Write auto generated input file to tmp

CHANGELOG.md

@@ -3,6 +3,17 @@ Changelog
 
 Bug Fixes
 
+- Fixes the possible permission error in `from_input_file` method of `Equilibrium`, `FourierRZToroidalSurface` and `FourierRZCurve` classes when used with a VMEC input file. Now the automatically generated DESC input file is written to a temporary file under `./tmp/`.
+
+v0.17.1
+-------
+
+This patch release updates package dependencies to resolve critical incompatibilities between jax-related libraries. DESC versions 0.16.0 and 0.17.0 contain a known bug when used alongside jax-finufft v1.3.0, and we recommend that users upgrade to DESC version 0.17.1 to ensure environment stability.
+
+If an immediate upgrade is not feasible, the issue can be mitigated by manually downgrading jax-finufft to version 1.2.0.
+
+Bug Fixes
+
 - Fixes incorrect units in the documentation of some curvature variables.
 - Fixes SyntaxError thrown when loading hdf5 data from file-like objects.
 

desc/input_reader.py

@@ -5,6 +5,7 @@
 import os
 import pathlib
 import re
+import tempfile
 import warnings
 from datetime import datetime
 
@@ -215,7 +216,9 @@
             isVMEC = re.search(r"&INDATA", line, re.IGNORECASE)
             if isVMEC:
                 print("Converting VMEC input to DESC input")
-                path = self.input_path + "_desc"
+                basename = os.path.basename(self.input_path) + "_desc"
+                tmpdir = tempfile.mkdtemp()
+                path = os.path.join(tmpdir, basename)
                 InputReader.vmec_to_desc_input(self.input_path, path)
                 print("Generated DESC input file {}:".format(path))
                 return self.parse_inputs(path)

tests/test_input_output.py

@@ -45,8 +45,6 @@ def test_vmec_input(tmpdir_factory):
     with pytest.warns(UserWarning):
         ir = InputReader(cl_args=[str(tmp_path)])
     vmec_inputs = ir.inputs
-    # ir makes a VMEC file automatically
-    path_converted_file = tmpdir.join("input.DSHAPE_desc")
     # also test making a DESC file from the ir.inputs manually
     path = tmpdir.join("desc_from_vmec")
     ir.write_desc_input(path, ir.inputs)
@@ -60,6 +58,12 @@ def test_vmec_input(tmpdir_factory):
     correct_file_path = ".//tests//inputs//input.DSHAPE_desc"
 
     # check DESC input file matches known correct one line-by-line
+    # above InputReader(cl_args=[str(tmp_path)]) generates a DESC input file
+    # inside unknown tmp folder, we re create the input file here at a specific
+    # location, so that we can compare
+    path_converted_file = tmpdir.join("input.DSHAPE_converted")
+    with pytest.warns(UserWarning):
+        InputReader.vmec_to_desc_input(input_path, str(path_converted_file))
     with open(correct_file_path) as f:
         lines_correct = f.readlines()
     with open(path) as f:
@@ -238,20 +242,30 @@ def test_near_axis_input_files():
         np.testing.assert_allclose(
             inputs_desc[arg], inputs_vmec[arg], rtol=1e-6, atol=1e-8
         )
-    if os.path.exists(".//tests//inputs//input.QSC_r2_5.5_vmec_desc"):
-        os.remove(".//tests//inputs//input.QSC_r2_5.5_vmec_desc")
 
 
 @pytest.mark.unit
-def test_from_input_file_equilibrium_desc_vmec_DSHAPE():
-    """Test that from_input_file works for DESC input files."""
-    vmec_path = ".//tests//inputs//input.DSHAPE"
+def test_from_input_file_equilibrium_desc_vmec_DSHAPE(tmp_path):
+    """Test that from_input_file works for DESC and VMEC input files."""
     desc_path = ".//tests//inputs//input.DSHAPE_desc"
     kwargs = {"spectral_indexing": "fringe"}
     with pytest.warns(UserWarning, match="Left handed"):
         eq = Equilibrium.from_input_file(desc_path, **kwargs)
-    with pytest.warns(UserWarning):
-        eq_VMEC = Equilibrium.from_input_file(vmec_path, **kwargs)
+
+    # load VMEC input from a read-only directory to ensure temp file handling works
+    # Related to issue #2139
+    vmec_src = ".//tests//inputs//input.DSHAPE"
+    locked_dir = tmp_path / "locked"
+    locked_dir.mkdir()
+    shutil.copy(vmec_src, locked_dir / "input.DSHAPE")
+    os.chmod(locked_dir, 0o555)
+    try:
+        with pytest.warns(UserWarning):
+            eq_VMEC = Equilibrium.from_input_file(
+                str(locked_dir / "input.DSHAPE"), **kwargs
+            )
+    finally:
+        os.chmod(locked_dir, 0o755)
 
     # make sure the loaded eqs are equivalent
     np.testing.assert_allclose(eq.R_lmn, eq_VMEC.R_lmn)
@@ -304,9 +318,6 @@ def test_from_input_file_equilibrium_desc_vmec():
     assert eq_VMEC.iota is None
     assert eq.sym == eq_VMEC.sym
 
-    if os.path.exists(".//tests//inputs//input.QSC_r2_5.5_vmec_desc"):
-        os.remove(".//tests//inputs//input.QSC_r2_5.5_vmec_desc")
-
 
 @pytest.mark.unit
 def test_vmec_input_surface_threshold():
@@ -814,7 +825,7 @@ def test_io_OmnigenousField(tmpdir_factory):
 
 @pytest.mark.unit
 def test_io_file_like_object(tmpdir_factory):
-    """Test loading an equilibrium from a file-like object (BytesIO)"""
+    """Test loading an equilibrium from a file-like object (BytesIO)."""
     file_path = "./tests/inputs/iotest_HELIOTRON.h5"
     with open(file_path, "rb") as f:
         file_like_obj = BytesIO(f.read())