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Merged
merged 6 commits into from
May 14, 2025
Merged

NFDI: provide source path as external variable #99

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2154258
NFDI: provide source path as external variable
jan-janssen May 14, 2025
16dc366
Update jupyter notebooks
jan-janssen May 14, 2025
a99b322
Remove hardcoded source path
jan-janssen May 14, 2025
efae48f
Update workflow.py
jan-janssen May 14, 2025
1000566
Update workflow.py
jan-janssen May 14, 2025
f3e8c0e
Update workflow.py
jan-janssen May 14, 2025
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364 changes: 1 addition & 363 deletions example_workflows/nfdi/aiida.ipynb
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2 changes: 1 addition & 1 deletion example_workflows/nfdi/jobflow.ipynb
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313 changes: 1 addition & 312 deletions example_workflows/nfdi/pyiron_base.ipynb
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10 changes: 8 additions & 2 deletions example_workflows/nfdi/workflow.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,26 @@
{"id": 4, "type": "function", "value": "workflow.substitute_macros"},
{"id": 5, "type": "function", "value": "workflow.compile_paper"},
{"id": 6, "type": "input", "value": 2.0, "name": "domain_size"},
{"id": 7, "type": "output", "name": "result"}
{"id": 7, "type": "input", "value": "source", "name": "source_directory"},
{"id": 8, "type": "output", "name": "result"}
],
"edges": [
{"target": 0, "targetPort": "domain_size", "source": 6, "sourcePort": null},
{"target": 0, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 1, "targetPort": "gmsh_output_file", "source": 0, "sourcePort": null},
{"target": 2, "targetPort": "meshio_output_xdmf", "source": 1, "sourcePort": "xdmf_file"},
{"target": 2, "targetPort": "meshio_output_h5", "source": 1, "sourcePort": "h5_file"},
{"target": 2, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 3, "targetPort": "poisson_output_pvd_file", "source": 2, "sourcePort": "pvd_file"},
{"target": 3, "targetPort": "poisson_output_vtu_file", "source": 2, "sourcePort": "vtu_file"},
{"target": 3, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 4, "targetPort": "pvbatch_output_file", "source": 3, "sourcePort": null},
{"target": 4, "targetPort": "ndofs", "source": 2, "sourcePort": "numdofs"},
{"target": 4, "targetPort": "domain_size", "source": 6, "sourcePort": null},
{"target": 4, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 5, "targetPort": "macros_tex", "source": 4, "sourcePort": null},
{"target": 5, "targetPort": "plot_file", "source": 3, "sourcePort": null},
{"target": 7, "targetPort": null, "source": 5, "sourcePort": null}
{"target": 5, "targetPort": "source_directory", "source": 7, "sourcePort": null},
{"target": 8, "targetPort": null, "source": 5, "sourcePort": null}
]
}
30 changes: 14 additions & 16 deletions example_workflows/nfdi/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,15 +2,13 @@
from conda_subprocess import check_output
import shutil

source_directory = os.path.join(os.path.dirname(os.path.abspath(__file__)), "source")


def generate_mesh(domain_size: float = 2.0) -> str:
def generate_mesh(domain_size: float, source_directory: str) -> str:
stage_name = "preprocessing"
gmsh_output_file_name = "square.msh"
source_file_name ="unit_square.geo"
os.makedirs(stage_name, exist_ok=True)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
_ = check_output(
[
"gmsh", "-2", "-setnumber", "domain_size", str(domain_size),
Expand Down Expand Up @@ -40,13 +38,13 @@ def convert_to_xdmf(gmsh_output_file : str) -> dict:
}


def poisson(meshio_output_xdmf: str, meshio_output_h5: str) -> 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"
source_file_name = "poisson.py"
os.makedirs(stage_name, exist_ok=True)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
_copy_file(stage_name=stage_name, source_file=meshio_output_xdmf)
_copy_file(stage_name=stage_name, source_file=meshio_output_h5)
_ = check_output(
Expand All @@ -65,12 +63,12 @@ def poisson(meshio_output_xdmf: str, meshio_output_h5: str) -> dict:
}


def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str) -> 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"
os.makedirs(stage_name, exist_ok=True)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
_copy_file(stage_name=stage_name, source_file=poisson_output_pvd_file)
_copy_file(stage_name=stage_name, source_file=poisson_output_vtu_file)
_ = check_output(
Expand All @@ -82,14 +80,14 @@ def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str) -
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) -> str:
def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float, source_directory: str) -> str:
stage_name = "postprocessing"
source_file_name = "prepare_paper_macros.py"
template_file_name = "macros.tex.template"
macros_output_file_name = "macros.tex"
os.makedirs(stage_name, exist_ok=True)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file_from_source(stage_name=stage_name, source_file_name=template_file_name)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
_copy_file_from_source(stage_name=stage_name, source_file_name=template_file_name, source_directory=source_directory)
_copy_file(stage_name=stage_name, source_file=pvbatch_output_file)
_ = check_output(
[
Expand All @@ -104,12 +102,12 @@ 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) -> 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"
os.makedirs(stage_name, exist_ok=True)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name, source_directory=source_directory)
_copy_file(stage_name=stage_name, source_file=macros_tex)
_copy_file(stage_name=stage_name, source_file=plot_file)
_ = check_output(
Expand All @@ -126,12 +124,12 @@ def _poisson_collect_output(numdofs_file: str) -> int:
return int(f.read())


def _copy_file(stage_name, source_file):
def _copy_file(stage_name: str, source_file: str):
input_file = os.path.join(os.path.abspath(stage_name), os.path.basename(source_file))
if input_file != source_file:
shutil.copyfile(source_file, input_file)


def _copy_file_from_source(stage_name, source_file_name):
def _copy_file_from_source(stage_name: str, source_file_name: str, source_directory: str):
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))
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