Merge branch 'main' into port-paper-to-documentation

Author: jeffbourdier

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.9.53
+current_version = 3.9.54
 commit = True
 tag = True
 

.cookiecutterrc

@@ -54,7 +54,7 @@ default_context:
     sphinx_doctest: "no"
     sphinx_theme: "sphinx-py3doc-enhanced-theme"
     test_matrix_separate_coverage: "no"
-    version: 3.9.53
+    version: 3.9.54
     version_manager: "bump2version"
     website: "https://github.com/NREL"
     year_from: "2023"

CHANGELOG.rst

@@ -7,6 +7,8 @@ GEOPHIRES v3 (2023-2025)
 
 3.9
 ^^^
+3.9.54: `List parameter read fix <https://github.com/NREL/GEOPHIRES-X/pull/418>`__ | `release <https://github.com/NREL/GEOPHIRES-X/releases/tag/v3.9.54>`__
+
 3.9.53: `Gringarten-Stehfest Precision <https://github.com/NREL/GEOPHIRES-X/pull/417>`__ | `release <https://github.com/NREL/GEOPHIRES-X/releases/tag/v3.9.53>`__
 
 3.9.50: `HIP-RA-X Print Output to Console parameter <https://github.com/NREL/GEOPHIRES-X/pull/416>`__ | `release <https://github.com/NREL/GEOPHIRES-X/releases/tag/v3.9.50>`__

README.rst

@@ -58,9 +58,9 @@ Free software: `MIT license <LICENSE>`__
     :alt: Supported implementations
     :target: https://pypi.org/project/geophires-x
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/softwareengineerprogrammer/GEOPHIRES-X/v3.9.53.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/softwareengineerprogrammer/GEOPHIRES-X/v3.9.54.svg
     :alt: Commits since latest release
-    :target: https://github.com/softwareengineerprogrammer/GEOPHIRES-X/compare/v3.9.53...main
+    :target: https://github.com/softwareengineerprogrammer/GEOPHIRES-X/compare/v3.9.54...main
 
 .. |docs| image:: https://readthedocs.org/projects/GEOPHIRES-X/badge/?style=flat
     :target: https://nrel.github.io/GEOPHIRES-X

docs/conf.py

@@ -18,7 +18,7 @@
 year = '2025'
 author = 'NREL'
 copyright = f'{year}, {author}'
-version = release = '3.9.53'
+version = release = '3.9.54'
 
 pygments_style = 'trac'
 templates_path = ['./templates']

setup.py

@@ -13,7 +13,7 @@ def read(*names, **kwargs):
 
 setup(
     name='geophires-x',
-    version='3.9.53',
+    version='3.9.54',
     license='MIT',
     description='GEOPHIRES is a free and open-source geothermal techno-economic simulator.',
     long_description='{}\n{}'.format(

src/geophires_x/Parameter.py

@@ -281,7 +281,7 @@ def __post_init__(self):
     json_parameter_type: str = _JSON_PARAMETER_TYPE_ARRAY
 
 
-def ReadParameter(ParameterReadIn: ParameterEntry, ParamToModify, model):
+def ReadParameter(ParameterReadIn: ParameterEntry, ParamToModify, model) -> None:
     """
     ReadParameter: A method to take a single ParameterEntry object and use it to update the associated Parameter.
     Does validation as well as Unit and Currency conversion
@@ -393,35 +393,8 @@ def default_parameter_value_message(new_val: Any, param_to_modify_name: str, def
             ParamToModify.Provided = True  # set provided to true because we are using a user provide value now
             ParamToModify.Valid = True  # set Valid to true because it passed the validation tests
     elif isinstance(ParamToModify, listParameter):
-        New_val = float(ParameterReadIn.sValue)
-        if (New_val < float(ParamToModify.Min)) or (New_val > float(ParamToModify.Max)):
-            # user provided value is out of range, so announce it, leave set to whatever it was set to (default value)
-            if len(ParamToModify.ErrMessage) > 0:
-                msg = (
-                    f'Parameter given ({str(New_val)}) for {ParamToModify.Name} outside of valid range.'
-                    f'GEOPHIRES will {ParamToModify.ErrMessage}'
-                )
-                print(f'Warning: {msg}')
-                model.logger.warning(msg)
-            model.logger.info(f'Complete {str(__name__)}: {sys._getframe().f_code.co_name}')
-            return
-        else:
-            if ' ' in ParamToModify.Name:
-                # Some list parameters are read in with enumerated parameter names;  in these cases we use the last
-                # character of the description to get the position i.e., "Gradient 1" is position 0.
-                parts = ParameterReadIn.Name.split(' ')
-                position = int(parts[1]) - 1
-                if position >= len(ParamToModify.value):
-                    ParamToModify.value.append(New_val)  # we are adding to the list, so use append
-                else:  # we are replacing a value, so pop the value we want to replace, then insert a new one
-                    ParamToModify.value.pop(position)
-                    ParamToModify.value.insert(position, New_val)
-            else:
-                # In an ideal world this would be handled in ParameterEntry such that its sValue and Comment are
-                # correct; however that would only be practical if ParameterEntry had typing information to know
-                # whether to treat text after a second comma as a comment or list entry.
-                ParamToModify.value = [float(x.strip()) for x in ParameterReadIn.raw_entry.split('--')[0].split(',')[1:]
-                                       if x.strip() != '']
+        _read_list_parameter(ParameterReadIn, ParamToModify, model)
+
     elif isinstance(ParamToModify, boolParameter):
         if ParameterReadIn.sValue == "0":
             New_val = False
@@ -449,6 +422,47 @@ def default_parameter_value_message(new_val: Any, param_to_modify_name: str, def
     model.logger.info(f'Complete {str(__name__)}: {sys._getframe().f_code.co_name}')
 
 
+def _read_list_parameter(ParameterReadIn: ParameterEntry, ParamToModify, model) -> None:
+    """
+    :type ParamToModify: :class:`~geophires_x.Parameter.Parameter`
+    :type model: :class:`~geophires_x.Model.Model`
+    """
+
+    if ' ' in ParamToModify.Name:
+        New_val = float(ParameterReadIn.sValue)
+        # Some list parameters are read in with enumerated parameter names;  in these cases we use the last
+        # character of the description to get the position i.e., "Gradient 1" is position 0.
+        parts = ParameterReadIn.Name.split(' ')
+        position = int(parts[1]) - 1
+        if position >= len(ParamToModify.value):
+            ParamToModify.value.append(New_val)  # we are adding to the list, so use append
+        else:  # we are replacing a value, so pop the value we want to replace, then insert a new one
+            ParamToModify.value.pop(position)
+            ParamToModify.value.insert(position, New_val)
+    else:
+        # In an ideal world this would be handled in ParameterEntry such that its sValue and Comment are
+        # correct; however that would only be practical if ParameterEntry had typing information to know
+        # whether to treat text after a second comma as a comment or list entry.
+        ParamToModify.value = [float(x.strip()) for x in ParameterReadIn.raw_entry.split('--')[0].split(',')[1:]
+                               if x.strip() != '']
+
+    ParamToModify.Provided = True
+
+    valid = True
+    for i in range(len(ParamToModify.value)):
+        New_val = ParamToModify.value[i]
+        if (New_val < float(ParamToModify.Min)) or (New_val > float(ParamToModify.Max)):
+            msg = (
+                f'Value given ({str(New_val)}) for {ParamToModify.Name} outside of valid range '
+                f'({ParamToModify.Min}–{ParamToModify.Max}).'
+            )
+            print(f'Warning: {msg}')
+            model.logger.warning(msg)
+            valid = False
+
+    ParamToModify.Valid = valid
+
+
 def ConvertUnits(ParamToModify, strUnit: str, model) -> str:
     """
     ConvertUnits gets called if a unit version is needed: either currency or standard units like F to C or m to ft

src/geophires_x/Reservoir.py

@@ -606,7 +606,14 @@ def read_parameters(self, model: Model) -> None:
                     elif ParameterToModify.Name.startswith('Thickness '):
                         parts = ParameterReadIn.Name.split(' ')
                         position = int(parts[1]) - 1
-                        model.reserv.layerthickness.value[position] = ParameterToModify.value
+                        num_segments = len(model.reserv.layerthickness.value)
+                        if position < num_segments:
+                            model.reserv.layerthickness.value[position] = ParameterToModify.value
+                        else:
+                            model.logger.error(f'Cannot set {ParameterToModify.Name} to {ParameterToModify.value} '
+                                               f'because only {num_segments} segments are defined.')
+                            # Don't raise exception since we can ignore and the user will see the incorrectly configured
+                            # segment(s) in the result.
 
                     elif ParameterToModify.Name.startswith("Fracture Separation"):
                         self.fracsepcalc.value = self.fracsep.value

src/geophires_x/__init__.py

@@ -1 +1 @@
-__version__ = '3.9.53'
+__version__ = '3.9.54'

tests/geophires_x_tests/test_reservoir.py

@@ -163,3 +163,68 @@ def _fractures_lcoe_net(r: GeophiresXResult) -> tuple[int, float, float]:
 
         self.assertGreater(net_production, 0)
         self.assertLess(net_production, 500)
+
+    def test_thicknesses_param(self):
+        def _get_result() -> GeophiresXResult:
+            return GeophiresXClient().get_geophires_result(
+                GeophiresInputParameters(
+                    from_file_path=self._get_test_file_path('generic-egs-case.txt'),
+                    params={
+                        'Number of Segments': 3,
+                        'Gradient 2': '40',
+                        'Gradient 3': '40',
+                        'Thicknesses': '2.5,0.49,0.87',
+                    },
+                )
+            )
+
+        r = _get_result()
+        summary = r.result['SUMMARY OF RESULTS']
+
+        expected = {
+            'Segment 1   Geothermal gradient': {'unit': 'degC/km', 'value': 36.7},
+            'Segment 1   Thickness': {'unit': 'kilometer', 'value': 2.5},
+            'Segment 2   Geothermal gradient': {'unit': 'degC/km', 'value': 40},
+            'Segment 2   Thickness': {'unit': 'kilometer', 'value': 0.49},
+            'Segment 3   Geothermal gradient': {'unit': 'degC/km', 'value': 40},
+            'Segment 3   Thickness': None,
+            'Segment 4   Geothermal gradient': None,
+        }
+
+        for k, v in expected.items():
+            self.assertEqual(summary[k], v)
+
+    def test_number_of_segments(self):
+        def _get_result() -> GeophiresXResult:
+            return GeophiresXClient().get_geophires_result(
+                GeophiresInputParameters(
+                    from_file_path=self._get_test_file_path('generic-egs-case.txt'),
+                    params={
+                        'Number of Segments': 3,
+                        'Gradient 2': '40',
+                        'Gradient 3': '40',
+                        'Gradient 4': '40',
+                        'Thickness 1': '2.5',
+                        'Thickness 2': '0.49',
+                        'Thicknesses': '2.5,0.49,0.87',
+                        'Thickness 3': '0.65',
+                        'Thickness 4': '0.85',
+                    },
+                )
+            )
+
+        r = _get_result()
+        summary = r.result['SUMMARY OF RESULTS']
+
+        expected = {
+            'Segment 1   Geothermal gradient': {'unit': 'degC/km', 'value': 36.7},
+            'Segment 1   Thickness': {'unit': 'kilometer', 'value': 2.5},
+            'Segment 2   Geothermal gradient': {'unit': 'degC/km', 'value': 40},
+            'Segment 2   Thickness': {'unit': 'kilometer', 'value': 0.49},
+            'Segment 3   Geothermal gradient': {'unit': 'degC/km', 'value': 40},
+            'Segment 3   Thickness': None,
+            'Segment 4   Geothermal gradient': None,
+        }
+
+        for k, v in expected.items():
+            self.assertEqual(summary[k], v)