Remove hardcoded source path

Author: jan-janssen

example_workflows/nfdi/workflow.py

@@ -2,10 +2,8 @@
 from conda_subprocess import check_output
 import shutil
 
-source_directory_global = os.path.join(os.path.dirname(os.path.abspath(__file__)), "source")
 
-
-def generate_mesh(domain_size: float = 2.0, source_directory: str = source_directory_global) -> str:
+def generate_mesh(domain_size: float = 2.0, source_directory: str) -> str:
     stage_name = "preprocessing"
     gmsh_output_file_name = "square.msh"
     source_file_name ="unit_square.geo"
@@ -40,7 +38,7 @@ def convert_to_xdmf(gmsh_output_file : str) -> dict:
     }
 
 
-def poisson(meshio_output_xdmf: str, meshio_output_h5: str, source_directory: str = source_directory_global) -> dict:
+def poisson(meshio_output_xdmf: str, meshio_output_h5: str, source_directory: str) -> dict:
     stage_name = "processing"
     poisson_output_pvd_file_name = "poisson.pvd"
     poisson_output_numdofs_file_name = "numdofs.txt"
@@ -65,7 +63,7 @@ def poisson(meshio_output_xdmf: str, meshio_output_h5: str, source_directory: st
     }
 
 
-def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str, source_directory: str = source_directory_global) -> str:
+def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str, source_directory: str) -> str:
     stage_name = "postprocessing"
     pvbatch_output_file_name = "plotoverline.csv"
     source_file_name = "postprocessing.py"
@@ -82,7 +80,7 @@ def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str, s
     return os.path.abspath(os.path.join("postprocessing", pvbatch_output_file_name))
 
 
-def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float = 2.0, source_directory: str = source_directory_global) -> str:
+def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float = 2.0, source_directory: str) -> str:
     stage_name = "postprocessing"
     source_file_name = "prepare_paper_macros.py"
     template_file_name = "macros.tex.template"
@@ -104,7 +102,7 @@ def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float =
     return os.path.abspath(os.path.join(stage_name, macros_output_file_name))
 
 
-def compile_paper(macros_tex: str, plot_file: str, source_directory: str = source_directory_global) -> str:
+def compile_paper(macros_tex: str, plot_file: str, source_directory: str) -> str:
     stage_name = "postprocessing"
     paper_output = "paper.pdf"
     source_file_name = "paper.tex"
@@ -134,4 +132,4 @@ def _copy_file(stage_name, source_file):
 
 def _copy_file_from_source(stage_name, source_file_name, source_directory: str = source_directory_global):
     source_file = os.path.join(source_directory, source_file_name)
-    shutil.copyfile(source_file, os.path.join(stage_name, source_file_name))
+    shutil.copyfile(source_file, os.path.join(stage_name, source_file_name))