Write auto generated input file to tmp

CHANGELOG.md

@@ -56,6 +56,17 @@ v0.17.1
 
 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.
 
 

desc/input_reader.py

@@ -215,10 +215,13 @@
             isVMEC = re.search(r"&INDATA", line, re.IGNORECASE)
             if isVMEC:
                 print("Converting VMEC input to DESC input")
-                path = self.input_path + "_desc"
-                InputReader.vmec_to_desc_input(self.input_path, path)
-                print("Generated DESC input file {}:".format(path))
-                return self.parse_inputs(path)
+                # use a buffer here to avoid having to read/write a file
+                # unnecessarily
+                buffer = io.StringIO()
+                InputReader.vmec_to_desc_input(self.input_path, buffer)
+                buffer.seek(0)
+                desc_file = buffer
+                return self.parse_inputs(desc_file)
 
             # extract numbers & words
             match = re.search(r"[!#]", line)
@@ -680,9 +683,11 @@
 
         """
         # open the file, unless its already open
+        opened_here = False
         if not isinstance(filename, io.IOBase):
             filename = os.path.expanduser(filename)
             f = open(filename, "w+")
+            opened_here = True
         else:
             f = filename
         f.seek(0)
@@ -783,7 +788,11 @@
         for n, R0, Z0 in inputs[0]["axis"]:
             f.write("n: {:3d}\tR0 = {:16.8E}\tZ0 = {:16.8E}\n".format(int(n), R0, Z0))
 
-        f.close()
+        # only close the file if we opened it here, as we also
+        # can use this function to write to an already open file
+        # or to an in-memory buffer
+        if opened_here:
+            f.close()
 
     @staticmethod
     def desc_output_to_input(  # noqa: C901 - fxn too complex

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 +58,13 @@ 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)]) uses a temp buffer
+    # instead of the old behavior of writing an intermediate file (#2148)
+    # so 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 +243,30 @@ 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 buffer 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 +319,6 @@ 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 +826,7 @@ 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())