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Use conda_subprocess in NFDI example #50

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merged 1 commit into from
Apr 6, 2025
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Use conda_subprocess in NFDI example #50

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1 change: 1 addition & 0 deletions environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@ dependencies:
- pyiron_base=0.11.8
- pygraphviz=1.14
- aiida-workgraph=0.5.1
- conda_subprocess =0.0.6
42 changes: 23 additions & 19 deletions nfdi_ing_workflow.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
import os
import subprocess
from conda_subprocess import check_output
import shutil

source_directory = os.path.join(os.path.dirname(os.path.abspath(__file__)), "source")
Expand All @@ -11,24 +11,26 @@ def generate_mesh(domain_size: float = 2.0) -> str:
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)
_ = subprocess.check_output(
_ = check_output(
[
"conda", "run", "-n", stage_name, "gmsh", "-2", "-setnumber",
"domain_size", str(domain_size), source_file_name, "-o", gmsh_output_file_name
"gmsh", "-2", "-setnumber", "domain_size", str(domain_size),
source_file_name, "-o", gmsh_output_file_name
],
prefix_name=stage_name,
cwd=stage_name,
universal_newlines=True,
).split("\n")
return os.path.abspath(os.path.join(stage_name, gmsh_output_file_name))


def convert_to_xdmf(gmsh_output_file : str) -> str:
def convert_to_xdmf(gmsh_output_file : str) -> dict:
stage_name = "preprocessing"
meshio_output_file_name = "square.xdmf"
os.makedirs(stage_name, exist_ok=True)
_copy_file(stage_name=stage_name, source_file=gmsh_output_file)
_ = subprocess.check_output(
["conda", "run", "-n", stage_name, "meshio", "convert", os.path.basename(gmsh_output_file), meshio_output_file_name],
_ = check_output(
["meshio", "convert", os.path.basename(gmsh_output_file), meshio_output_file_name],
prefix_name=stage_name,
cwd=stage_name,
universal_newlines=True,
).split("\n")
Expand All @@ -47,12 +49,12 @@ def poisson(meshio_output_xdmf: str, meshio_output_h5: str) -> dict:
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file(stage_name=stage_name, source_file=meshio_output_xdmf)
_copy_file(stage_name=stage_name, source_file=meshio_output_h5)
_ = subprocess.check_output(
_ = check_output(
[
"conda", "run", "-n", stage_name, "python", "poisson.py",
"--mesh", os.path.basename(meshio_output_xdmf), "--degree", "2",
"python", "poisson.py", "--mesh", os.path.basename(meshio_output_xdmf), "--degree", "2",
"--outputfile", poisson_output_pvd_file_name, "--num-dofs", poisson_output_numdofs_file_name
],
prefix_name=stage_name,
cwd=stage_name,
universal_newlines=True,
).split("\n")
Expand All @@ -71,8 +73,9 @@ def plot_over_line(poisson_output_pvd_file: str, poisson_output_vtu_file: str) -
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file(stage_name=stage_name, source_file=poisson_output_pvd_file)
_copy_file(stage_name=stage_name, source_file=poisson_output_vtu_file)
_ = subprocess.check_output(
["conda", "run", "-n", stage_name, "pvbatch", source_file_name, os.path.basename(poisson_output_pvd_file), pvbatch_output_file_name],
_ = check_output(
["pvbatch", source_file_name, os.path.basename(poisson_output_pvd_file), pvbatch_output_file_name],
prefix_name=stage_name,
cwd=stage_name,
universal_newlines=True,
).split("\n")
Expand All @@ -88,13 +91,13 @@ def substitute_macros(pvbatch_output_file: str, ndofs: int, domain_size: float =
_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(stage_name=stage_name, source_file=pvbatch_output_file)
_ = subprocess.check_output(
_ = check_output(
[
"conda", "run", "-n", stage_name, "python", "prepare_paper_macros.py",
"--macro-template-file", template_file_name, "--plot-data-path", os.path.basename(pvbatch_output_file),
"--domain-size", str(domain_size), "--num-dofs", str(ndofs),
"--output-macro-file", macros_output_file_name,
"python", "prepare_paper_macros.py", "--macro-template-file", template_file_name,
"--plot-data-path", os.path.basename(pvbatch_output_file), "--domain-size", str(domain_size),
"--num-dofs", str(ndofs), "--output-macro-file", macros_output_file_name,
],
prefix_name=stage_name,
cwd=stage_name,
universal_newlines=True,
).split("\n")
Expand All @@ -109,8 +112,9 @@ def compile_paper(macros_tex: str, plot_file: str) -> str:
_copy_file_from_source(stage_name=stage_name, source_file_name=source_file_name)
_copy_file(stage_name=stage_name, source_file=macros_tex)
_copy_file(stage_name=stage_name, source_file=plot_file)
_ = subprocess.check_output(
["conda", "run", "-n", stage_name, "tectonic", source_file_name],
_ = check_output(
["tectonic", source_file_name],
prefix_name=stage_name,
universal_newlines=True,
cwd=stage_name,
).split("\n")
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