ConfigManager class with update_config functionality

.github/workflows/test_suite.yml

@@ -50,7 +50,10 @@ jobs:
 
       - name: 'Clone the PyGEM-notebooks repo'
         run: |
-          git clone --depth 1 https://github.com/pygem-community/PyGEM-notebooks.git
+          # 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
           echo "PYGEM_NOTEBOOKS_DIRPATH=$(pwd)/PyGEM-notebooks" >> $GITHUB_ENV
 
       - name: 'Run tests'

pygem/bin/op/duplicate_gdirs.py

@@ -11,11 +11,11 @@
 import os
 import shutil
 # 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()
 
 def main():
     parser = argparse.ArgumentParser(description="Script to make duplicate oggm glacier directories - primarily to avoid corruption if parellelizing runs on a single glacier")

pygem/bin/op/initialize.py

@@ -11,25 +11,11 @@
 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(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 +122,7 @@ 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
 

pygem/bin/op/list_failed_simulations.py

@@ -15,11 +15,11 @@
 import argparse
 import numpy as np
 # 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
 
 def run(reg, simpath, gcm, scenario, calib_opt, bias_adj, gcm_startyear, gcm_endyear):

pygem/bin/postproc/postproc_binned_monthly_mass.py

@@ -21,9 +21,11 @@
 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()
+# read the config
+pygem_prms = config_manager.read_config()
 
 # ----- FUNCTIONS -----
 def getparser():

pygem/bin/postproc/postproc_compile_simulations.py

@@ -21,11 +21,11 @@
 
 # pygem imports
 import pygem
-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
 
 rgi_reg_dict = {'all':'Global',

pygem/bin/postproc/postproc_distribute_ice.py

@@ -24,9 +24,11 @@
 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()
+# 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

pygem/bin/postproc/postproc_monthly_mass.py

@@ -25,9 +25,11 @@
 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()
+# read the config
+pygem_prms = config_manager.read_config()
 import pygem.pygem_modelsetup as modelsetup
 
 

pygem/bin/preproc/preproc_fetch_mbdata.py

@@ -19,11 +19,11 @@
 # oggm
 from oggm import utils
 # 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
 
 

pygem/bin/preproc/preproc_wgms_estimate_kp.py

@@ -22,11 +22,11 @@
 from scipy.stats import median_abs_deviation
 # pygem imports
 from pygem import class_climate
-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
 
 

pygem/bin/run/run_calibration.py

@@ -31,11 +31,11 @@
 import sklearn.model_selection
 
 # 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()
 from pygem import mcmc
 from pygem import class_climate
 from pygem.massbalance import PyGEMMassBalance

pygem/bin/run/run_calibration_frontalablation.py

@@ -24,11 +24,11 @@
 from scipy.stats import linregress
 import xarray as xr
 # 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
 from pygem.massbalance import PyGEMMassBalance
 from pygem.glacierdynamics import MassRedistributionCurveModel

pygem/bin/run/run_calibration_reg_glena.py

@@ -22,11 +22,11 @@
 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()
+# 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

pygem/bin/run/run_mcmc_priors.py

@@ -13,11 +13,11 @@
 from scipy import stats
 
 # 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
 
 # Region dictionary for titles

pygem/bin/run/run_simulation.py

@@ -35,11 +35,11 @@
 
 # pygem imports
 import pygem
-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.gcmbiasadj as gcmbiasadj
 import pygem.pygem_modelsetup as modelsetup
 from pygem.massbalance import PyGEMMassBalance

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():
     """

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):

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()
 

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):

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"

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:

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

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']):