Add option to pass subdirectory

docs/demo_dolfinx.py

@@ -10,11 +10,12 @@
 
 # First we try to generate the mean shape from the UK Biobank atlas
 
-folder_mean = Path("mean")
-subprocess.run(["ukb-atlas", str(folder_mean), "--mesh"])
+folder = Path("data")
+subdir = "mean"
+subprocess.run(["ukb-atlas", str(folder), "--mesh", "--subdir", subdir])
 
 comm = MPI.COMM_WORLD
-msh_file = folder_mean / "ED.msh"
+msh_file = folder / subdir / "ED.msh"
 gmsh.initialize()
 gmsh.model.add("Mesh from file")
 gmsh.merge(str(msh_file))
@@ -50,12 +51,13 @@
 
 
 # Now lets us perturb the mean shape with the second mode
-
-folder_mean = Path("mode_1")
-subprocess.run(["ukb-atlas", str(folder_mean), "--mesh", "--mode", "1", "--std", "1.5"])
+subdir = "mode_1"
+subprocess.run(
+    ["ukb-atlas", str(folder), "--mesh", "--mode", "1", "--std", "1.5", "--subdir", subdir]
+)
 
 comm = MPI.COMM_WORLD
-msh_file = folder_mean / "ED.msh"
+msh_file = folder / subdir / "ED.msh"
 gmsh.initialize()
 gmsh.model.add("Mesh from file")
 gmsh.merge(str(msh_file))

src/ukb/cli.py

@@ -18,6 +18,12 @@ def get_parser() -> argparse.ArgumentParser:
         type=Path,
         help="Directory to save the generated surfaces and meshes.",
     )
+    parser.add_argument(
+        "--subdir",
+        type=Path,
+        default=None,
+        help="Directory to save the generated surfaces and meshes.",
+    )
     parser.add_argument(
         "-a",
         "--all",
@@ -85,8 +91,11 @@ def main(argv: typing.Sequence[str] | None = None) -> int:
         default=lambda o: str(o),
     )
 
-    unique_id = hashlib.md5(args_json.encode()).hexdigest()
-    outdir = main_outdir / unique_id
+    if args["subdir"]:
+        outdir = main_outdir / args["subdir"]
+    else:
+        unique_id = hashlib.md5(args_json.encode()).hexdigest()
+        outdir = main_outdir / unique_id
     outdir.mkdir(exist_ok=True, parents=True)
 
     (outdir / "parameters.json").write_text(args_json)

tests/test_cli.py

@@ -5,7 +5,7 @@
 
 
 def test_generate_surfaces_mean_healthy(tmp_path):
-    ukb.cli.main([str(tmp_path)])
+    ukb.cli.main([str(tmp_path), "--subdir", "."])
     assert (tmp_path / "UKBRVLV.h5").exists()
     assert (tmp_path / "parameters.json").exists()
     for name in ukb.surface.surfaces:
@@ -17,7 +17,7 @@ def test_generate_surfaces_mean_healthy(tmp_path):
 def test_generate_surfaces_non_mean_healthy(tmp_path):
     mode = 1
     std = 0.3
-    ukb.cli.main([str(tmp_path), "--mode", str(mode), "--std", str(std)])
+    ukb.cli.main([str(tmp_path), "--mode", str(mode), "--std", str(std), "--subdir", "."])
     assert (tmp_path / "UKBRVLV.h5").exists()
     assert (tmp_path / "parameters.json").exists()
     params = json.loads((tmp_path / "parameters.json").read_text())
@@ -32,7 +32,7 @@ def test_generate_surfaces_non_mean_healthy(tmp_path):
 
 @pytest.mark.xfail(reason="I think we have the wrong template")
 def test_generate_surfaces_mean_all(tmp_path):
-    ukb.cli.main([str(tmp_path), "--all"])
+    ukb.cli.main([str(tmp_path), "--all", "--subdir", "."])
     assert (tmp_path / "UKBRVLV_ALL.h5").exists()
     assert (tmp_path / "parameters.json").exists()
     for name in ukb.surface.surfaces: