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scepter/setup/scepter_helperFxns.py

@@ -11,8 +11,8 @@
 import re
 import shutil
 import subprocess
+
 import pandas as pd
-
 
 # %%
 # --------------------------------------------------------------------------
@@ -178,28 +178,25 @@ def copy_files(src_dir: str, dst_dir: str):
             # print(f"Copied {src_file} to {dst_file}")
 
 
-
-def generate_timesteps(total_duration: float, 
-                       timestep: float
-                      ) -> list:
-    '''
-    Create a list of time steps given a total duration for 
+def generate_timesteps(total_duration: float, timestep: float) -> list:
+    """
+    Create a list of time steps given a total duration for
     a scepter run and a timestep. (for use in multi-run only).
 
     Parameters
     ----------
     total_duration : float
-        [years] value denoting the total duration of the 
+        [years] value denoting the total duration of the
         SCEPTER simulation
     timestep : float
-        
+
 
     Returns
     -------
     list
-        list of start times for SCEPTER simulations 
+        list of start times for SCEPTER simulations
         for ex: [0,2,4,6,...]
-    '''
+    """
     timesteparr = []
     current_time = 0
     while current_time <= (total_duration - timestep):
@@ -208,50 +205,50 @@ def generate_timesteps(total_duration: float,
     return timesteparr
 
 
-
-def write_iter_file_with_marker(values: list, 
-                                current_index: int, 
-                                filename: str,
-                                ):
-    '''
+def write_iter_file_with_marker(
+    values: list,
+    current_index: int,
+    filename: str,
+):
+    """
     Write a file showing all timesteps and an arrow
     toward the specific timestep handled by the given
     scepter run (for use in multi-run only)
 
     Parameters
     ----------
     values : list
-        list of timesteps, generally the output of the 
+        list of timesteps, generally the output of the
         generate_timesteps function
     current_index : int
-        the run number in the sequence of simulations 
+        the run number in the sequence of simulations
         (set by the 'counter' in the multi-run loop)
     filename : str
         the path to the file that notes which timestep is
         used. default in the scepter multi-run script is
         "multiyear-iter.res"
-        
+
 
     Returns
     -------
-    '''
-    with open(filename, 'w') as file:
-        file.write(f"year \n")
+    """
+    with open(filename, "w") as file:
+        file.write("year \n")
         for i, value in enumerate(values):
             if i == current_index:
                 file.write(f"{value} <--- \n")
             else:
                 file.write(f"{value}\n")
 
 
-
-def update_clim(inputfile: str, 
-                outputfile: str, 
-                timezero: float,
-                ):
-    '''
-    SCEPTER climatology always starts at year zero. When you run a multi-year 
-    run you need to modify t=0 depending on the timestep (e.g., for the run 
+def update_clim(
+    inputfile: str,
+    outputfile: str,
+    timezero: float,
+):
+    """
+    SCEPTER climatology always starts at year zero. When you run a multi-year
+    run you need to modify t=0 depending on the timestep (e.g., for the run
     spanning years 2-4, climatology year 2 must become year zero). this function
     updates the climatology to match the multi-run index and saves the result
     in the new run's directory. (for use in multi-run only)
@@ -264,33 +261,33 @@ def update_clim(inputfile: str,
         location where we'll write the output climatology file (the new timestep dir)
     timezero : float
         the time value that gets set to zero in this iteration
-        
+
 
     Returns
     -------
-    '''
+    """
     # open the input and output files
-    with open(inputfile, 'r') as f_in, open(outputfile, 'w') as f_out:
+    with open(inputfile, "r") as f_in, open(outputfile, "w") as f_out:
         # skip the header line and copy it to new file
         header = next(f_in)
         f_out.write(header)  # write to output
         # read the file line by line
         for line in f_in:
             # split each line into year and climate value
-            year, clim = line.strip().split('\t')  # Adjust the delimiter as needed
-    
+            year, clim = line.strip().split("\t")  # Adjust the delimiter as needed
+
             # convert year to an integer and subtract 5
             year = float(year) - timezero
-            
+
             # check if the adjusted year is greater than or equal to tstep
             if year >= 0:
                 formatted_yr = "{:.7f}".format(float(year))
                 formatted_clim = "{:.7f}".format(float(clim))
                 # write the adjusted year and temperature to the output file
                 # print(f"{formatted_yr}\t{formatted_clim}\n")
-                f_out.write(f"{formatted_yr}\t{formatted_clim}\n")  # Adjust the delimiter as needed
-
-
+                f_out.write(
+                    f"{formatted_yr}\t{formatted_clim}\n"
+                )  # Adjust the delimiter as needed
 
 
 def remove_duplicates(input_file: str):
@@ -312,10 +309,17 @@ def remove_duplicates(input_file: str):
     with open(input_file, "r") as f:
         lines = f.readlines()
         header = lines[0]  # Save the header
-        lines_without_tabs = [line.replace('\t', '') for line in lines]  # remove tabs before comparing
+        lines_without_tabs = [
+            line.replace("\t", "") for line in lines
+        ]  # remove tabs before comparing
         # add '\n' if a line doesn't have it (just for comparison sake)
-        lines_without_tabs2 = [element if element.endswith('\n') else element + '\n' for element in lines_without_tabs]
-        unique_lines = set(lines_without_tabs2[1:])  # remove duplicates from mineral names
+        lines_without_tabs2 = [
+            element if element.endswith("\n") else element + "\n"
+            for element in lines_without_tabs
+        ]
+        unique_lines = set(
+            lines_without_tabs2[1:]
+        )  # remove duplicates from mineral names
 
     # check if the last entry ends with "\n" and remove it if needed
     last_entry = list(unique_lines)[-1]