crunchflow 2.0.0__tar.gz → 2.0.2__tar.gz

{crunchflow-2.0.0 → crunchflow-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: crunchflow
-Version: 2.0.0
+Version: 2.0.2
 Summary: A Python toolbox for working with the CrunchFlow reactive transport code
 License: GPL-3.0-or-later
 Author: Zach Perzan
@@ -12,7 +12,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: matplotlib (>=3.9.0,<4.0.0)
+Requires-Dist: matplotlib (>=3.7.0,<4.0.0)
 Requires-Dist: numpy (>=2.0.0,<3.0.0)
 Requires-Dist: pandas (>=2.2.2,<3.0.0)
 Description-Content-Type: text/markdown

{crunchflow-2.0.0 → crunchflow-2.0.2}/crunchflow/input/blocks.py

@@ -169,7 +169,7 @@ class Output(KeywordBlock):
             else:
                 result.append(f"time_series_print      {self.time_series_print}")
         for ts in self.time_series:
-                result.append(f"time_series            {ts}")
+            result.append(f"time_series            {ts}")
         for key, value in self.other.items():
             result.append(f"{key:<22} {value}")
         return "\n".join(result)
@@ -292,9 +292,9 @@ class Flow(KeywordBlock):
         self.gravity = ''
         self.infiltration = ''
         self.initialize_hydrostatic = ''
-        self.permeability_x = ''
-        self.permeability_y = ''
-        self.permeability_z = ''
+        self.permeability_x = []
+        self.permeability_y = []
+        self.permeability_z = []
         self.porosity_update = ''
         self.pressure = []
         self.pump = ''
@@ -307,7 +307,7 @@ class Flow(KeywordBlock):
     def set_parameters(self, parameters):
         for key, value in parameters.items():
             key = key.lower()
-            if key == 'pressure':
+            if key in ['pressure', 'permeability_x', 'permeability_y', 'permeability_z']:
                 self.pressure.append(value)
             elif hasattr(self, key):
                 setattr(self, key, value)
@@ -315,20 +315,33 @@ class Flow(KeywordBlock):
                 self.other[key] = value
 
     def __str__(self):
+        exceptions = ['other', 'pressure', 'permeability_x', 'permeability_y', 'permeability_z']
         result = []
         for attr, value in self.__dict__.items():
-            if attr not in ['other', 'pressure'] and (value or isinstance(value, bool)):
+            if attr not in exceptions and (value or isinstance(value, bool)):
                 if isinstance(value, list):
                     result.append(f"{attr:<22} {' '.join(map(str, value))}")
                 elif isinstance(value, bool):
                     result.append(f"{attr:<22} {str(value).lower()}")
                 else:
                     result.append(f"{attr:<22} {value}")
+
+        # Print pressure, since it can be defined multiple times
         for press in self.pressure:
             line = f"pressure               "
             for p in press.split():
                 line += f"{p:<8} "
             result.append(line.strip())
+
+        # Print permeability, since it can be defined multiple times
+        for perm in self.permeability_x:
+            result.append(f"permeability_x         {perm}")
+        for perm in self.permeability_y:
+            result.append(f"permeability_y         {perm}")
+        for perm in self.permeability_z:
+            result.append(f"permeability_z         {perm}")
+
+        # Finally, the other category
         for key, value in self.other.items():
             result.append(f"{key:<22} {value}")
         return "\n".join(result)

{crunchflow-2.0.0 → crunchflow-2.0.2}/crunchflow/input/inputfile.py

@@ -5,6 +5,7 @@ from crunchflow.input.blocks import (
     PrimarySpecies, SecondarySpecies, Gases, Minerals, AqueousKinetics,
     Isotopes, DatabaseBlock
 )
+from importlib.metadata import version
 import os
 
 
@@ -118,7 +119,8 @@ class InputFile:
         full_path = os.path.join(path, filename)
         with open(full_path, 'w') as file:
             file.write('! CrunchFlow input file\n')
-            file.write('! Generated automatically by python-crunchflow \n')
+            cf_version = version("crunchflow")
+            file.write('! Generated automatically by python-crunchflow v%s\n' % cf_version)
             file.write(str(self) + "\n")
 
         # Update PestControl.ant if requested
@@ -162,7 +164,8 @@ class InputFile:
 
         # Some attributes can be set multiple times within a single block
         multiply_defined = ['time_series', 'pressure', 'mineral',
-                            'primary', 'D_25', 'tortuosityMP']
+                            'primary', 'D_25', 'tortuosityMP',
+                            'permeability_x', 'permeability_y', 'permeability_z']
 
         # List of condition attributes that are not species
         condition_attributes = ['units', 'equilibrate_surface', 'temperature',

{crunchflow-2.0.0 → crunchflow-2.0.2}/crunchflow/output/timeseries.py

@@ -1,4 +1,5 @@
 import os
+import re
 import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
@@ -17,21 +18,38 @@ def get_ts_coords(tsfile):
     -------
     coords : tuple of int
         Coordinates of the form (x, y, z)"""
-    
+
     # Open the file and read in the first line
     with open(tsfile) as f:
-        for i, line in enumerate(f):
-            if i == 0:
-                fields = line.split()[-3:]
-                
-                # Final 3 fields are x, y, and z
-                x = int(fields[0])
-                y = int(fields[1])
-                z = int(fields[2])
-    
-    # Return tuple
-    coords = (x, y, z)
-    
+        firstline = f.readline()
+        if 'Flux weighted' in firstline:
+            # First split on colon
+            coord_str = firstline.split(':')[-1]
+
+            # Then split on both space and hyphen. Sometimes CrunchFlow outputs
+            # these coordinates as "1-100" and sometimes as "1- 100"
+            raw_coord_list = re.split(r'[-\s]', coord_str)
+
+            # Remove empty strings
+            coord_list = [x for x in raw_coord_list if x]
+
+            if len(coord_list) == 6:
+                coords = ('%s-%s' % (coord_list[0], coord_list[1]),
+                          '%s-%s' % (coord_list[2], coord_list[3]),
+                          '%s-%s' % (coord_list[4], coord_list[5]))
+            else:
+                coords = coord_str
+
+        else:
+            # Final 3 fields are x, y, and z
+            fields = firstline.split()[-3:]
+            x = int(fields[0])
+            y = int(fields[1])
+            z = int(fields[2])
+
+            # Return tuple
+            coords = (x, y, z)
+
     return coords
 
 

{crunchflow-2.0.0 → crunchflow-2.0.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "crunchflow"
-version = "2.0.0"
+version = "2.0.2"
 description = "A Python toolbox for working with the CrunchFlow reactive transport code"
 authors = ["Zach Perzan <zach.perzan@unlv.edu>"]
 license = "GPL-3.0-or-later"
@@ -9,7 +9,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = "^3.9"
 numpy = "^2.0.0"
-matplotlib = "^3.9.0"
+matplotlib = "^3.7.0"
 pandas = "^2.2.2"
 
 [tool.poetry.group.test]