "calib": dict,
+        "calib.option_calibration": str,
+        "calib.priors_reg_fn": str,
+        "calib.HH2015_params": dict,
+        "calib.HH2015_params.tbias_init": int,
+        "calib.HH2015_params.tbias_step": int,
+        "calib.HH2015_params.kp_init": float,
+        "calib.HH2015_params.kp_bndlow": float,
+        "calib.HH2015_params.kp_bndhigh": int,
+        "calib.HH2015_params.ddfsnow_init": float,
+        "calib.HH2015_params.ddfsnow_bndlow": float,
+        "calib.HH2015_params.ddfsnow_bndhigh": float,
+        "calib.HH2015mod_params": dict,
+        "calib.HH2015mod_params.tbias_init": int,
+        "calib.HH2015mod_params.tbias_step": float,
+        "calib.HH2015mod_params.kp_init": int,
+        "calib.HH2015mod_params.kp_bndlow": float,
+        "calib.HH2015mod_params.kp_bndhigh": int,
+        "calib.HH2015mod_params.ddfsnow_init": float,
+        "calib.HH2015mod_params.method_opt": str,
+        "calib.HH2015mod_params.params2opt": list,
+        "calib.HH2015mod_params.ftol_opt": float,
+        "calib.HH2015mod_params.eps_opt": float,
+        "calib.emulator_params": dict,
+        "calib.emulator_params.emulator_sims": int,
+        "calib.emulator_params.overwrite_em_sims": bool,
+        "calib.emulator_params.opt_hh2015_mod": bool,
+        "calib.emulator_params.tbias_step": float,
+        "calib.emulator_params.tbias_init": int,
+        "calib.emulator_params.kp_init": int,
+        "calib.emulator_params.kp_bndlow": float,
+        "calib.emulator_params.kp_bndhigh": int,
+        "calib.emulator_params.ddfsnow_init": float,
+        "calib.emulator_params.option_areaconstant": bool,
+        "calib.emulator_params.tbias_disttype": str,
+        "calib.emulator_params.tbias_sigma": int,
+        "calib.emulator_params.kp_gamma_alpha": int,
+        "calib.emulator_params.kp_gamma_beta": int,
+        "calib.emulator_params.ddfsnow_disttype": str,
+        "calib.emulator_params.ddfsnow_mu": float,
+        "calib.emulator_params.ddfsnow_sigma": float,
+        "calib.emulator_params.ddfsnow_bndlow": int,
+        "calib.emulator_params.ddfsnow_bndhigh": float,
+        "calib.emulator_params.method_opt": str,
+        "calib.emulator_params.params2opt": list,
+        "calib.emulator_params.ftol_opt": float,
+        "calib.emulator_params.eps_opt": float,
+        "calib.MCMC_params": dict,
+        "calib.MCMC_params.option_use_emulator": bool,
+        "calib.MCMC_params.emulator_sims": int,
+        "calib.MCMC_params.tbias_step": float,
+        "calib.MCMC_params.tbias_stepsmall": float,
+        "calib.MCMC_params.option_areaconstant": bool,
+        "calib.MCMC_params.mcmc_step": float,
+        "calib.MCMC_params.n_chains": int,
+        "calib.MCMC_params.mcmc_sample_no": int,
+        "calib.MCMC_params.mcmc_burn_pct": int,
+        "calib.MCMC_params.thin_interval": int,
+        "calib.MCMC_params.ddfsnow_disttype": str,
+        "calib.MCMC_params.ddfsnow_mu": float,
+        "calib.MCMC_params.ddfsnow_sigma": float,
+        "calib.MCMC_params.ddfsnow_bndlow": int,
+        "calib.MCMC_params.ddfsnow_bndhigh": float,
+        "calib.MCMC_params.kp_disttype": str,
+        "calib.MCMC_params.tbias_disttype": str,
+        "calib.MCMC_params.tbias_mu": int,
+        "calib.MCMC_params.tbias_sigma": int,
+        "calib.MCMC_params.tbias_bndlow": int,
+        "calib.MCMC_params.tbias_bndhigh": int,
+        "calib.MCMC_params.kp_gamma_alpha": int,
+        "calib.MCMC_params.kp_gamma_beta": int,
+        "calib.MCMC_params.kp_lognorm_mu": int,
+        "calib.MCMC_params.kp_lognorm_tau": int,
+        "calib.MCMC_params.kp_mu": int,
+        "calib.MCMC_params.kp_sigma": float,
+        "calib.MCMC_params.kp_bndlow": float,
+        "calib.MCMC_params.kp_bndhigh": float,
+        "calib.data": dict,
+        "calib.data.massbalance": dict,
+        "calib.data.massbalance.hugonnet2021_relpath": str,
+        "calib.data.massbalance.hugonnet2021_fn": str,
+        "calib.data.massbalance.hugonnet2021_facorrected_fn": str,
+        "calib.data.oib": dict,
+        "calib.data.oib.oib_relpath": str,
+        "calib.data.oib.oib_rebin": int,
+        "calib.data.oib.oib_filter_pctl": int,
+        "calib.data.frontalablation": dict,
+        "calib.data.frontalablation.frontalablation_relpath": str,
+        "calib.data.frontalablation.frontalablation_cal_fn": str,
+        "calib.data.icethickness": dict,
+        "calib.data.icethickness.h_consensus_relpath": str,
+        "calib.icethickness_cal_frac_byarea": float,
+        "sim": dict,
+        "sim.option_dynamics": (str, type(None)),
+        "sim.option_bias_adjustment": int,
+        "sim.nsims": int,
+        "sim.out": dict,
+        "sim.out.sim_stats": list,
+        "sim.out.export_all_simiters": bool,
+        "sim.out.export_extra_vars": bool,
+        "sim.out.export_binned_data": bool,
+        "sim.out.export_binned_components": bool,
+        "sim.out.export_binned_area_threshold": int,
+        "sim.oggm_dynamics": dict,
+        "sim.oggm_dynamics.cfl_number": float,
+        "sim.oggm_dynamics.cfl_number_calving": float,
+        "sim.oggm_dynamics.glena_reg_relpath": str,
+        "sim.oggm_dynamics.use_reg_glena": bool,
+        "sim.oggm_dynamics.fs": int,
+        "sim.oggm_dynamics.glen_a_multiplier": int,
+        "sim.icethickness_advancethreshold": int,
+        "sim.terminus_percentage": int,
+        "sim.params": dict,
+        "sim.params.use_constant_lapserate": bool,
+        "sim.params.kp": int,
+        "sim.params.tbias": int,
+        "sim.params.ddfsnow": float,
+        "sim.params.ddfsnow_iceratio": float,
+        "sim.params.precgrad": float,
+        "sim.params.lapserate": float,
+        "sim.params.tsnow_threshold": int,
+        "sim.params.calving_k": float,
+        "mb": dict,
+        "mb.option_surfacetype_initial": int,
+        "mb.include_firn": bool,
+        "mb.include_debris": bool,
+        "mb.debris_relpath": str,
+        "mb.option_elev_ref_downscale": str,
+        "mb.option_temp2bins": int,
+        "mb.option_adjusttemp_surfelev": int,
+        "mb.option_prec2bins": int,
+        "mb.option_preclimit": int,
+        "mb.option_accumulation": int,
+        "mb.option_ablation": int,
+        "mb.option_ddf_firn": int,
+        "mb.option_refreezing": str,
+        "mb.Woodard_rf_opts": dict,
+        "mb.Woodard_rf_opts.rf_month": int,
+        "mb.HH2015_rf_opts": dict,
+        "mb.HH2015_rf_opts.rf_layers": int,
+        "mb.HH2015_rf_opts.rf_dz": int,
+        "mb.HH2015_rf_opts.rf_dsc": int,
+        "mb.HH2015_rf_opts.rf_meltcrit": float,
+        "mb.HH2015_rf_opts.pp": float,
+        "mb.HH2015_rf_opts.rf_dens_top": int,
+        "mb.HH2015_rf_opts.rf_dens_bot": int,
+        "mb.HH2015_rf_opts.option_rf_limit_meltsnow": int,
+        "rgi": dict,
+        "rgi.rgi_relpath": str,
+        "rgi.rgi_lat_colname": str,
+        "rgi.rgi_lon_colname": str,
+        "rgi.elev_colname": str,
+        "rgi.indexname": str,
+        "rgi.rgi_O1Id_colname": str,
+        "rgi.rgi_glacno_float_colname": str,
+        "rgi.rgi_cols_drop": list,
+        "time": dict,
+        "time.option_leapyear": int,
+        "time.startmonthday": str,
+        "time.endmonthday": str,
+        "time.wateryear_month_start": int,
+        "time.winter_month_start": int,
+        "time.summer_month_start": int,
+        "time.option_dates": int,
+        "time.timestep": str,
+        "constants": dict,
+        "constants.density_ice": int,
+        "constants.density_water": int,
+        "constants.area_ocean": float,
+        "constants.k_ice": float,
+        "constants.k_air": float,
+        "constants.ch_ice": int,
+        "constants.ch_air": int,
+        "constants.Lh_rf": int,
+        "constants.tolerance": float,
+        "constants.gravity": float,
+        "constants.pressure_std": int,
+        "constants.temp_std": float,
+        "constants.R_gas": float,
+        "constants.molarmass_air": float,
+        "debug": dict,
+        "debug.refreeze": bool,
+        "debug.mb": bool,
+    }
 
-        _check(default_config, user_config)
\ No newline at end of file
+    # expected types of elements in lists
+    LIST_ELEMENT_TYPES = {
+        "setup.rgi_region01": int,
+        "setup.glac_no_skip": float,
+        "setup.glac_no": float,
+        "calib.HH2015mod_params.params2opt": str,
+        "calib.emulator_params.params2opt": str,
+        "sim.out.sim_stats": str,
+        "rgi.rgi_cols_drop": str,
+    }
diff --git a/pygem/tests/test_config.py b/pygem/tests/test_config.py
index 6aa19080..8e1a727c 100644
--- a/pygem/tests/test_config.py
+++ b/pygem/tests/test_config.py
@@ -1,115 +1,129 @@
-import os
-import shutil
+import pathlib
+import pytest
+import yaml
 from pygem.setup.config import ConfigManager
 
-def test_create_config():
-    """Test that create_config creates the config file."""
-    test_dir = os.path.join(os.getcwd(), "test_config")
-    os.makedirs(test_dir, exist_ok=True)
-    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
-    
-    config_manager.create_config()
-    assert os.path.isfile(config_manager.config_path), "Config file was not created"
-    
-    # Clean up
-    shutil.rmtree(test_dir)
 
-def test_ensure_config_no_overwrite():
-    """Test that create_config does not overwrite the existing config file when overwrite=False."""
-    test_dir = os.path.join(os.getcwd(), "test_config")
-    os.makedirs(test_dir, exist_ok=True)
-    
-    # First, create the config file with overwrite=True
-    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
-    config_manager.create_config()  # This will create the file
+class TestConfigManager:
+    """Tests for the ConfigManager class."""
     
-    # Now, try initializing ConfigManager without overwrite=True
-    config_manager_no_overwrite = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=False)
+    @pytest.fixture(autouse=True)
+    def setup(self, tmp_path):
+        """Setup a ConfigManager instance for each test."""
+        self.config_manager = ConfigManager(
+            config_filename='config.yaml',
+            base_dir=tmp_path,
+            overwrite=True
+        )
     
-    # Try to ensure the config - it should not overwrite the existing file
-    try:
-        config_manager_no_overwrite.ensure_config()
-        # If it doesn't raise any exceptions, check that the file exists and is not modified
-        assert os.path.isfile(config_manager_no_overwrite.config_path), "Config file should exist"
-        original_mtime = os.path.getmtime(config_manager.config_path)
-        
-        # Trigger ensure_config again to confirm it does not modify the existing file
-        config_manager_no_overwrite.ensure_config()
-        assert os.path.getmtime(config_manager_no_overwrite.config_path) == original_mtime, "Config file should not be modified"
-    except Exception as e:
-        assert False, f"Unexpected error: {e}"
-    
-    # Clean up
-    shutil.rmtree(test_dir)
+    def test_config_created(self, tmp_path):
+        config_path = pathlib.Path(tmp_path) / 'config.yaml'
+        assert config_path.is_file()
 
-def test_update_config():
-    """Test updating keys in the config file."""
-    test_dir = os.path.join(os.getcwd(), "test_config")
-    os.makedirs(test_dir, exist_ok=True)
-    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
+    def test_read_config(self):
+        config = self.config_manager.read_config()
+        assert isinstance(config, dict)
+        assert "sim" in config
+        assert "nsims" in config["sim"]
 
-    updates = {
-        "sim.nsims": "5",
-        "user.email": "updated@example.com",
-        "constants.density_ice": "850"
-    }
-    
-    config_manager.update_config(updates)
-    config = config_manager.read_config()
+    def test_update_config_unrecognized_key_error(self):
+        """Test that a KeyError is raised when updating a value with an unrecognized key."""
+        with pytest.raises(KeyError, match="Unrecognized configuration key: invalid_key"):
+            self.config_manager.update_config({"invalid_key": None})
 
-    # Assert the updates were made correctly
-    assert config["sim"]["nsims"] == 5
-    assert config["user"]["email"] == "updated@example.com"
-    assert config["constants"]["density_ice"] == 850
-    
-    # Clean up
-    shutil.rmtree(test_dir)
+    @pytest.mark.parametrize("key, invalid_value, expected_type, invalid_type", [
+        ("sim.nsims", [1, 2, 3], "int", "list"),
+        ("calib.HH2015_params.kp_init", "0.5", "float", "str"),
+        ("setup.include_landterm", -999, "bool", "int"),
+        ("rgi.rgi_cols_drop", "not-a-list", "list", "str"),
+    ])
+    def test_update_config_type_error(self, key, invalid_value, expected_type, invalid_type):
+        """
+        Test that a TypeError is raised when updating a value with a new value of a
+        wrong type.
+        """
+        with pytest.raises(
+            TypeError, 
+            match=f"Invalid type for '{key.replace('.', '\\.')}':"
+                  f" expected.*{expected_type}.*, not.*{invalid_type}.*"
+        ):
+            self.config_manager.update_config({key: invalid_value})
 
-def test_update_config_key_error():
-    """Test that update_config raises an error if a key doesn't exist."""
-    test_dir = os.path.join(os.getcwd(), "test_config")
-    os.makedirs(test_dir, exist_ok=True)
-    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
-    
-    try:
-        config_manager.update_config({"nonexistent.key": "value"})
-    except KeyError:
-        pass  # Expected error
-    else:
-        assert False, "KeyError not raised"
-    
-    # Clean up
-    shutil.rmtree(test_dir)
+    def test_update_config_list_element_type_error(self):
+        """
+        Test that a TypeError is raised when updating a value with a new list value
+        containing elements of a different type than expected.
+        """
+        key = "rgi.rgi_cols_drop"
+        invalid_value = ["a", "b", 100]
+        expected_type = "str"
 
-def test_update_config_type_error():
-    """Test that update_config raises an error if there is a type mismatch."""
-    test_dir = os.path.join(os.getcwd(), "test_config")
-    os.makedirs(test_dir, exist_ok=True)
-    config_manager = ConfigManager(config_filename='config.yaml', base_dir=test_dir, overwrite=True)
-    
-    # try setting a dictionary key-value with an value that is not a dictionary
-    try:
-        config_manager.update_config({"sim": "not a dict"})
-    except TypeError:
-        pass  # Expected error
-    else:
-        assert False, "TypeError not raised"
-    
-    # try setting a bool key-value type with a non-bool value type
-    try:
-        config_manager.update_config({"setup.include_tidewater": -999})
-    except TypeError:
-        pass  # Expected error
-    else:
-        assert False, "TypeError not raised"
-    
-    # try setting a string key-value type with a non-string value type
-    try:
-        config_manager.update_config({"root": -999})
-    except TypeError:
-        pass  # Expected error
-    else:
-        assert False, "TypeError not raised"
-    
-    # Clean up
-    shutil.rmtree(test_dir)
\ No newline at end of file
+        with pytest.raises(
+            TypeError, 
+            match=f"Invalid type for elements in '{key.replace('.', '\\.')}':"
+                  f" expected all elements to be .*{expected_type}.*, but got.*{invalid_value}.*"
+        ):
+            self.config_manager.update_config({key: invalid_value})
+
+    def test_compare_with_source(self):
+        """Test that compare_with_source detects missing keys."""
+        # Remove a key from the config file
+        with open(self.config_manager.config_path, 'r') as f:
+            config = yaml.safe_load(f)
+        del config['sim']['nsims']
+        with open(self.config_manager.config_path, 'w') as f:
+            yaml.dump(config, f)
+
+        with pytest.raises(KeyError, match=r"Missing required key in configuration: sim\.nsims"):
+            self.config_manager.read_config(validate=True)
+
+    def test_update_config(self):
+        """Test that update_config updates the config file for all data types."""
+        updates = {
+            "sim.nsims": 5,                             # int
+            "calib.HH2015_params.kp_init": 0.5,         # float
+            "user.email": "updated@example.com",        # str
+            "setup.include_landterm": False,            # bool
+            "rgi.rgi_cols_drop": ['Item1', 'Item2'],    # list
+        }
+
+        # Values before updating
+        config = self.config_manager.read_config()
+        assert config["sim"]["nsims"] == 1
+        assert config["calib"]["HH2015_params"]["kp_init"] == 1.5
+        assert config["user"]["email"] == "drounce@cmu.edu"
+        assert config["setup"]["include_landterm"] == True
+        assert config["rgi"]["rgi_cols_drop"] == ["GLIMSId", "BgnDate", "EndDate", "Status", "Linkages", "Name"]
+        
+        self.config_manager.update_config(updates)
+        config = self.config_manager.read_config()
+
+        # Values after updating
+        assert config["sim"]["nsims"] == 5
+        assert config["calib"]["HH2015_params"]["kp_init"] == 0.5
+        assert config["setup"]["include_landterm"] == False
+        assert config["user"]["email"] == "updated@example.com"
+        assert config["rgi"]["rgi_cols_drop"] == ["Item1", "Item2"]
+
+    def test_update_config_dict(self):
+        """Test that update_config updates the config file for nested dictionaries."""
+        # Values before updating
+        config = self.config_manager.read_config()
+        assert config["user"]["name"] == "David Rounce"
+        assert config["user"]["email"] == "drounce@cmu.edu"
+        assert config["user"]["institution"] == "Carnegie Mellon University, Pittsburgh PA"
+
+        updates = {
+            "user": {
+                "name": "New Name",
+                "email": "New email",
+                "institution": "New Institution",
+            }
+        }
+        self.config_manager.update_config(updates)
+
+        # Values after updating
+        config = self.config_manager.read_config()
+        assert config["user"]["name"] == "New Name"
+        assert config["user"]["email"] == "New email"
+        assert config["user"]["institution"] == "New Institution"
diff --git a/pygem/tests/test_notebooks.py b/pygem/tests/test_notebooks.py
new file mode 100644
index 00000000..350a2a20
--- /dev/null
+++ b/pygem/tests/test_notebooks.py
@@ -0,0 +1,20 @@
+import os
+import subprocess
+
+import pytest
+
+# Get all notebooks in the PyGEM-notebooks repository
+nb_dir = os.environ.get("PYGEM_NOTEBOOKS_DIRPATH") or os.path.join(
+    os.path.expanduser("~"), "PyGEM-notebooks"
+)
+notebooks = [f for f in os.listdir(nb_dir) if f.endswith(".ipynb")]
+
+
+@pytest.mark.parametrize("notebook", notebooks)
+def test_notebook(notebook):
+    # TODO #54: Test all notebooks
+    if notebook not in ("simple_test.ipynb", "advanced_test.ipynb"):
+        pytest.skip()
+    subprocess.check_call(
+        ["pytest", "--nbmake", os.path.join(nb_dir, notebook)]
+    )
\ No newline at end of file
diff --git a/pygem/tests/test_oggm_compat.py b/pygem/tests/test_oggm_compat.py
deleted file mode 100755
index 28c8afff..00000000
--- a/pygem/tests/test_oggm_compat.py
+++ /dev/null
@@ -1,78 +0,0 @@
-from pygem import oggm_compat
-import numpy as np
-
-do_plot = False
-
-
-def test_single_flowline_glacier_directory():
-
-    rid = 'RGI60-15.03473'
-    gdir = oggm_compat.single_flowline_glacier_directory(rid)
-    assert gdir.rgi_area_km2 == 61.054
-
-    if do_plot:
-        from oggm import graphics
-        import matplotlib.pyplot as plt
-        f, (ax1, ax2) = plt.subplots(1, 2)
-        graphics.plot_googlemap(gdir, ax=ax1)
-        graphics.plot_inversion(gdir, ax=ax2)
-        plt.show()
-
-
-def test_get_glacier_zwh():
-
-    rid = 'RGI60-15.03473'
-    gdir = oggm_compat.single_flowline_glacier_directory(rid)
-    df = oggm_compat.get_glacier_zwh(gdir)
-
-    # Ref area km2
-    ref_area = gdir.rgi_area_km2
-    ref_area_m2 = ref_area * 1e6
-
-    # Check that glacier area is conserved at 0.1%
-    np.testing.assert_allclose((df.w * df.dx).sum(), ref_area_m2, rtol=0.001)
-
-    # Check that volume is within VAS at 25%
-    vas_vol = 0.034 * ref_area**1.375
-    vas_vol_m3 = vas_vol * 1e9
-    np.testing.assert_allclose((df.w * df.dx * df.h).sum(), vas_vol_m3,
-                               rtol=0.25)
-
-
-def test_random_mb_run():
-
-    rid = 'RGI60-15.03473'
-    gdir = oggm_compat.single_flowline_glacier_directory(rid, prepro_border=80)
-    
-    # This initializes the mass balance model, but does not run it
-    mbmod = oggm_compat.RandomLinearMassBalance(gdir, seed=1, sigma_ela=300,
-                                                h_perc=55)
-    # HERE CAN BE THE LOOP SUCH THAT EVERYTHING IS ALREADY LOADED
-    for i in [1,2,3,4]:
-        # Change the model parameter
-        mbmod.param1 = i
-        # Run the mass balance model with fixed geometry
-        ts_mb = mbmod.get_specific_mb(years=[2000,2001,2002]) 
-
-    # Run the glacier flowline model with a mass balance model
-    from oggm.core.flowline import robust_model_run
-    flmodel = robust_model_run(gdir, mb_model=mbmod, ys=0, ye=700)
-
-    # Check that "something" is computed
-    import xarray as xr
-    ds = xr.open_dataset(gdir.get_filepath('model_diagnostics'))
-    assert ds.isel(time=-1).volume_m3 > 0
-
-    if do_plot:
-        import matplotlib.pyplot as plt
-        from oggm import graphics
-        graphics.plot_modeloutput_section(flmodel)
-        f, (ax1, ax2, ax3) = plt.subplots(1, 3, figsize=(12, 4))
-        (ds.volume_m3 * 1e-9).plot(ax=ax1)
-        ax1.set_ylabel('Glacier volume (km$^{3}$)')
-        (ds.area_m2 * 1e-6).plot(ax=ax2)
-        ax2.set_ylabel('Glacier area (km$^{2}$)')
-        (ds.length_m * 1e3).plot(ax=ax3)
-        ax3.set_ylabel('Glacier length (km)')
-        plt.tight_layout()
-        plt.show()
diff --git a/pyproject.toml b/pyproject.toml
index b661a0b2..7ecc8490 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,6 +34,9 @@ jupyter = "^1.1.1"
 arviz = "^0.20.0"
 oggm = "^1.6.2"
 ruamel-yaml = "^0.18.10"
+pytest = ">=8.3.4"
+pytest-cov = ">=6.0.0"
+nbmake = ">=1.5.5"
 
 [tool.poetry.scripts]
 initialize = "pygem.bin.op.initialize:main"
@@ -53,4 +56,9 @@ duplicate_gdirs = "pygem.bin.op.duplicate_gdirs:main"
 
 [build-system]
 requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
\ No newline at end of file
+build-backend = "poetry.core.masonry.api"
+
+[tool.coverage.report]
+omit = ["pygem/tests/*"]
+show_missing = true
+skip_empty = true
\ No newline at end of file

From f8f62049893c2099d2380dc6b366291ef44bc029 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 16:39:11 -0500
Subject: [PATCH 19/29] clean up imports

Co-authored-by: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
---
 pygem/setup/config.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 1e793ab3..72e8d82e 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -7,8 +7,6 @@
 """
 import os
 import shutil
-import yaml
-import argparse
 import ruamel.yaml
 
 class ConfigManager:

From 7207d048b53c3197f9053ee241a92b5979820a7b Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 16:45:02 -0500
Subject: [PATCH 20/29] add `advanced_test_tw.ipynb` test

---
 pygem/tests/test_notebooks.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pygem/tests/test_notebooks.py b/pygem/tests/test_notebooks.py
index 350a2a20..b443267c 100644
--- a/pygem/tests/test_notebooks.py
+++ b/pygem/tests/test_notebooks.py
@@ -13,8 +13,8 @@
 @pytest.mark.parametrize("notebook", notebooks)
 def test_notebook(notebook):
     # TODO #54: Test all notebooks
-    if notebook not in ("simple_test.ipynb", "advanced_test.ipynb"):
+    if notebook not in ("simple_test.ipynb", "advanced_test.ipynb", "advanced_test_tw.ipynb):
         pytest.skip()
     subprocess.check_call(
         ["pytest", "--nbmake", os.path.join(nb_dir, notebook)]
-    )
\ No newline at end of file
+    )

From 4d745b7842c07f64e5dbec0e2ef70f4bcb21d4be Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 16:46:17 -0500
Subject: [PATCH 21/29] typo fix

---
 pygem/tests/test_notebooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygem/tests/test_notebooks.py b/pygem/tests/test_notebooks.py
index b443267c..2eb5c020 100644
--- a/pygem/tests/test_notebooks.py
+++ b/pygem/tests/test_notebooks.py
@@ -13,7 +13,7 @@
 @pytest.mark.parametrize("notebook", notebooks)
 def test_notebook(notebook):
     # TODO #54: Test all notebooks
-    if notebook not in ("simple_test.ipynb", "advanced_test.ipynb", "advanced_test_tw.ipynb):
+    if notebook not in ("simple_test.ipynb", "advanced_test.ipynb", "advanced_test_tw.ipynb"):
         pytest.skip()
     subprocess.check_call(
         ["pytest", "--nbmake", os.path.join(nb_dir, notebook)]

From 43adb9ca66caeae19e35318a9fd0232aa410c564 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 16:47:44 -0500
Subject: [PATCH 22/29] add __all__ variable

Co-authored-by: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
---
 pygem/setup/config.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 72e8d82e..faf8d6ce 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -9,6 +9,9 @@
 import shutil
 import ruamel.yaml
 
+__all__ = ["ConfigManager"]
+
+
 class ConfigManager:
     def __init__(self, config_filename='config.yaml', base_dir=None, overwrite=False):
         """initialize the ConfigManager class"""

From 8f57b642830ea9b39dcda812bbd04deef174a1f6 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 16:48:05 -0500
Subject: [PATCH 23/29] cleanup commenting

Co-authored-by: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
---
 pygem/setup/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index faf8d6ce..510925a7 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -38,7 +38,7 @@ def read_config(self, validate=True):
         """Read the configuration file and return its contents as a dictionary while preserving formatting."""
         ryaml = ruamel.yaml.YAML()
         with open(self.config_path, 'r') as f:
-            user_config = ryaml.load(f)  # Using ruamel.yaml for preservation
+            user_config = ryaml.load(f)
 
         if validate:
             self.validate_config(user_config)

From 8319561f11cf62fe4d12f67026eb18cc1b62617e Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 16:48:21 -0500
Subject: [PATCH 24/29] cleanup commenting

Co-authored-by: Davor Dundovic <33790330+ddundo@users.noreply.github.com>
---
 pygem/setup/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 510925a7..40a2fd32 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -54,7 +54,7 @@ def write_config(self, config):
     
     def update_config(self, updates):
         """Update multiple keys in the YAML configuration file while preserving quotes and original types."""
-        config = self.read_config(validate=False)  # Read existing config
+        config = self.read_config(validate=False)
         
         for key, value in updates.items():
             if key not in self.EXPECTED_TYPES:

From 3fefb4399baba697e087c18ba988ff6ce6d1515f Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 17:01:20 -0500
Subject: [PATCH 25/29] more descriptive variable in validate_config

---
 pygem/setup/config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 40a2fd32..8784348b 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -69,11 +69,11 @@ def update_config(self, updates):
         self.validate_config(config)
         self.write_config(config)
     
-    def validate_config(self, data):
+    def validate_config(self, config):
         """Validate the configuration file against expected types and required keys"""
         for key, expected_type in self.EXPECTED_TYPES.items():
             keys = key.split(".")
-            sub_data = data
+            sub_data = config
             for sub_key in keys:
                 if isinstance(sub_data, dict) and sub_key in sub_data:
                     sub_data = sub_data[sub_key]

From e87e35e7531136b8c5cfc7e64684bbf85bafe92b Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 17:15:40 -0500
Subject: [PATCH 26/29] private methods and expanded docstrings

---
 pygem/setup/config.py | 53 +++++++++++++++++++++++++++++++------------
 1 file changed, 38 insertions(+), 15 deletions(-)

diff --git a/pygem/setup/config.py b/pygem/setup/config.py
index 8784348b..108f6fb9 100644
--- a/pygem/setup/config.py
+++ b/pygem/setup/config.py
@@ -13,21 +13,29 @@
 
 
 class ConfigManager:
+    """Manages PyGEMs configuration file, ensuring it exists, reading, updating, and validating its contents."""
     def __init__(self, config_filename='config.yaml', base_dir=None, overwrite=False):
-        """initialize the ConfigManager class"""
+        """
+        Initialize the ConfigManager class.
+
+        Parameters:
+        config_filename (str, optional): Name of the configuration file. Defaults to 'config.yaml'.
+        base_dir (str, optional): Directory where the configuration file is stored. Defaults to '~/PyGEM'.
+        overwrite (bool, optional): Whether to overwrite an existing configuration file. Defaults to False.
+        """
         self.config_filename = config_filename
         self.base_dir = base_dir or os.path.join(os.path.expanduser('~'), 'PyGEM')
         self.config_path = os.path.join(self.base_dir, self.config_filename)
         self.source_config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "config.yaml")
         self.overwrite = overwrite
-        self.ensure_config()
+        self._ensure_config()
     
-    def ensure_config(self):
+    def _ensure_config(self):
         """Ensure the configuration file exists, creating or overwriting it if necessary"""
         if not os.path.isfile(self.config_path) or self.overwrite:
-            self.copy_source_config()
+            self._copy_source_config()
 
-    def copy_source_config(self):
+    def _copy_source_config(self):
         """Copy the default configuration file to the expected location"""
 
         os.makedirs(self.base_dir, exist_ok=True)
@@ -35,25 +43,36 @@ def copy_source_config(self):
         print(f"Copied default configuration to {self.config_path}")
         
     def read_config(self, validate=True):
-        """Read the configuration file and return its contents as a dictionary while preserving formatting."""
+        """Read the configuration file and return its contents as a dictionary while preserving formatting.
+        Parameters:
+        validate (bool): Whether to validate the configuration file contents. Defaults to True.
+        """
         ryaml = ruamel.yaml.YAML()
         with open(self.config_path, 'r') as f:
             user_config = ryaml.load(f)
 
         if validate:
-            self.validate_config(user_config)
+            self._validate_config(user_config)
 
         return user_config
 
-    def write_config(self, config):
-        """Write the configuration dictionary to the file while preserving quotes."""
+    def _write_config(self, config):
+        """Write the configuration dictionary to the file while preserving quotes.
+
+        Parameters:
+        config (dict): configuration dictionary object
+        """
         ryaml = ruamel.yaml.YAML()
         ryaml.preserve_quotes = True
         with open(self.config_path, 'w') as file:
-            ryaml.dump(config, file)  # This will preserve quotes
+            ryaml.dump(config, file)
     
     def update_config(self, updates):
-        """Update multiple keys in the YAML configuration file while preserving quotes and original types."""
+        """Update multiple keys in the YAML configuration file while preserving quotes and original types.
+        
+        Parameters:
+        updates (dict): Key-Value pairs to be updated
+        """
         config = self.read_config(validate=False)
         
         for key, value in updates.items():
@@ -66,11 +85,15 @@ def update_config(self, updates):
 
             d[keys[-1]] = value
         
-        self.validate_config(config)
-        self.write_config(config)
+        self._validate_config(config)
+        self._write_config(config)
     
-    def validate_config(self, config):
-        """Validate the configuration file against expected types and required keys"""
+    def _validate_config(self, config):
+        """Validate the configuration dictionary against expected types and required keys.
+        
+        Parameters:
+        config (dict): The configuration dictionary to be validated.
+        """
         for key, expected_type in self.EXPECTED_TYPES.items():
             keys = key.split(".")
             sub_data = config

From b9694a52c94cc8aaf94947ad1f04c92c3e47bfc6 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 18:16:02 -0500
Subject: [PATCH 27/29] swap PyGEM-Notebooks clone repo back to main branch

---
 .github/workflows/test_suite.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
index ffd583f6..c060e5d3 100644
--- a/.github/workflows/test_suite.yml
+++ b/.github/workflows/test_suite.yml
@@ -50,8 +50,7 @@ jobs:
 
       - name: 'Clone the PyGEM-notebooks repo'
         run: |
-          git clone -b 11_config_update --depth 1 https://github.com/pygem-community/PyGEM-notebooks.git
-
+          git clone --depth 1 https://github.com/pygem-community/PyGEM-notebooks.git
           echo "PYGEM_NOTEBOOKS_DIRPATH=$(pwd)/PyGEM-notebooks" >> $GITHUB_ENV
 
       - name: 'Run tests'

From a0a91beb432cca05034205efbf9a6dcf350a55a3 Mon Sep 17 00:00:00 2001
From: "Brandon S. Tober" <tobers.brandon@gmail.com>
Date: Sun, 2 Mar 2025 22:45:53 -0500
Subject: [PATCH 28/29] clone appropriate PyGEM-notebook brach

---
 .github/workflows/test_suite.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
index c060e5d3..4620f58b 100644
--- a/.github/workflows/test_suite.yml
+++ b/.github/workflows/test_suite.yml
@@ -50,7 +50,9 @@ jobs:
 
       - name: 'Clone the PyGEM-notebooks repo'
         run: |
-          git clone --depth 1 https://github.com/pygem-community/PyGEM-notebooks.git
+          BRANCH=${GITHUB_REF#refs/heads/}
+          git clone --depth 1 --branch $([[ "$BRANCH" == "master" ]] && echo "main" || echo "dev") \
+            https://github.com/pygem-community/PyGEM-notebooks.git
           echo "PYGEM_NOTEBOOKS_DIRPATH=$(pwd)/PyGEM-notebooks" >> $GITHUB_ENV
 
       - name: 'Run tests'

From 47b1bd78e3936bbee151f6ed28fd14a7e9bc354d Mon Sep 17 00:00:00 2001
From: btobers <tobers.brandon@gmail.com>
Date: Mon, 3 Mar 2025 07:43:02 -0500
Subject: [PATCH 29/29] comment added

---
 .github/workflows/test_suite.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
index 4620f58b..2a9f2bf0 100644
--- a/.github/workflows/test_suite.yml
+++ b/.github/workflows/test_suite.yml
@@ -50,6 +50,7 @@ jobs:
 
       - name: 'Clone the PyGEM-notebooks repo'
         run: |
+          # Use PyGEM-notebook:main for master branch and PyGEM-notebooks:dev otherwise
           BRANCH=${GITHUB_REF#refs/heads/}
           git clone --depth 1 --branch $([[ "$BRANCH" == "master" ]] && echo "main" || echo "dev") \
             https://github.com/pygem-community/PyGEM-notebooks.git