fiqus 2025.2.0__py3-none-any.whl → 2025.11.0__py3-none-any.whl

fiqus/pro_templates/combined/Multipole_template.pro

@@ -214,7 +214,7 @@ Group {
     {% endif %}
 
     {% if dm.magnet.geometry.electromagnetics.with_iron_yoke %}
-      {% for name, number in zip(rm_EM.iron.vol.names, rm_EM.iron.vol.numbers) %}
+      {% for name, number in zip(rm_EM.iron_yoke.vol.names, rm_EM.iron_yoke.vol.numbers) %}
         <<name>> = Region[ <<number>> ];
       {% endfor %}
     {% endif %}
@@ -231,7 +231,7 @@ Group {
                  {% if rm_EM.powered['r2_a2'].vol.names %}, <<rm_EM.powered['r2_a2'].vol.names|join(', ')>>{% endif %}} ];
 
     {% if dm.magnet.geometry.electromagnetics.with_iron_yoke %}
-      <<nc.omega>><<nc.iron>>_EM = Region[ {<<rm_EM.iron.vol.names|join(', ')>>} ];
+      <<nc.omega>><<nc.iron>>_EM = Region[ {<<rm_EM.iron_yoke.vol.names|join(', ')>>} ];
     {% endif %}
 
     {% if dm.magnet.geometry.electromagnetics.with_wedges %}
@@ -317,7 +317,7 @@ Group {
   {% endif %}
 
   {% if dm.magnet.geometry.thermal.with_iron_yoke %}
-    {% for name, number in zip(rm_TH.iron.vol.names, rm_TH.iron.vol.numbers) %}
+    {% for name, number in zip(rm_TH.iron_yoke.vol.names, rm_TH.iron_yoke.vol.numbers) %}
       <<name>> = Region[ <<number>> ];
     {% endfor %}
   {% endif %}
@@ -340,7 +340,7 @@ Group {
   {% endfor %}
     <<nc.omega>><<nc.powered>>_TH = Region[ {<<nc.omega>><<nc.powered>>_<<dm.conductors.keys()|join('_TH, ' + nc.omega + nc.powered + '_')>>_TH} ];
   {% if dm.magnet.geometry.thermal.with_iron_yoke %}
-    <<nc.omega>><<nc.iron>>_TH = Region[ {<<rm_TH.iron.vol.names|join(', ')>>} ];
+    <<nc.omega>><<nc.iron>>_TH = Region[ {<<rm_TH.iron_yoke.vol.names|join(', ')>>} ];
   {% endif %}
   {% if dm.magnet.geometry.thermal.with_wedges %}
     <<nc.omega>><<nc.induced>>_TH = Region[ {
@@ -491,7 +491,7 @@ Function {
       nu [ Region[{<<rm_EM.air.vol.name>>, <<nc.omega>><<nc.powered>>_EM, <<rm_EM.air_far_field.vol.names[0]>>{% if dm.magnet.geometry.electromagnetics.with_wedges %}, <<nc.omega>><<nc.induced>>_EM{% endif %}}] ]  = 1. / mu0;
 
     {% if dm.magnet.geometry.electromagnetics.with_iron_yoke %}
-      {% for name in rm_EM.iron.vol.names %}
+      {% for name in rm_EM.iron_yoke.vol.names %}
         nu [ <<name>> ]  = nu<<name>>[$1];
         dnuIronYoke [ <<name>> ]  = dnu<<name>>[$1];
       {% endfor %}

fiqus/utils/Utils.py

@@ -131,7 +131,7 @@ class FilesAndFolders:
                 os.remove(dummy_yaml_file_to_create_ruamel_object)
 
                 def iterate_fields(model, ruamel_yaml_object):
-                    for currentPydanticKey, value in model.__fields__.items():
+                    for currentPydanticKey, value in model.model_fields.items():
                         if value.alias and by_alias:
                             currentDictionaryKey = value.alias
                         else:
@@ -143,7 +143,7 @@ class FilesAndFolders:
                                 currentDictionaryKey,
                             )
 
-                        if hasattr(getattr(model, currentPydanticKey), "__fields__"):
+                        if hasattr(getattr(model, currentPydanticKey), "model_fields"):
                             new_ruamel_yaml_object = iterate_fields(
                                 getattr(model, currentPydanticKey),
                                 ruamel_yaml_object[currentDictionaryKey],
@@ -153,7 +153,7 @@ class FilesAndFolders:
 
                         elif isinstance(getattr(model, currentPydanticKey), list):
                             for i, item in enumerate(getattr(model, currentPydanticKey)):
-                                if hasattr(item, "__fields__"):
+                                if hasattr(item, "model_fields"):
                                     new_ruamel_yaml_object = iterate_fields(
                                         item,
                                         ruamel_yaml_object[currentDictionaryKey][i],
@@ -164,13 +164,13 @@ class FilesAndFolders:
                     return ruamel_yaml_object
 
                 iterate_fields(data_model, ruamel_yaml_object)
-                for currentPydanticKey, value in data_model.__fields__.items():
+                for currentPydanticKey, value in data_model.model_fields.items():
                     if value.alias and by_alias:
                         currentDictionaryKey = value.alias
                     else:
                         currentDictionaryKey = currentPydanticKey
 
-                    if hasattr(getattr(data_model, currentPydanticKey), "__fields__"):
+                    if hasattr(getattr(data_model, currentPydanticKey), "model_fields"):
                         ruamel_yaml_object[currentDictionaryKey] = iterate_fields(
                             getattr(data_model, currentPydanticKey),
                             ruamel_yaml_object[currentDictionaryKey],
@@ -726,7 +726,9 @@ def initialize_logger(work_folder: str = None, time_stamp: str = None, verbose:
     logger = logging.getLogger()
 
     while logger.hasHandlers():
-        logger.removeHandler(logger.handlers[0])
+        handler = logger.handlers[0]
+        logger.removeHandler(handler)
+        handler.close()
 
     if verbose:
         logger.setLevel(logging.INFO)
@@ -805,7 +807,10 @@ def get_data_settings(GetDP_path=None, settings=None):
         if GetDP_path:
             settings.GetDP_path = GetDP_path
     elif platform.system() == 'Linux':
-        settings.GetDP_path = 'getdp'
+        if GetDP_path:
+            settings.GetDP_path = GetDP_path
+        else:
+            settings.GetDP_path = 'getdp'
     elif platform.system() == 'Darwin':
         if GetDP_path:
             settings.GetDP_path = GetDP_path

{fiqus-2025.2.0.dist-info → fiqus-2025.11.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fiqus
-Version: 2025.2.0
+Version: 2025.11.0
 Summary: Source code for STEAM FiQuS tool
 Home-page: https://gitlab.cern.ch/steam/fiqus
 Author: STEAM Team
@@ -10,72 +10,74 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: gmsh==4.13.1
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-Requires-Dist: mplcursors==0.5.3
-Requires-Dist: numpy==1.26.4
-Requires-Dist: pandas==2.2.1
-Requires-Dist: pydantic==2.6.4
-Requires-Dist: ruamel.yaml==0.18.6
-Requires-Dist: ruamel.yaml.clib==0.2.8
-Requires-Dist: scipy==1.14.1
-Requires-Dist: tqdm==4.66.2
-Requires-Dist: typing-extensions==4.10.0
+Requires-Dist: gmsh ==4.13.1
+Requires-Dist: h5py ==3.10.0
+Requires-Dist: Jinja2 ==3.1.3
+Requires-Dist: matplotlib ==3.8.3
+Requires-Dist: mplcursors ==0.5.3
+Requires-Dist: numpy ==1.26.4
+Requires-Dist: pandas ==2.2.1
+Requires-Dist: pydantic ==2.6.4
+Requires-Dist: ruamel.yaml ==0.18.6
+Requires-Dist: ruamel.yaml.clib ==0.2.8
+Requires-Dist: scipy ==1.14.1
+Requires-Dist: tqdm ==4.66.2
+Requires-Dist: typing-extensions ==4.10.0
 Provides-Extra: all
-Requires-Dist: gmsh==4.13.1; extra == "all"
-Requires-Dist: h5py==3.10.0; extra == "all"
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 Provides-Extra: build
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 Provides-Extra: docs
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 Provides-Extra: tests
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 ![FiQuS logo](https://gitlab.cern.ch/steam/fiqus/-/raw/master/docs/images/FiQuS_name_logo.svg)
 

fiqus-2025.11.0.dist-info/RECORD

@@ -0,0 +1,86 @@
+fiqus/MainFiQuS.py,sha256=dyhSz6VZQrZ2zbaATanfKeqDtHw1hkc8SJ0XbA_IojA,21069
+fiqus/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/data/DataConductor.py,sha256=MUrGvH9I_rs7iHuVNUP-FFrtA7KE7i-Cagocfq7_lQo,17653
+fiqus/data/DataFiQuS.py,sha256=rOxuYzVk1Gsscnrf1hoyQ8RRRhPOAgGG7xjKWlsOLKQ,5728
+fiqus/data/DataFiQuSCCT.py,sha256=__3AEMvalYm_YgCV9RK-hr9T7e_Dvvx3fBcqbToQWUw,7285
+fiqus/data/DataFiQuSConductor.py,sha256=HpPelDwQsGbgNoX3SdwHQYcTMCHq8vMmi0C-EGpxWeA,3392
+fiqus/data/DataFiQuSConductorAC_Strand.py,sha256=SLERW3APmEiwt0U5DQfqneTaktGetzW5eML3pLQWVGE,38184
+fiqus/data/DataFiQuSMultipole.py,sha256=_rX9zP-xNTZioVmu4NCaFVWF66ipesp8cSiB0pmKsG4,32377
+fiqus/data/DataFiQuSPancake3D.py,sha256=czgDU-h_XBq3OLqFOllr8zLx_MxQoCiWo84DsyOhhbo,136611
+fiqus/data/DataModelCommon.py,sha256=UoMdZSaHTghal0X9DeNiGUzMNdjolwMy9IRNaQQh38s,23491
+fiqus/data/DataMultipole.py,sha256=-UUxtgdn32NKxZt3-p-3p5lDcdxlGN9uPlVeLJB9u2E,6323
+fiqus/data/DataRoxieParser.py,sha256=2qlyUmrFOJw7CT2CDs3psv_B7GNtpkTcJoRwpVHr_C0,9277
+fiqus/data/DataSettings.py,sha256=zs5sEYUk4xjeMc_j8gt3PMji7V0yyMYizpXxBKv0aB0,3799
+fiqus/data/DataWindingsCCT.py,sha256=qqqxO4VG6rsKpNEImkA1hjrUMyS4UFNfVG_ioQd4ML8,1709
+fiqus/data/RegionsModelFiQuS.py,sha256=6FTJBE0D4snVivMnKpS4NPJFFrdoZjmpR4KmMNF74R4,6795
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+fiqus/pre_processors/PreProcessCCT.py,sha256=BDRei7uLdOHxNnsg-r17HcjtvvrST8HUj_lQ1GSmVZo,9217
+fiqus/pre_processors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/pro_assemblers/ProAssembler.py,sha256=DrVd1wiuv-7PIj3G38crBu07aMPyE3FOapODJN7wl9E,3572
+fiqus/pro_assemblers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/pro_material_functions/ironBHcurves.pro,sha256=0Tz1KzZ63G_zaS6dYQ5NYwa9EAtJna0jR61OxsM9J_E,17835
+fiqus/pro_templates/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/pro_templates/combined/CCT_template.pro,sha256=gZKoLj6ZefuSzM7dYkEJW49qlzfiUqEwmifaJP4kOzc,13878
+fiqus/pro_templates/combined/ConductorAC_template.pro,sha256=RN69ycY4vGGPp8YmCHICVGRNfvuEHGB50FxmEeEzrXA,94008
+fiqus/pro_templates/combined/Multipole_template.pro,sha256=H0H_R7sa69EL2lHtIQ0kmz-0Ov0MbZZIpnu1L0pAhPM,97994
+fiqus/pro_templates/combined/Pancake3D_template.pro,sha256=OjWWWAZel5Yk_k4FEFFNkkSFkCv1N0rM2-DRvilH6dc,215797
+fiqus/pro_templates/combined/TSA_materials.pro,sha256=I8zVOP2ZEFqR0y3JcpSQJWaE6I4UeeMU22PtSD8ExCc,12244
+fiqus/pro_templates/combined/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/pro_templates/combined/materials.pro,sha256=D-cBOIMaQyYffIfoR4yRiK69Z6sxHu2QtyjhDIKFiXc,7038
+fiqus/pro_templates/separated/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/utils/Utils.py,sha256=HPEN92OxtMxk_xrMD4nfvBsA2BuKuk9_x1Yoy2bF2tw,35613
+fiqus/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+fiqus/utils/update_data_settings.py,sha256=Cl_vP-7MXFHG3LiDE8nVtL7CwK9DUvDhxXV7sabP9to,1295
+tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/test_FiQuS.py,sha256=mlY5eRp-sE_ubaPG7HHAEsC4Q3iQwI76nfOclPg7m-M,15529
+tests/test_geometry_generators.py,sha256=CknRmySOjTbOfmTm4nC_X7K0FJRytjq2HKzQVKTKD2c,9116
+tests/test_mesh_generators.py,sha256=Qa1wJ8-0vCInkt300iM_tGVkioBHi4jVBKid9LAKfAM,10881
+tests/test_solvers.py,sha256=k2VX19GV2yTCec01ieW-6Z2NAMyMqB9rk5CAp9Ye0Ow,12815
+tests/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tests/utils/fiqus_test_classes.py,sha256=ynCjYknWGI_pa-lRWQ01aL2SjHz0GTrN4bICW5GlR34,30395
+tests/utils/generate_reference_files_ConductorAC.py,sha256=_jEE6xcqiz52bnmY6Is11QmG-bZ2vdH0k99p733t4N4,1676
+tests/utils/generate_reference_files_Pancake3D.py,sha256=9sULcDOmbotrbYHz8DqGv6Km7ThfltnCHFojHUx193U,3126
+tests/utils/helpers.py,sha256=BQxdHr8N4rGXc2C_YNEeOXxTIDJSUeRyyxLkvWfhiJY,4149
+fiqus-2025.11.0.dist-info/LICENSE.txt,sha256=gcuuhKKc5-dwvyvHsXjlC9oM6N5gZ6umYbC8ewW1Yvg,35821
+fiqus-2025.11.0.dist-info/METADATA,sha256=68b71oEsx-HfExyCFDOMeEywFZOheUalzKGvrF5yvFQ,8370
+fiqus-2025.11.0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+fiqus-2025.11.0.dist-info/top_level.txt,sha256=oGzSIyoVc1zYg14o67zI3QFwWsJvqNzNT0-te9WbUQc,12
+fiqus-2025.11.0.dist-info/RECORD,,

{fiqus-2025.2.0.dist-info → fiqus-2025.11.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.45.1)
+Generator: bdist_wheel (0.41.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

tests/test_geometry_generators.py

@@ -86,6 +86,10 @@ class TestGeometryGenerators(FiQuSGeometryTests):
                 reference_geometry_yaml_file = self.get_path_to_reference_file(
                     data_model=data_model, file_name='GeometryModel', file_extension="yaml"
                 )
+                print('Comparing:'
+                      f'{geometry_yaml_file}'
+                      ' with'
+                      f'{reference_geometry_yaml_file}')
                 self.compare_json_or_yaml_files(geometry_yaml_file, reference_geometry_yaml_file, tolerance=1e-9)
 
     def test_Multipole(self):

tests/test_mesh_generators.py

@@ -94,6 +94,11 @@ class TestMeshGenerators(FiQuSMeshTests):
                     file_name=model_name,
                     file_extension="regions",
                 )
+                print('Comparing'
+                      f'{regions_file}'
+                      'with'
+                      f'{reference_regions_file}'
+                      )
                 self.compare_json_or_yaml_files(regions_file, reference_regions_file)
 
     # def test_CCT(self):

tests/test_solvers.py

@@ -2,6 +2,12 @@ import unittest
 from tests.utils.fiqus_test_classes import FiQuSSolverTests
 from fiqus.data.DataFiQuS import FDM
 import fiqus.data.DataFiQuSPancake3D as Pancake3D
+import os
+import platform
+from pathlib import Path
+
+linux_getdp_prefix_path = Path("/bin/cerngetdp/")
+windows_getdp_prefix_path = Path("C:/cerngetdp/")
 
 
 class TestSolvers(FiQuSSolverTests):
@@ -10,6 +16,16 @@ class TestSolvers(FiQuSSolverTests):
         Checks if Pancake3D solvers work correctly by comparing the results to the
         reference results that were checked manually.
         """
+        if os.getenv("CERNGETDP_VERSION_PANCAKE3D") is not None:
+            os_name = platform.system()
+
+            if os_name == "Linux":
+                self.getdp_path = linux_getdp_prefix_path / Path(f"pancake3d/bin/getdp_{os.getenv('CERNGETDP_VERSION_PANCAKE3D')}")
+            else:
+                self.getdp_path = windows_getdp_prefix_path / Path(f"pancake3d/getdp_{os.getenv('CERNGETDP_VERSION_PANCAKE3D')}.exe")
+        else:
+            print("CERNGETDP_VERSION_PANCAKE3D is not set. Using default getdp path from data settings.")
+
         model_names = [
             "TEST_Pancake3D_REF",
             "TEST_Pancake3D_REFStructured",
@@ -111,6 +127,17 @@ class TestSolvers(FiQuSSolverTests):
         Checks if CACStrand solvers work correctly by comparing the results to the
         reference results that were checked manually.
         """
+        if os.getenv("CERNGETDP_VERSION_CAC_STRAND") is not None:
+            os_name = platform.system()
+
+            if os_name == "Linux":
+                self.getdp_path = linux_getdp_prefix_path / Path(f"cac_strand/bin/getdp_{os.getenv('CERNGETDP_VERSION_CAC_STRAND')}")
+            else:
+                self.getdp_path = windows_getdp_prefix_path / Path(f"cac_strand/getdp_{os.getenv('CERNGETDP_VERSION_CAC_STRAND')}.exe")
+        else:
+            print("CERNGETDP_VERSION_CAC_STRAND is not set. Using default getdp path from data settings.")
+
+
         model_names = [
             "TEST_CAC_Strand_hexFilaments",
             "TEST_CAC_Strand_adaptiveMesh",
@@ -140,12 +167,12 @@ class TestSolvers(FiQuSSolverTests):
                 # Compare the magnetic flux density files:
                 pos_file = self.get_path_to_generated_file(
                     data_model=data_model,
-                    file_name="b",
+                    file_name="b_Omega",
                     file_extension="pos",
                 )
                 reference_pos_file = self.get_path_to_reference_file(
                     data_model=data_model,
-                    file_name="b",
+                    file_name="b_Omega",
                     file_extension="pos",
                 )
                 self.compare_pos_files(pos_file, reference_pos_file, rel_tolerance=1e-3, abs_tolerance=1e-10)
@@ -153,12 +180,12 @@ class TestSolvers(FiQuSSolverTests):
                 # Compare the current density files:
                 pos_file = self.get_path_to_generated_file(
                     data_model=data_model,
-                    file_name="j",
+                    file_name="j_OmegaC",
                     file_extension="pos",
                 )
                 reference_pos_file = self.get_path_to_reference_file(
                     data_model=data_model,
-                    file_name="j",
+                    file_name="j_OmegaC",
                     file_extension="pos",
                 )
                 self.compare_pos_files(pos_file, reference_pos_file, rel_tolerance=1e-3, abs_tolerance=1e-10)
@@ -169,6 +196,16 @@ class TestSolvers(FiQuSSolverTests):
         Checks if Multipole solvers work correctly by comparing the results to the
         reference results that were checked manually.
         """
+        if os.getenv("CERNGETDP_VERSION_MULTIPOLE") is not None:
+            os_name = platform.system()
+
+            if os_name == "Linux":
+                self.getdp_path = linux_getdp_prefix_path / Path(f"multipole/bin/getdp_{os.getenv('CERNGETDP_VERSION_MULTIPOLE')}")
+            else:
+                self.getdp_path = windows_getdp_prefix_path / Path(f"multipole/getdp_{os.getenv('CERNGETDP_VERSION_MULTIPOLE')}.exe")
+        else:
+            print("CERNGETDP_VERSION_MULTIPOLE is not set. Using default getdp path from data settings.")
+
         model_names = [
             "TEST_MULTIPOLE_MBH_1in1_TSA_withQH",
             "TEST_MULTIPOLE_MBH_1in1_TSA",

tests/utils/fiqus_test_classes.py

@@ -155,12 +155,21 @@ class BaseClassesForTests(unittest.TestCase):
             )
 
         # Run FiQuS:
-        MainFiQuS(
-            model_folder=model_folder,
-            input_file_path=self.get_input_file_path(model_name),
-            fdm=data_model,
-            # verbose=False,
-        )
+        if hasattr(self, "getdp_path"):
+            MainFiQuS(
+                model_folder=model_folder,
+                input_file_path=self.get_input_file_path(model_name),
+                fdm=data_model,
+                GetDP_path=self.getdp_path
+                # verbose=False,
+            )
+        else:
+            MainFiQuS(
+                model_folder=model_folder,
+                input_file_path=self.get_input_file_path(model_name),
+                fdm=data_model,
+                # verbose=False,
+            )
 
     def get_path_to_generated_file(
         self,

tests/utils/generate_reference_files_ConductorAC.py

@@ -1,57 +1,57 @@
-import os
-import shutil
-import sys
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../'))) # Add the path to the fiqus package to the system path
-from fiqus.data.DataFiQuS import FDM
-from fiqus.utils.Utils import FilesAndFolders as Util
-from fiqus import MainFiQuS as mf
-
-
-# Generate reference files for the models below:
-model_names = [
-    "TEST_CAC_Strand_adaptiveMesh",
-    "TEST_CAC_Strand_hexFilaments",
-    "TEST_CAC_wireInChannel",
-]
-# The run types for the models above:
-run_types = [
-    'geometry_and_mesh', 
-    'start_from_yaml', 
-    'start_from_yaml',
-]
-
-for model_name, run_type in zip(model_names, run_types):
-    # get path to the input file:
-    input_file = os.path.join(
-        os.path.dirname(os.path.dirname(__file__)),
-        "_inputs",
-        model_name,
-        f"{model_name}.yaml",
-    )
-
-    # select _references folder as the output folder:
-    output_folder = os.path.join(
-        os.path.dirname(os.path.dirname(__file__)), "_references", model_name
-    )
-
-    # if the output folder exists, remove it:
-    if os.path.exists(output_folder):
-        shutil.rmtree(output_folder)
-
-    # Create the output folder:
-    os.makedirs(output_folder)
-
-    # Cast input yaml file to FDM
-    data_model: FDM = Util.read_data_from_yaml(input_file, FDM)
-
-    data_model.run.overwrite = True
-
-    # Make the run type start_from_yaml:
-    data_model.run.type = run_type
-
-    fiqus_instance = mf.MainFiQuS(
-        fdm=data_model, model_folder=output_folder, input_file_path=input_file
-    )
-
-    # remove fiqus_instance to avoid memory issues:
-    del fiqus_instance
+import os
+import shutil
+import sys
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../'))) # Add the path to the fiqus package to the system path
+from fiqus.data.DataFiQuS import FDM
+from fiqus.utils.Utils import FilesAndFolders as Util
+from fiqus import MainFiQuS as mf
+
+
+# Generate reference files for the models below:
+model_names = [
+    "TEST_CAC_Strand_adaptiveMesh",
+    "TEST_CAC_Strand_hexFilaments",
+    "TEST_CAC_wireInChannel",
+]
+# The run types for the models above:
+run_types = [
+    'geometry_and_mesh', 
+    'start_from_yaml', 
+    'start_from_yaml',
+]
+
+for model_name, run_type in zip(model_names, run_types):
+    # get path to the input file:
+    input_file = os.path.join(
+        os.path.dirname(os.path.dirname(__file__)),
+        "_inputs",
+        model_name,
+        f"{model_name}.yaml",
+    )
+
+    # select _references folder as the output folder:
+    output_folder = os.path.join(
+        os.path.dirname(os.path.dirname(__file__)), "_references", model_name
+    )
+
+    # if the output folder exists, remove it:
+    if os.path.exists(output_folder):
+        shutil.rmtree(output_folder)
+
+    # Create the output folder:
+    os.makedirs(output_folder)
+
+    # Cast input yaml file to FDM
+    data_model: FDM = Util.read_data_from_yaml(input_file, FDM)
+
+    data_model.run.overwrite = True
+
+    # Make the run type start_from_yaml:
+    data_model.run.type = run_type
+
+    fiqus_instance = mf.MainFiQuS(
+        fdm=data_model, model_folder=output_folder, input_file_path=input_file
+    )
+
+    # remove fiqus_instance to avoid memory issues:
+    del fiqus_instance