Use conda_subprocess in NFDI example (#50)

Author: jan-janssen

environment.yml

@@ -6,3 +6,4 @@ dependencies:
 - pyiron_base=0.11.8
 - pygraphviz=1.14
 - aiida-workgraph=0.5.1
+- conda_subprocess =0.0.6

nfdi_ing_workflow.py

@@ -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")
@@ -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")
@@ -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")
@@ -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")
@@ -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")
@@ -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")