Rnc/pr edits to zk tars refactor

.gitignore

@@ -229,3 +229,6 @@ examples/mesh_plot/
 thincurr_scratch/
 scratch/
 synthwave/vessel_caches
+
+# No figure storage to git, at least of pdfs
+*.pdf

.pre-commit-config.yaml

@@ -10,19 +10,19 @@ repos:
         entry: uv run jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
       - id: ruff_format
         name: ruff_format 
-        entry: uv run ruff format
+        entry: uv run --no-sync ruff format
         language: system
         types: [python]
         files: "^synthwave/"
       - id: ruff_check
         name: ruff_check
-        entry: uv run ruff check --fix
+        entry: uv run --no-sync ruff check --fix
         language: system
         types: [python]
         files: "^synthwave/"
       - id: isort
         name: isort
-        entry: uv run isort
+        entry: uv run --no-sync isort
         language: system
         types: [python]
         files: "^synthwave/"

synthwave/tests/conftest.py

@@ -9,6 +9,7 @@
 import gc
 
 import pytest
+from OpenFUSIONToolkit import OFT_env
 
 
 def pytest_configure(config):
@@ -27,3 +28,9 @@ def _serial_gc(request):
     yield
     if request.node.get_closest_marker("serial"):
         gc.collect()
+
+
+# Fixture for OFT environment so only one is created for all tests.
+@pytest.fixture(scope="session")
+def oft_env():
+    return OFT_env(nthreads=2)

synthwave/tests/test_direct_response.py

@@ -17,7 +17,6 @@
 import numpy as np
 import pytest
 import xarray as xr
-from OpenFUSIONToolkit import OFT_env
 
 from synthwave import PACKAGE_ROOT
 from synthwave.magnetic_geometry.equilibrium_field import (
@@ -35,7 +34,10 @@
     direct_response_thincurr,
 )
 
-# ThinCurr / OFT_env hold global C++ state that cannot be shared across workers
+# All tests in this file use the OpenFUSIONToolkit C++ library which has
+# global state (OFT_env, ThinCurr) that cannot be shared across concurrent
+# workers.  Mark the entire module serial so the conftest fixture forces
+# sequential execution and GC cleanup between tests.
 pytestmark = pytest.mark.serial
 
 _CMOD_DIR = os.path.join(PACKAGE_ROOT, "input_data", "cmod")
@@ -48,11 +50,6 @@
 _BASE_NUM_POINTS = 100
 
 
-@pytest.fixture(scope="module")
-def oft_env():
-    return OFT_env(nthreads=2)
-
-
 @pytest.fixture(scope="module")
 def sensor_details():
     """Load the C-Mod Mirnov set and conform it to the OFT/Biot-Savart schema.
@@ -169,7 +166,7 @@ def test_thincurr_phase_matches_biot_savart(oft_env, direct_response_inputs):
         gen_OFT_filament_and_eta_file(
             working_directory=tmpdir,
             filament_list=filament_list,
-            resistivity_list=[1e-6] * len(filament_list),
+            resistivity_list=[1e-6],
         )
         sensor_file_path = gen_OFT_sensors_file(
             sensor_details=sensor_details,

synthwave/tests/test_equilibrium_field.py

@@ -262,6 +262,21 @@ def test_detect_cocos_cmod(self, eqdsk_cmod):
                 f"Expected COCOS {expected_cocos} for C-Mod, got {cocos}"
             )
 
+        @pytest.mark.skipif(
+            condition=not os.path.exists(
+                os.path.join(
+                    PACKAGE_ROOT,
+                    "..",
+                    "submodules",
+                    "OpenFUSIONToolkit",
+                    "examples",
+                    "TokaMaker",
+                    "DIIID",
+                    "g192185.02440",
+                )
+            ),
+            reason="Test requires DIII-D data which is not open source",
+        )
         def test_detect_cocos_d3d(self, eqdsk_d3d):
             """DIII-D uses EFIT convention (sigma_RphiZ=+1, e_Bp=0, psi increasing).
             COCOS depends on sign(Ip) and sign(B0)
@@ -345,7 +360,24 @@ def eqdsk(self, request):
             "eqdsk",
             [
                 "eqdsk_cmod",
-                "eqdsk_d3d",
+                pytest.param(
+                    "eqdsk_d3d",
+                    marks=pytest.mark.skipif(
+                        condition=not os.path.exists(
+                            os.path.join(
+                                PACKAGE_ROOT,
+                                "..",
+                                "submodules",
+                                "OpenFUSIONToolkit",
+                                "examples",
+                                "TokaMaker",
+                                "DIIID",
+                                "g192185.02440",
+                            )
+                        ),
+                        reason="Test requires DIII-D data which is not open source",
+                    ),
+                ),
                 pytest.param(
                     "eqdsk_tcv",
                     marks=pytest.mark.skipif(
@@ -392,7 +424,24 @@ def test_convert_cocos_same(self, eqdsk):
             "eqdsk",
             [
                 "eqdsk_cmod",
-                "eqdsk_d3d",
+                pytest.param(
+                    "eqdsk_d3d",
+                    marks=pytest.mark.skipif(
+                        condition=not os.path.exists(
+                            os.path.join(
+                                PACKAGE_ROOT,
+                                "..",
+                                "submodules",
+                                "OpenFUSIONToolkit",
+                                "examples",
+                                "TokaMaker",
+                                "DIIID",
+                                "g192185.02440",
+                            )
+                        ),
+                        reason="Test requires DIII-D data which is not open source",
+                    ),
+                ),
                 pytest.param(
                     "eqdsk_tcv",
                     marks=pytest.mark.skipif(
@@ -449,7 +498,24 @@ def test_convert_cocos_internal(self, eqdsk):
             "eqdsk",
             [
                 "eqdsk_cmod",
-                "eqdsk_d3d",
+                pytest.param(
+                    "eqdsk_d3d",
+                    marks=pytest.mark.skipif(
+                        condition=not os.path.exists(
+                            os.path.join(
+                                PACKAGE_ROOT,
+                                "..",
+                                "submodules",
+                                "OpenFUSIONToolkit",
+                                "examples",
+                                "TokaMaker",
+                                "DIIID",
+                                "g192185.02440",
+                            )
+                        ),
+                        reason="Test requires DIII-D data which is not open source",
+                    ),
+                ),
                 pytest.param(
                     "eqdsk_tcv",
                     marks=pytest.mark.skipif(

synthwave/tests/test_thincurr.py

@@ -5,7 +5,6 @@
 import numpy as np
 import pytest
 import xarray as xr
-from OpenFUSIONToolkit import OFT_env
 from sympy import nextprime
 
 from synthwave import PACKAGE_ROOT
@@ -31,13 +30,6 @@
 pytestmark = pytest.mark.serial
 
 
-# Fixture for oft environment so only one is created for all tests
-@pytest.fixture(scope="session")
-def oft_env_fixture():
-    oft_env = OFT_env(nthreads=2)
-    return oft_env
-
-
 @pytest.mark.parametrize(
     "mode",
     [
@@ -49,7 +41,7 @@ def oft_env_fixture():
     ],
     ids=["m2n1", "m3n2", "m-3n2", "m3n1", "m4n3"],
 )
-def test_toroidal_angles(mode, oft_env_fixture):
+def test_toroidal_angles(mode, oft_env):
     tolerance_tight = np.deg2rad(1)
     tolerance_loose = np.deg2rad(
         5
@@ -171,7 +163,7 @@ def test_toroidal_angles(mode, oft_env_fixture):
         )
 
         total_response, direct_response, _vessel_response = frequency_response_thincurr(
-            oft_env=oft_env_fixture,
+            oft_env=oft_env,
             tracer=toroidal_tracer,
             freq=10e3,
             mesh_file=torus_mesh_file,
@@ -317,7 +309,7 @@ def test_gen_OFT_sensors_file():
         assert len(content) > 0
 
 
-def test_direct_response_thincurr_matches_frequency_response(oft_env_fixture):
+def test_direct_response_thincurr_matches_frequency_response(oft_env):
     """direct_response_thincurr must return the same direct component as frequency_response_thincurr."""
 
     major_radius = 1
@@ -370,13 +362,11 @@ def test_direct_response_thincurr_matches_frequency_response(oft_env_fixture):
         filament_list, current_list = toroidal_tracer.get_filament_list(
             num_filaments=num_filaments
         )
-        gen_OFT_filament_and_eta_file(
-            working_directory, filament_list, [1e-6] * len(filament_list)
-        )
+        gen_OFT_filament_and_eta_file(working_directory, filament_list, [1e-6])
 
         total_response, direct_response_freq, vessel_response = (
             frequency_response_thincurr(
-                oft_env=oft_env_fixture,
+                oft_env=oft_env,
                 tracer=toroidal_tracer,
                 freq=10e3,
                 mesh_file=torus_mesh_file,
@@ -386,7 +376,7 @@ def test_direct_response_thincurr_matches_frequency_response(oft_env_fixture):
         )
 
         direct_response_only = direct_response_thincurr(
-            oft_env=oft_env_fixture,
+            oft_env=oft_env,
             tracer=toroidal_tracer,
             mesh_file=torus_mesh_file,
             sensor_details=sensor_details,