PyGEM-Community · btobers · Nov 5, 2025 · Sep 22, 2025 · Oct 7, 2025 · Oct 7, 2025
diff --git a/.github/workflows/test_suite.yml b/.github/workflows/test_suite.yml
@@ -3,7 +3,7 @@ name: 'Install PyGEM and Run Test Suite'
 on:
   push:
     branches:
-      - master
+      - main
       - dev
     paths:
       - '**.py'
@@ -58,7 +58,7 @@ jobs:
       - name: 'Clone the PyGEM-notebooks repo'
         run: |
           BRANCH=${GITHUB_REF#refs/heads/}
-          if [ "$BRANCH" = "master" ]; then
+          if [ "$BRANCH" = "main" ]; then
             NOTEBOOK_BRANCH="main"
           else
             NOTEBOOK_BRANCH="dev"
@@ -73,4 +73,5 @@ jobs:
           python3 -m pytest --cov=pygem -v --durations=20 pygem/tests/test_01_basics.py
           python3 -m pytest --cov=pygem -v --durations=20 pygem/tests/test_02_config.py
           python3 -m pytest --cov=pygem -v --durations=20 pygem/tests/test_03_notebooks.py
-          python3 -m pytest --cov=pygem -v --durations=20 pygem/tests/test_04_postproc.py
+          python3 -m pytest --cov=pygem -v --durations=20 pygem/tests/test_04_auxiliary.py
+          python3 -m pytest --cov=pygem -v --durations=20 pygem/tests/test_05_postproc.py
diff --git a/config.yaml b/config.yaml
diff --git a/docs/_static/elev_change_1d/01.00570_elev_change_1d.csv b/docs/_static/elev_change_1d/01.00570_elev_change_1d.csv
@@ -0,0 +1,11 @@
+bin_start,bin_stop,bin_area,date_start,date_end,dh,dh_sigma,ref_dem,ref_dem_year
+1300.0,1400.0,79778.125,2016-06-01,2017-06-01,-4.50164794921875,2.37652587890625,COP30,2013
+1400.0,1500.0,107009.375,2016-06-01,2017-06-01,-3.091949462890625,1.5350341796875,COP30,2013
+1500.0,1600.0,96590.625,2016-06-01,2017-06-01,-2.728790283203125,1.53717041015625,COP30,2013
+1600.0,1700.0,138362.5,2016-06-01,2017-06-01,-1.95526123046875,3.421600341796875,COP30,2013
+1700.0,1800.0,176418.75,2016-06-01,2017-06-01,-2.159393310546875,7.1052093505859375,COP30,2013
+1800.0,1900.0,231671.875,2016-06-01,2017-06-01,-1.4642333984375,1.008819580078125,COP30,2013
+1900.0,2000.0,270537.5,2016-06-01,2017-06-01,-1.630615234375,1.78204345703125,COP30,2013
+2000.0,2100.0,218462.5,2016-06-01,2017-06-01,-1.223602294921875,1.511993408203125,COP30,2013
+2100.0,2200.0,137959.375,2016-06-01,2017-06-01,-1.411376953125,1.4329833984375,COP30,2013
+2200.0,2300.0,100803.125,2016-06-01,2017-06-01,-1.162353515625,2.39971923828125,COP30,2013
diff --git a/docs/_static/elev_change_1d/01.00570_elev_change_1d.json b/docs/_static/elev_change_1d/01.00570_elev_change_1d.json
@@ -0,0 +1 @@
+{"ref_dem": "COP30", "ref_dem_year": 2013, "dates": [["2016-06-01", "2017-06-01"]], "bin_edges": [1300.0, 1400.0, 1500.0, 1600.0, 1700.0, 1800.0, 1900.0, 2000.0, 2100.0, 2200.0, 2300.0], "bin_centers": [1350.0, 1450.0, 1550.0, 1650.0, 1750.0, 1850.0, 1950.0, 2050.0, 2150.0, 2250.0], "bin_area": [79778.125, 107009.375, 96590.625, 138362.5, 176418.75, 231671.875, 270537.5, 218462.5, 137959.375, 100803.125], "dh": [[-4.50164794921875, -3.091949462890625, -2.728790283203125, -1.95526123046875, -2.159393310546875, -1.4642333984375, -1.630615234375, -1.223602294921875, -1.411376953125, -1.162353515625]], "dh_sigma": [[2.37652587890625, 1.5350341796875, 1.53717041015625, 3.421600341796875, 7.1052093505859375, 1.008819580078125, 1.78204345703125, 1.511993408203125, 1.4329833984375, 2.39971923828125]]}
diff --git a/docs/_static/elev_change_1d/README.txt b/docs/_static/elev_change_1d/README.txt
@@ -0,0 +1,9 @@
+"""
+Python Glacier Evolution Model (PyGEM)
+
+copyright © 2025 Brandon Tober <btober@cmu.edu>, David Rounce <drounce@cmu.edu>
+
+Distributed under the MIT license
+"""
+
+This directory contains example 1d elevation change data following the format specifications of PyGEM.
diff --git a/docs/_static/example_meltextent_and_snowline_1d/sample_melt_extent_elev.csv b/docs/_static/example_meltextent_and_snowline_1d/sample_melt_extent_elev.csv
diff --git a/docs/_static/example_meltextent_and_snowline_1d/sample_snowline_elev.csv b/docs/_static/example_meltextent_and_snowline_1d/sample_snowline_elev.csv
diff --git a/docs/calibration_options.md b/docs/calibration_options.md
@@ -6,11 +6,10 @@ Several calibration options exist, which vary with respect to complexity and com
 
 | Calibration option | Overview | Reference |
 | :--- | :--- | :--- |
-| ['HH2015'](HH2015_target) | Finds single set of parameters.<br>Varies in order: $f_{snow}$, $k_{p}$, $T_{bias}$ | [Huss and Hock (2015)](https://www.frontiersin.org/articles/10.3389/feart.2015.00054/full) |
-| ['HH2015mod'](HH2015mod_target) | Finds single set of parameters.<br>Varies in order: $k_{p}$, $T_{bias}$ | [Rounce et al. 2020](https://www.cambridge.org/core/journals/journal-of-glaciology/article/quantifying-parameter-uncertainty-in-a-largescale-glacier-evolution-model-using-bayesian-inference-application-to-high-mountain-asia/61D8956E9A6C27CC1A5AEBFCDADC0432) |
-| ['emulator'](emulator_target) | Creates emulator for ['MCMC'](MCMC_target).<br>Finds single set of parameters with emulator following ['HH2015mod'](HH2015mod_target) | [Rounce et al. 2023](https://www.science.org/doi/10.1126/science.abo1324) |
-| ['MCMC'](MCMC_target) | Finds multiple sets of parameters using Bayesian inference with [emulator](emulator_target).<br> Varies $f_{snow}$, $k_{p}$, $T_{bias}$ | [Rounce et al. 2023](https://www.science.org/doi/10.1126/science.abo1324) |
-| ['MCMC_fullsim'](MCMC_target) | Finds multiple sets of parameters using Bayesian inference with full model simulations.<br> Varies $f_{snow}$, $k_{p}$, $T_{bias}$ | [Rounce et al. 2020](https://www.cambridge.org/core/journals/journal-of-glaciology/article/quantifying-parameter-uncertainty-in-a-largescale-glacier-evolution-model-using-bayesian-inference-application-to-high-mountain-asia/61D8956E9A6C27CC1A5AEBFCDADC0432) |
+| ['HH2015'](HH2015_target) | Finds single set of parameters.<br>Varies in order: $f_{snow}$, $k_{p}$, $T_{bias}$ | [Huss and Hock, 2015](https://www.frontiersin.org/articles/10.3389/feart.2015.00054/full) |
+| ['HH2015mod'](HH2015mod_target) | Finds single set of parameters.<br>Varies in order: $k_{p}$, $T_{bias}$ | [Rounce et al., 2020](https://www.cambridge.org/core/journals/journal-of-glaciology/article/quantifying-parameter-uncertainty-in-a-largescale-glacier-evolution-model-using-bayesian-inference-application-to-high-mountain-asia/61D8956E9A6C27CC1A5AEBFCDADC0432) |
+| ['emulator'](emulator_target) | Creates emulator for ['MCMC'](MCMC_target).<br>Finds single set of parameters with emulator following ['HH2015mod'](HH2015mod_target) | [Rounce et al., 2023](https://www.science.org/doi/10.1126/science.abo1324) |
+| ['MCMC'](MCMC_target) | Finds many sets of parameters using Bayesian inference. Setting `calib.MCMC_params.option_use_emulator=True` in ~/PyGEM/config.yaml will run Bayesian inference using the mass balance emulator. Setting `calib.MCMC_params.option_use_emulator=False` (or when performing dynamical calibration against elevation change data)$^*$ will run Bayesian inference calibration with full model simulations.<br>Varies $f_{snow}$, $k_{p}$, $T_{bias}$, (optionally $\rho_{ablation}$, $\rho_{accumulation}$)$^*$ |  [Rounce et al., 2020](https://www.cambridge.org/core/journals/journal-of-glaciology/article/quantifying-parameter-uncertainty-in-a-largescale-glacier-evolution-model-using-bayesian-inference-application-to-high-mountain-asia/61D8956E9A6C27CC1A5AEBFCDADC0432); [2023](https://www.science.org/doi/10.1126/science.abo1324) |
 | [Future options](cal_custom_target) | Stay tuned for new options coming in 2023/2024! | | 
 
 The output of each calibration is a .json file that holds a dictionary of the calibration options and the subsequent model parameters.  Thus, the .json file will store several calibration options.  Each calibration option is a key to the dictionary. The model parameters are also stored in a dictionary (i.e., a dictionary within a dictionary) with each model parameter being a key to the dictionary that provides access to a list of values for that specific model parameter. The following shows an example of how to print a list of the precipitation factors ($k_{p}$) for the calibration option specified in the input file:

diff --git a/docs/install_pygem.md b/docs/install_pygem.md
@@ -12,7 +12,7 @@ Next, choose your preferred PyGEM installation option:<br>
 
 (stable_install_target)=
 ## Stable install
-The simplest **stable** installation method is to use an environment file. Right-click and save PyGEM's recommended environment file from [this link](https://raw.githubusercontent.com/PyGEM-Community/PyGEM/refs/heads/master/docs/pygem_environment.yml).
+The simplest **stable** installation method is to use an environment file. Right-click and save PyGEM's recommended environment file from [this link](https://raw.githubusercontent.com/PyGEM-Community/PyGEM/refs/heads/main/docs/pygem_environment.yml).
 
 From the folder where you saved the file, run `conda env create -f pygem_environment.yml`.
 ```{note}

diff --git a/docs/model_structure.md b/docs/model_structure.md
@@ -32,9 +32,9 @@ If you use a different file structure and do not update the relative file paths
 The model code itself is heavily commented with the hope that the code is easy to follow and develop further. After [installing PyGEM](install_pygem_target), downloading the required [input files](model_inputs_target), and setting up the [directory structure](directory_structure_target) (or modifying the *~/PyGEM/config.yaml* with your preferred directory structure) you are ready to run the code! Generally speaking, the workflow includes:
 * [Pre-process data](preprocessing_target) <em>(optional if including more data)</em>
 * [Set up configuration file](config_workflow_target)
-* [Calibrate frontal ablation parameter](workflow_cal_frontalablation_target) <em>(optional for marine-terimating glaciers)</em>
 * [Calibrate climatic mass balance parameters](workflow_cal_prms_target)
-* [Calibrate ice viscosity parameter](workflow_cal_glena_target)
+* [Calibrate frontal ablation parameter](workflow_cal_frontalablation_target) <em>(optional for marine-terimating glaciers)</em>
+* [Calibrate ice viscosity parameter](workflow_run_inversion_target)
 * [Run model simulation](workflow_sim_target)
 * [Post-process output](workflow_post_target)
 * [Analyze output](workflow_analyze_target)
@@ -92,17 +92,14 @@ Circularity issues exist in calibrating the frontal ablation parameter as the ma
 ```
 
 
-(workflow_cal_glena_target)=
+(workflow_run_inversion_target)=
 ### Calibrate ice viscosity model parameter
 The ice viscosity ("Glen A") model parameter is calibrated such that the ice volume estimated using the calibrated mass balance gradients are consistent with the reference ice volume estimates ([Farinotti et al. (2019)](https://www.nature.com/articles/s41561-019-0300-3)) for each RGI region. This is done by running the following:
 ```
-run_calibration_reg_glena
+run_inversion
 ```
 
-If successful, the script will run without error and output the following:
-* ../Output/calibration/‘glena_region.csv’ 
-
-For more details, see the [run_calibration_reg_glena.py Script Overview](run_calibration_reg_glena_overview_target).
+For more details, see the [run_inversion.py Script Overview](run_inversion_overview_target).
 
 
 (workflow_sim_target)=
@@ -130,7 +127,7 @@ For more details, see the [run_simulation.py Script Overview](run_simulation_tar
 There are currently several scripts available to post-process PyGEM simulations. To aggregate simulations by RGI region, climate scenario, and variable, run the *postproc_compile_simulations.py* script. For example to compile all Alaska's glacier mass, area, runoff, etc. for various scenarios we would run the following:
 
  ```
-compile_simulations -rgi_region 01 -scenario ssp245 ssp370 ssp585
+postproc_compile_simulations -rgi_region 01 -scenario ssp245 ssp370 ssp585
  ```
 
 (workflow_analyze_target)=

diff --git a/docs/run_calibration_reg_glena_overview.md b/docs/run_calibration_reg_glena_overview.md
diff --git a/docs/run_inversion_overview.md b/docs/run_inversion_overview.md
@@ -0,0 +1,22 @@
+(run_inversion_overview_target)=
+# run_inversion.py
+This script will perform ice thickness inversion while calibrating the ice viscosity ("Glen A") model parameter such that the modeled ice volume roughly matches the ice volume estimates from [Farinotti et al. (2019)](https://www.nature.com/articles/s41561-019-0300-3) for each RGI region. Run the script as follows:
+
+```
+run_inversion -rgi_region01 <region>
+```
+
+## Script Structure
+
+Broadly speaking, the script follows:
+* Load glaciers
+* Load climate data
+* Compute apparent mass balance and invert for initial ice thickness
+* Use minimization to find agreement between our modeled and [Farinotti et al. (2019)](https://www.nature.com/articles/s41561-019-0300-3) modeled ice thickness estimates for each RGI region
+* Export the calibrated parameters
+
+## Special Considerations
+The regional Glen A value is calibrated by inverting for the ice thickness of all glaciers in a given region without considering calving (all glaciers are considered land-terminating). After the "best" Glen A value is determined, a final round of ice thickness inversion is performed for tidewater glaciers with calving turned **on**. Running this script will by default export the regionally calibrated Glen A values to the path specfied by `sim.oggm_dynamics.glen_a_regional_relpath` in *~/PyGEM/config.yaml'*. The calibrated inversion parameters also get stored within a given glacier directories *diagnostics.json* file, e.g.:
+```
+{"dem_source": "COPDEM90", "flowline_type": "elevation_band", "apparent_mb_from_any_mb_residual": 2893.2237556771674, "inversion_glen_a": 3.784593106855888e-24, "inversion_fs": 0}
+```
diff --git a/docs/scripts_overview.md b/docs/scripts_overview.md
@@ -9,7 +9,7 @@ maxdepth: 1
 ---
 
 run_calibration_frontalablation_overview
+run_inversion_overview
 run_calibration_overview
-run_calibration_reg_glena_overview
 run_simulation_overview
 ```
diff --git a/pygem/__init__.py b/pygem/__init__.py
@@ -3,7 +3,7 @@
 
 copyright © 2018 David Rounce <drounce@cmu.edu
 
-Distrubted under the MIT lisence
+Distributed under the MIT license
 """
 
 from importlib.metadata import version

diff --git a/pygem/bin/op/compress_gdirs.py b/pygem/bin/op/compress_gdirs.py
@@ -3,7 +3,7 @@
 
 copyright © 2024 Brandon Tober <btober@cmu.edu> David Rounce <drounce@cmu.edu>
 
-Distrubted under the MIT lisence
+Distributed under the MIT license
 
 compress OGGM glacier directories
 """
@@ -24,19 +24,15 @@
 
 # Initialize OGGM subprocess
 cfg.initialize(logging_level='WARNING')
-cfg.PATHS['working_dir'] = (
-    f'{pygem_prms["root"]}/{pygem_prms["oggm"]["oggm_gdir_relpath"]}'
-)
+cfg.PATHS['working_dir'] = f'{pygem_prms["root"]}/{pygem_prms["oggm"]["oggm_gdir_relpath"]}'
 cfg.PARAMS['border'] = pygem_prms['oggm']['border']
 cfg.PARAMS['use_multiprocessing'] = True
 
 
 def compress_region(region):
     print(f'\n=== Compressing glacier directories for RGI Region: {region} ===')
     # Get glacier IDs from the RGI shapefile
-    rgi_ids = gpd.read_file(
-        utils.get_rgi_region_file(str(region).zfill(2), version='62')
-    )['RGIId'].tolist()
+    rgi_ids = gpd.read_file(utils.get_rgi_region_file(str(region).zfill(2), version='62'))['RGIId'].tolist()
 
     # Initialize glacier directories
     gdirs = workflow.init_glacier_directories(rgi_ids)
@@ -52,9 +48,7 @@ def compress_region(region):
 
 
 def main():
-    parser = argparse.ArgumentParser(
-        description='Script to compress and store OGGM glacier directories'
-    )
+    parser = argparse.ArgumentParser(description='Script to compress and store OGGM glacier directories')
     # add arguments
     parser.add_argument(
         '-rgi_region01',

diff --git a/pygem/bin/op/duplicate_gdirs.py b/pygem/bin/op/duplicate_gdirs.py
@@ -3,7 +3,7 @@
 
 copyright © 2024 Brandon Tober <btober@cmu.edu> David Rounce <drounce@cmu.edu>
 
-Distrubted under the MIT lisence
+Distributed under the MIT license
 
 duplicate OGGM glacier directories
 """

diff --git a/pygem/bin/op/initialize.py b/pygem/bin/op/initialize.py
@@ -3,7 +3,7 @@
 
 copyright © 2024 Brandon Tober <btober@cmu.edu> David Rounce <drounce@cmu.edu>
 
-Distrubted under the MIT lisence
+Distributed under the MIT license
 
 initialization script (ensure config.yaml and get sample datasets)
 """
@@ -16,10 +16,8 @@
 
 from pygem.setup.config import ConfigManager
 
-# instantiate ConfigManager
+# instantiate ConfigManager - store new config.yaml file
 config_manager = ConfigManager(overwrite=True)
-# read the config
-pygem_prms = config_manager.read_config()
 
 
 def print_file_tree(start_path, indent=''):
@@ -88,9 +86,7 @@ def download_and_unzip_from_google_drive(file_id, output_dir):
             response = session.get(base_url, params={'id': file_id}, stream=True)
             token = get_confirm_token(response)
             if token:
-                response = session.get(
-                    base_url, params={'id': file_id, 'confirm': token}, stream=True
-                )
+                response = session.get(base_url, params={'id': file_id, 'confirm': token}, stream=True)
             save_response_content(response, zip_path)
 
         # Unzip the file
@@ -99,11 +95,7 @@ def download_and_unzip_from_google_drive(file_id, output_dir):
             zip_ref.extractall(tmppath)
 
         # get root dir name of zipped files
-        dir = [
-            item
-            for item in os.listdir(tmppath)
-            if os.path.isdir(os.path.join(tmppath, item))
-        ][0]
+        dir = [item for item in os.listdir(tmppath) if os.path.isdir(os.path.join(tmppath, item))][0]
         unzip_dir = os.path.join(tmppath, dir)
         # get unique name if root dir name already exists in output_dir
         output_dir = get_unique_folder_name(os.path.join(output_dir, dir))
@@ -121,7 +113,7 @@ def main():
     # Define the base directory
     basedir = os.path.join(os.path.expanduser('~'), 'PyGEM')
     # Google Drive file id for sample dataset
-    file_id = '1Wu4ZqpOKxnc4EYhcRHQbwGq95FoOxMfZ'
+    file_id = '1cRVG__7dVclut42LdQBjnXKpTvyYWBuK'
     # download and unzip
     out = download_and_unzip_from_google_drive(file_id, basedir)
 

diff --git a/pygem/bin/op/list_failed_simulations.py b/pygem/bin/op/list_failed_simulations.py
@@ -3,7 +3,7 @@
 
 copyright © 2018 David Rounce <drounce@cmu.edu>
 
-Distrubted under the MIT lisence
+Distributed under the MIT license
 
 script to check for failed glaciers for a given simulation and export a pickle file containing a list of said glacier numbers to be reprocessed
 """
@@ -63,18 +63,14 @@ def run(
     # instantiate list of galcnos that are not in sim_dir
     failed_glacnos = []
 
-    fps = glob.glob(
-        sim_dir + f'*_{calib_opt}_ba{bias_adj}_*_{sim_startyear}_{sim_endyear}_all.nc'
-    )
+    fps = glob.glob(sim_dir + f'*_{calib_opt}_ba{bias_adj}_*_{sim_startyear}_{sim_endyear}_all.nc')
 
     # Glaciers with successful runs to process
     glacno_ran = [x.split('/')[-1].split('_')[0] for x in fps]
     glacno_ran = [x.split('.')[0].zfill(2) + '.' + x[-5:] for x in glacno_ran]
 
     # print stats of successfully simualated glaciers
-    main_glac_rgi = main_glac_rgi_all.loc[
-        main_glac_rgi_all.apply(lambda x: x.rgino_str in glacno_ran, axis=1)
-    ]
+    main_glac_rgi = main_glac_rgi_all.loc[main_glac_rgi_all.apply(lambda x: x.rgino_str in glacno_ran, axis=1)]
     print(
         f'{gcm} {str(sim_climate_scenario).replace("None", "")} glaciers successfully simulated:\n  - {main_glac_rgi.shape[0]} of {main_glac_rgi_all.shape[0]} glaciers ({np.round(main_glac_rgi.shape[0] / main_glac_rgi_all.shape[0] * 100, 3)}%)'
     )
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		{"ref_dem": "COP30", "ref_dem_year": 2013, "dates": [["2016-06-01", "2017-06-01"]], "bin_edges": [1300.0, 1400.0, 1500.0, 1600.0, 1700.0, 1800.0, 1900.0, 2000.0, 2100.0, 2200.0, 2300.0], "bin_centers": [1350.0, 1450.0, 1550.0, 1650.0, 1750.0, 1850.0, 1950.0, 2050.0, 2150.0, 2250.0], "bin_area": [79778.125, 107009.375, 96590.625, 138362.5, 176418.75, 231671.875, 270537.5, 218462.5, 137959.375, 100803.125], "dh": [[-4.50164794921875, -3.091949462890625, -2.728790283203125, -1.95526123046875, -2.159393310546875, -1.4642333984375, -1.630615234375, -1.223602294921875, -1.411376953125, -1.162353515625]], "dh_sigma": [[2.37652587890625, 1.5350341796875, 1.53717041015625, 3.421600341796875, 7.1052093505859375, 1.008819580078125, 1.78204345703125, 1.511993408203125, 1.4329833984375, 2.39971923828125]]}