From d6199f98c15a8262f4e9a21f7199e7d0edc5a46d Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Fri, 13 Dec 2024 22:35:19 +0100
Subject: [PATCH 01/13] Boozer tests

---
 tests/libneo/python/test_boozer.py | 37 +++++++++++++++++++-----------
 1 file changed, 23 insertions(+), 14 deletions(-)

diff --git a/tests/libneo/python/test_boozer.py b/tests/libneo/python/test_boozer.py
index 109fd25..25ce820 100644
--- a/tests/libneo/python/test_boozer.py
+++ b/tests/libneo/python/test_boozer.py
@@ -1,22 +1,31 @@
-# %%
-from libneo import BoozerFile
-from libneo import read_eqdsk, FluxConverter
+import pytest
+
+from pathlib import Path
+import os
 import numpy as np
 import matplotlib.pyplot as plt
 
-trial_boozer_file = "/temp/AG-plasma/archive/2023/andfmar/Boozer_files_perturbation_field/ASDEX_U/30835_rmpm90/out_neo-2_rmp_m90-n0"
-trial_eqdsk_file = "/proj/plasma/DATA/AUG/EQDSK/g30835.3200_ed6"
-bc = BoozerFile(trial_boozer_file)
-eqdsk = read_eqdsk(trial_eqdsk_file)
+from libneo import BoozerFile
+from libneo import read_eqdsk, FluxConverter
+
+data_path = Path(os.environ["DATA"])
+
+trial_boozer_file = data_path / "AUG/BOOZER/30835/out_neo-2_rmp_90-n0"
+trial_eqdsk_file = data_path / "AUG/EQDSK/g30835.3200_ed6"
+bc = BoozerFile(trial_boozer_file.as_posix())
+eqdsk = read_eqdsk(trial_eqdsk_file.as_posix())
 converter = FluxConverter(eqdsk["qprof"])
-no_edges = slice(10,-10)
+no_edges = slice(10, -10)
+
 
 def test_iota():
     stor_bc = bc.s[no_edges]
     iota_bc = np.array(bc.iota[no_edges])
-    stor_eqdsk = converter.sqrtspol2stor(np.sqrt(eqdsk["rho_poloidal"]))
-    iota_eqdsk = np.interp(stor_bc, stor_eqdsk, 1/eqdsk["qprof"])
-    assert np.allclose(iota_eqdsk, -iota_bc, atol=1e-2) # .bc file has only positive itota
+    stor_eqdsk = converter.sqrtspol2stor(np.sqrt(eqdsk["s_pol"]))
+    iota_eqdsk = np.interp(stor_bc, stor_eqdsk, 1 / eqdsk["qprof"])
+    assert np.allclose(
+        iota_eqdsk, -iota_bc, atol=1e-2
+    )  # .bc file has only positive itota
 
 
 def test_get_rho_poloidal():
@@ -24,6 +33,6 @@ def test_get_rho_poloidal():
     sqrtspol_control = converter.stor2sqrtspol(bc.s)[no_edges]
     assert np.allclose(sqrtspol, sqrtspol_control, atol=1e-2)
 
-if __name__=="__main__":
-    test_iota()
-    test_get_rho_poloidal()
\ No newline at end of file
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-s"])

From 28bb67449ac5ab07b4972f585f5ceb8b99fb8b7f Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Fri, 13 Dec 2024 22:46:45 +0100
Subject: [PATCH 02/13] Final newline

---
 .vscode/settings.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 3221a8a..4245d76 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -40,5 +40,6 @@
     "testing.openTesting": "neverOpen",
     "github.codespaces.devcontainerChangedNotificationStyle": "none",
     "mesonbuild.selectRootDir": false,
-    "testing.automaticallyOpenTestResults": "neverOpen"
+    "testing.automaticallyOpenTestResults": "neverOpen",
+    "files.insertFinalNewline": true
 }

From 315780e61b0dd03bffa449157ab2fc8869f06d2c Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Fri, 13 Dec 2024 22:48:15 +0100
Subject: [PATCH 03/13] Modernize tests

---
 tests/libneo/python/conftest.py    |  8 +++++++
 tests/libneo/python/test_boozer.py | 37 +++++++++++++++++++-----------
 2 files changed, 31 insertions(+), 14 deletions(-)
 create mode 100644 tests/libneo/python/conftest.py

diff --git a/tests/libneo/python/conftest.py b/tests/libneo/python/conftest.py
new file mode 100644
index 0000000..2019d3a
--- /dev/null
+++ b/tests/libneo/python/conftest.py
@@ -0,0 +1,8 @@
+import pytest
+
+import os
+from pathlib import Path
+
+@pytest.fixture
+def data_path():
+    return Path(os.environ["DATA"])
diff --git a/tests/libneo/python/test_boozer.py b/tests/libneo/python/test_boozer.py
index 25ce820..7fceb01 100644
--- a/tests/libneo/python/test_boozer.py
+++ b/tests/libneo/python/test_boozer.py
@@ -1,6 +1,5 @@
 import pytest
 
-from pathlib import Path
 import os
 import numpy as np
 import matplotlib.pyplot as plt
@@ -8,19 +7,29 @@
 from libneo import BoozerFile
 from libneo import read_eqdsk, FluxConverter
 
-data_path = Path(os.environ["DATA"])
-
-trial_boozer_file = data_path / "AUG/BOOZER/30835/out_neo-2_rmp_90-n0"
-trial_eqdsk_file = data_path / "AUG/EQDSK/g30835.3200_ed6"
-bc = BoozerFile(trial_boozer_file.as_posix())
-eqdsk = read_eqdsk(trial_eqdsk_file.as_posix())
-converter = FluxConverter(eqdsk["qprof"])
 no_edges = slice(10, -10)
 
 
-def test_iota():
-    stor_bc = bc.s[no_edges]
-    iota_bc = np.array(bc.iota[no_edges])
+@pytest.fixture
+def boozer(data_path):
+    trial_boozer_file = data_path / "AUG/BOOZER/30835/out_neo-2_rmp_90-n0"
+    return BoozerFile(trial_boozer_file.as_posix())
+
+
+@pytest.fixture
+def eqdsk(data_path):
+    trial_eqdsk_file = data_path / "AUG/EQDSK/g30835.3200_ed6"
+    return read_eqdsk(trial_eqdsk_file.as_posix())
+
+
+@pytest.fixture
+def converter(eqdsk):
+    return FluxConverter(eqdsk["qprof"])
+
+
+def test_iota(boozer, eqdsk, converter):
+    stor_bc = boozer.s[no_edges]
+    iota_bc = np.array(boozer.iota[no_edges])
     stor_eqdsk = converter.sqrtspol2stor(np.sqrt(eqdsk["s_pol"]))
     iota_eqdsk = np.interp(stor_bc, stor_eqdsk, 1 / eqdsk["qprof"])
     assert np.allclose(
@@ -28,9 +37,9 @@ def test_iota():
     )  # .bc file has only positive itota
 
 
-def test_get_rho_poloidal():
-    sqrtspol = bc.get_rho_poloidal()[no_edges]
-    sqrtspol_control = converter.stor2sqrtspol(bc.s)[no_edges]
+def test_get_rho_poloidal(boozer, converter):
+    sqrtspol = boozer.get_rho_poloidal()[no_edges]
+    sqrtspol_control = converter.stor2sqrtspol(boozer.s)[no_edges]
     assert np.allclose(sqrtspol, sqrtspol_control, atol=1e-2)
 
 

From eb4724b2c592a3ebb2b88ef8eae309a45bde50c4 Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Fri, 13 Dec 2024 23:35:15 +0100
Subject: [PATCH 04/13] Modernize tests

---
 tests/libneo/python/conftest.py    |  8 ----
 tests/libneo/python/paths.py       |  5 +++
 tests/libneo/python/test_boozer.py | 10 ++---
 tests/libneo/python/test_eqdsk.py  | 61 +++++++++++++++---------------
 4 files changed, 40 insertions(+), 44 deletions(-)
 delete mode 100644 tests/libneo/python/conftest.py
 create mode 100644 tests/libneo/python/paths.py

diff --git a/tests/libneo/python/conftest.py b/tests/libneo/python/conftest.py
deleted file mode 100644
index 2019d3a..0000000
--- a/tests/libneo/python/conftest.py
+++ /dev/null
@@ -1,8 +0,0 @@
-import pytest
-
-import os
-from pathlib import Path
-
-@pytest.fixture
-def data_path():
-    return Path(os.environ["DATA"])
diff --git a/tests/libneo/python/paths.py b/tests/libneo/python/paths.py
new file mode 100644
index 0000000..183fc15
--- /dev/null
+++ b/tests/libneo/python/paths.py
@@ -0,0 +1,5 @@
+import os
+from pathlib import Path
+
+code_path = Path(os.environ["CODE"])
+data_path = Path(os.environ["DATA"])
diff --git a/tests/libneo/python/test_boozer.py b/tests/libneo/python/test_boozer.py
index 7fceb01..91bbb9d 100644
--- a/tests/libneo/python/test_boozer.py
+++ b/tests/libneo/python/test_boozer.py
@@ -1,25 +1,25 @@
 import pytest
 
-import os
 import numpy as np
 import matplotlib.pyplot as plt
 
 from libneo import BoozerFile
 from libneo import read_eqdsk, FluxConverter
+from paths import data_path
 
 no_edges = slice(10, -10)
 
 
 @pytest.fixture
-def boozer(data_path):
+def boozer():
     trial_boozer_file = data_path / "AUG/BOOZER/30835/out_neo-2_rmp_90-n0"
-    return BoozerFile(trial_boozer_file.as_posix())
+    return BoozerFile(str(trial_boozer_file))
 
 
 @pytest.fixture
-def eqdsk(data_path):
+def eqdsk():
     trial_eqdsk_file = data_path / "AUG/EQDSK/g30835.3200_ed6"
-    return read_eqdsk(trial_eqdsk_file.as_posix())
+    return read_eqdsk(str(trial_eqdsk_file))
 
 
 @pytest.fixture
diff --git a/tests/libneo/python/test_eqdsk.py b/tests/libneo/python/test_eqdsk.py
index 6b29320..113637d 100644
--- a/tests/libneo/python/test_eqdsk.py
+++ b/tests/libneo/python/test_eqdsk.py
@@ -6,37 +6,31 @@
 
 import json
 import gzip
-import os.path
 
 from libneo import eqdsk
+from paths import code_path, data_path
 
-# Directory where the golden records are stored for regression tests
-golden_record_dir = "/proj/plasma/DATA/TESTS/libneo/eqdsk"
 
+golden_record_path = data_path / "TESTS/libneo/eqdsk"
 
-test_files = [
-    
-    # Local
-    "libneo/tests/resources/input_efit_file.dat",
 
-    # PROCESS code
-    "/proj/plasma/DATA/DEMO/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
+@pytest.fixture
+def test_files():
+    return {
+        "local": code_path / "libneo/test/resources/input_efit_file.dat",
+        "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
+        "standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
+        # TODO: "CHEASE": data_path / "DEMO/teams/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
+    }
 
-    # Standardized
-    "/proj/plasma/DATA/DEMO/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
 
-    # TODO: CHEASE
-    # "/proj/plasma/DATA/DEMO/teams/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT"
-]
-
-
-def test_eqdsk_read():
-    for test_file in test_files:
+def test_eqdsk_read(test_files):
+    for test_file in test_files.values():
         _ = eqdsk.eqdsk_file(test_file)
 
 
-def test_eqdsk_golden_records():
-    for test_file in test_files:
+def test_eqdsk_golden_records(test_files):
+    for test_file in test_files.values():
         eqdsk_object = eqdsk.eqdsk_file(test_file)
 
         data = eqdsk_object.__dict__
@@ -45,33 +39,34 @@ def test_eqdsk_golden_records():
         assert are_dicts_equal(data, get_golden_record(test_file))
 
 
-def get_golden_record(filename):
+def get_golden_record(file_path):
     """
     Returns the golden record for the given test file.
     """
 
-    file_base, _ = os.path.splitext(os.path.basename(filename))
-    with gzip.open(f"{golden_record_dir}/{file_base}.json.gz", "rb") as f:
+    file_base = file_path.stem
+    with gzip.open(golden_record_path / f"{file_base}.json.gz", "rb") as f:
         compressed_data = f.read()
         json_data = compressed_data.decode("utf-8")
         return json.loads(json_data)
 
 
-def store_golden_records():
+def store_golden_records(file_paths):
     """
     Stores reference data for regression tests. Call only manually after fixing
     a bug and checking that the new results are correct.
     """
 
-    for file in test_files:
-        basedir = os.path.dirname(file)
-        file_base, ext = os.path.splitext(os.path.basename(file))
-        data = eqdsk.eqdsk_file(f"{basedir}/{file_base}{ext}").__dict__
+    for f in file_paths:
+        basedir = f.parent
+        file_base = f.stem
+        ext = f.suffix
+        data = eqdsk.eqdsk_file(str(f)).__dict__
         replace_array_members_by_lists(data)
 
-        outfile = f"{golden_record_dir}/{file_base}.json.gz"
+        outfile = golden_record_path / f"{file_base}.json.gz"
 
-        if os.path.isfile(outfile):
+        if outfile.exists():
             raise RuntimeError(f"Golden record file {outfile} already exists.")
 
         with gzip.open(outfile, "wb") as f:
@@ -137,4 +132,8 @@ def are_float_lists_equal(list1, list2, tolerance=1e-9):
         elif isinstance(a, list) and isinstance(b, list):
             if not are_float_lists_equal(a, b, tolerance):
                 return False
-    return True
\ No newline at end of file
+    return True
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-s"])

From d705b6b091505e78efb16c30290db2954d3f9610 Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Fri, 13 Dec 2024 23:46:57 +0100
Subject: [PATCH 05/13] MGRID test modernized

---
 tests/libneo/python/test_mgrid.py | 58 +++++++++++++++++++------------
 1 file changed, 36 insertions(+), 22 deletions(-)

diff --git a/tests/libneo/python/test_mgrid.py b/tests/libneo/python/test_mgrid.py
index c1ca27e..1aaa904 100644
--- a/tests/libneo/python/test_mgrid.py
+++ b/tests/libneo/python/test_mgrid.py
@@ -1,33 +1,47 @@
+import pytest
+
 import numpy as np
 
 from libneo.mgrid import MgridFile
+from paths import data_path
+
+testfile_path = data_path / "LHD/VMEC/makegrid_alternative/mgrid_lhd_nfp10.nc"
+
+
+@pytest.fixture
+def mgrid():
+    return MgridFile.from_file(testfile_path)
+
 
 def test_mgrid_read():
-    f = MgridFile.from_file('/proj/plasma/DATA/LHD/albert/vmec/makegrid_alternative/mgrid_lhd_nfp10.nc')
+    f = MgridFile.from_file(testfile_path)
     print(f)
 
-def test_mgrid_read_write():
-    f = MgridFile.from_file('/proj/plasma/DATA/LHD/albert/vmec/makegrid_alternative/mgrid_lhd_nfp10.nc')
-    f.write('/tmp/mgrid_test.nc')
+
+def test_mgrid_read_write(mgrid):
+    mgrid.write("/tmp/mgrid_test.nc")
 
 
-def test_mgrid_read_write_read():
-    f = MgridFile.from_file('/proj/plasma/DATA/LHD/albert/vmec/makegrid_alternative/mgrid_lhd_nfp10.nc')
-    f.write('/tmp/mgrid_test.nc')
-    g = MgridFile.from_file('/tmp/mgrid_test.nc')
+def test_mgrid_read_write_read(mgrid):
+    mgrid.write("/tmp/mgrid_test.nc")
+    g = MgridFile.from_file("/tmp/mgrid_test.nc")
 
     # Assert if all variables are the same
-    assert f.ir == g.ir
-    assert f.jz == g.jz
-    assert f.kp == g.kp
-    assert f.nfp == g.nfp
-    assert f.rmin == g.rmin
-    assert f.zmin == g.zmin
-    assert f.rmax == g.rmax
-    assert f.zmax == g.zmax
-    assert f.mgrid_mode == g.mgrid_mode
-    assert np.array_equal(f.coil_group, g.coil_group)
-    assert np.array_equal(f.coil_current, g.coil_current)
-    assert np.array_equal(f.br, g.br)
-    assert np.array_equal(f.bp, g.bp)
-    assert np.array_equal(f.bz, g.bz)
+    assert mgrid.ir == g.ir
+    assert mgrid.jz == g.jz
+    assert mgrid.kp == g.kp
+    assert mgrid.nfp == g.nfp
+    assert mgrid.rmin == g.rmin
+    assert mgrid.zmin == g.zmin
+    assert mgrid.rmax == g.rmax
+    assert mgrid.zmax == g.zmax
+    assert mgrid.mgrid_mode == g.mgrid_mode
+    assert np.array_equal(mgrid.coil_group, g.coil_group)
+    assert np.array_equal(mgrid.coil_current, g.coil_current)
+    assert np.array_equal(mgrid.br, g.br)
+    assert np.array_equal(mgrid.bp, g.bp)
+    assert np.array_equal(mgrid.bz, g.bz)
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-s"])

From f4b5c75e2a94d5a6b098a99f352b78e4cdeeb5c3 Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 00:03:23 +0100
Subject: [PATCH 06/13] EQDSK testing runs

---
 tests/libneo/python/test_efit_to_boozer.py |  0
 tests/libneo/python/test_eqdsk.py          | 18 ++++++++++++------
 2 files changed, 12 insertions(+), 6 deletions(-)
 create mode 100644 tests/libneo/python/test_efit_to_boozer.py

diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/libneo/python/test_eqdsk.py b/tests/libneo/python/test_eqdsk.py
index 113637d..ef33360 100644
--- a/tests/libneo/python/test_eqdsk.py
+++ b/tests/libneo/python/test_eqdsk.py
@@ -13,24 +13,28 @@
 
 golden_record_path = data_path / "TESTS/libneo/eqdsk"
 
-
 @pytest.fixture
 def test_files():
     return {
         "local": code_path / "libneo/test/resources/input_efit_file.dat",
         "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
         "standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
+        "AUG": data_path / "AUG/EQDSK/g30835.3200_ed6",
+        # TODO: "MASTU": data_path / "MASTU/EQDSK/MAST_47051_450ms.geqdsk",
         # TODO: "CHEASE": data_path / "DEMO/teams/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
     }
 
 
 def test_eqdsk_read(test_files):
-    for test_file in test_files.values():
+    for key, test_file in test_files.items():
+        print(f"Testing {key} EQDSK file: {test_file}")
         _ = eqdsk.eqdsk_file(test_file)
 
 
-def test_eqdsk_golden_records(test_files):
-    for test_file in test_files.values():
+def test_eqdsk_golden_records(eqdsk_test_files):
+    store_golden_records(eqdsk_test_files.values())
+
+    for test_file in eqdsk_test_files.values():
         eqdsk_object = eqdsk.eqdsk_file(test_file)
 
         data = eqdsk_object.__dict__
@@ -51,7 +55,7 @@ def get_golden_record(file_path):
         return json.loads(json_data)
 
 
-def store_golden_records(file_paths):
+def store_golden_records(file_paths, force_overwrite=False):
     """
     Stores reference data for regression tests. Call only manually after fixing
     a bug and checking that the new results are correct.
@@ -67,7 +71,9 @@ def store_golden_records(file_paths):
         outfile = golden_record_path / f"{file_base}.json.gz"
 
         if outfile.exists():
-            raise RuntimeError(f"Golden record file {outfile} already exists.")
+            print(f"Golden record {outfile} exists.")
+            if not force_overwrite:
+                continue
 
         with gzip.open(outfile, "wb") as f:
             json_data = json.dumps(data, indent=4)

From d7198373bd04fe914e64514edfaae46df94c6789 Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 00:39:20 +0100
Subject: [PATCH 07/13] Testing EFIT to Boozer

---
 tests/libneo/python/test_efit_to_boozer.py | 80 ++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
index e69de29..97480fd 100644
--- a/tests/libneo/python/test_efit_to_boozer.py
+++ b/tests/libneo/python/test_efit_to_boozer.py
@@ -0,0 +1,80 @@
+import pytest
+
+import os
+import tempfile
+from pathlib import Path
+import numpy as np
+import matplotlib.pyplot as plt
+
+from paths import code_path, data_path
+
+import _efit_to_boozer as efit_to_boozer
+from libneo.boozer import get_angles_and_transformation
+
+efit_to_boozer_input = """3600      nstep    - number of integration steps
+500       nlabel   - grid size over radial variable 
+500       ntheta   - grid size over poloidal angle
+10000     nsurfmax - number of starting points for separarix search
+2000      nsurf    - number of flux surfaces in Boozer file
+12        mpol     - number of poloidal modes in Boozer file
+2119063900.d0 psimax - psi of plasma boundary
+"""
+
+field_divB0_input = """0                                 ipert        ! 0=eq only, 1=vac, 2,3=vac+plas
+1                                 iequil       ! 0=pert. alone, 1=with equil.
+1.00                              ampl         ! amplitude of perturbation, a.u.
+72                                ntor         ! number of toroidal harmonics
+0.99                              cutoff       ! inner cutoff in psi/psi_a units
+4                                 icftype      ! type of coil file
+'{gfile}'                         gfile        ! equilibrium file
+'unused_field.dat'                pfile        ! coil        file
+'unused_convexwall.dat'           convexfile   ! convex file for stretchcoords
+'UNUSED_FLUXDATA'                 fluxdatapath ! directory with data in flux coord.
+0                                 window size for filtering of psi array over R
+0                                 window size for filtering of psi array over Z
+"""
+
+@pytest.fixture
+def test_files():
+    return {
+        "CHEASE": data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
+        "AUG": data_path / "AUG/EQDSK/g30835.3200_ed6",
+        "MASTU": data_path / "MASTU/EQDSK/MAST_47051_450ms.geqdsk",
+        "local": code_path / "libneo/test/resources/input_efit_file.dat",
+        "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
+        "standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
+    }
+
+
+def test_angles_and_transformation(test_files):
+    stor = 0.4
+    num_theta = 64
+    for key, test_file in test_files.items():
+        print(f"Testing {key} EQDSK file: {test_file}")
+        tmp_path = init_run_path(test_file)
+        print(f"Running in {tmp_path}")
+        os.chdir(tmp_path)
+        efit_to_boozer.efit_to_boozer.init()
+        th_boozers, th_geoms, Gs = get_angles_and_transformation(stor, num_theta)
+
+        plt.figure()
+        plt.plot(th_boozers, th_geoms)
+
+
+def init_run_path(gfile):
+    tmp_path = Path(tempfile.mkdtemp())
+    write_input_files(tmp_path, gfile)
+    return tmp_path
+
+
+def write_input_files(tmp_path, gfile):
+    efit_to_boozer_input_file = tmp_path / "efit_to_boozer.inp"
+    efit_to_boozer_input_file.write_text(efit_to_boozer_input)
+
+    field_divB0_input_file = tmp_path / "field_divB0.inp"
+    field_divB0_input_file.write_text(field_divB0_input.format(gfile=gfile))
+
+
+if __name__ == "__main__":
+    pytest.main([__file__, "-s"])
+    plt.show()

From d47d7eafd15a8c606a9e422c12e7072d36dc868d Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 14:07:17 +0100
Subject: [PATCH 08/13] Fix fixtures

---
 tests/conftest.py                          | 12 ++++++++++++
 tests/libneo/python/paths.py               |  5 -----
 tests/libneo/python/test_boozer.py         |  5 ++---
 tests/libneo/python/test_efit_to_boozer.py |  4 +---
 tests/libneo/python/test_eqdsk.py          | 22 ++++++++++------------
 tests/libneo/python/test_mgrid.py          |  9 +++++----
 6 files changed, 30 insertions(+), 27 deletions(-)
 create mode 100644 tests/conftest.py
 delete mode 100644 tests/libneo/python/paths.py

diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..035d0df
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,12 @@
+import pytest
+
+import os
+from pathlib import Path
+
+@pytest.fixture
+def code_path():
+    return Path(os.environ["CODE"])
+
+@pytest.fixture
+def data_path():
+    return Path(os.environ["DATA"])
diff --git a/tests/libneo/python/paths.py b/tests/libneo/python/paths.py
deleted file mode 100644
index 183fc15..0000000
--- a/tests/libneo/python/paths.py
+++ /dev/null
@@ -1,5 +0,0 @@
-import os
-from pathlib import Path
-
-code_path = Path(os.environ["CODE"])
-data_path = Path(os.environ["DATA"])
diff --git a/tests/libneo/python/test_boozer.py b/tests/libneo/python/test_boozer.py
index 91bbb9d..4bf6bbe 100644
--- a/tests/libneo/python/test_boozer.py
+++ b/tests/libneo/python/test_boozer.py
@@ -5,19 +5,18 @@
 
 from libneo import BoozerFile
 from libneo import read_eqdsk, FluxConverter
-from paths import data_path
 
 no_edges = slice(10, -10)
 
 
 @pytest.fixture
-def boozer():
+def boozer(data_path):
     trial_boozer_file = data_path / "AUG/BOOZER/30835/out_neo-2_rmp_90-n0"
     return BoozerFile(str(trial_boozer_file))
 
 
 @pytest.fixture
-def eqdsk():
+def eqdsk(data_path):
     trial_eqdsk_file = data_path / "AUG/EQDSK/g30835.3200_ed6"
     return read_eqdsk(str(trial_eqdsk_file))
 
diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
index 97480fd..74b43bf 100644
--- a/tests/libneo/python/test_efit_to_boozer.py
+++ b/tests/libneo/python/test_efit_to_boozer.py
@@ -6,8 +6,6 @@
 import numpy as np
 import matplotlib.pyplot as plt
 
-from paths import code_path, data_path
-
 import _efit_to_boozer as efit_to_boozer
 from libneo.boozer import get_angles_and_transformation
 
@@ -35,7 +33,7 @@
 """
 
 @pytest.fixture
-def test_files():
+def test_files(code_path, data_path):
     return {
         "CHEASE": data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
         "AUG": data_path / "AUG/EQDSK/g30835.3200_ed6",
diff --git a/tests/libneo/python/test_eqdsk.py b/tests/libneo/python/test_eqdsk.py
index ef33360..fe54c25 100644
--- a/tests/libneo/python/test_eqdsk.py
+++ b/tests/libneo/python/test_eqdsk.py
@@ -8,13 +8,10 @@
 import gzip
 
 from libneo import eqdsk
-from paths import code_path, data_path
 
 
-golden_record_path = data_path / "TESTS/libneo/eqdsk"
-
 @pytest.fixture
-def test_files():
+def test_files(code_path, data_path):
     return {
         "local": code_path / "libneo/test/resources/input_efit_file.dat",
         "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
@@ -31,31 +28,32 @@ def test_eqdsk_read(test_files):
         _ = eqdsk.eqdsk_file(test_file)
 
 
-def test_eqdsk_golden_records(eqdsk_test_files):
-    store_golden_records(eqdsk_test_files.values())
+def test_eqdsk_golden_records(data_path, test_files):
+    golden_record_path = data_path / "TESTS/libneo/eqdsk"
+    store_golden_records(test_files.values(), golden_record_path)
 
-    for test_file in eqdsk_test_files.values():
+    for test_file in test_files.values():
         eqdsk_object = eqdsk.eqdsk_file(test_file)
 
         data = eqdsk_object.__dict__
         replace_array_members_by_lists(data)
 
-        assert are_dicts_equal(data, get_golden_record(test_file))
+        assert are_dicts_equal(data, get_golden_record(test_file, golden_record_path))
 
 
-def get_golden_record(file_path):
+def get_golden_record(file_path, storage_path):
     """
     Returns the golden record for the given test file.
     """
 
     file_base = file_path.stem
-    with gzip.open(golden_record_path / f"{file_base}.json.gz", "rb") as f:
+    with gzip.open(storage_path / f"{file_base}.json.gz", "rb") as f:
         compressed_data = f.read()
         json_data = compressed_data.decode("utf-8")
         return json.loads(json_data)
 
 
-def store_golden_records(file_paths, force_overwrite=False):
+def store_golden_records(file_paths, storage_path, force_overwrite=False):
     """
     Stores reference data for regression tests. Call only manually after fixing
     a bug and checking that the new results are correct.
@@ -68,7 +66,7 @@ def store_golden_records(file_paths, force_overwrite=False):
         data = eqdsk.eqdsk_file(str(f)).__dict__
         replace_array_members_by_lists(data)
 
-        outfile = golden_record_path / f"{file_base}.json.gz"
+        outfile = storage_path / f"{file_base}.json.gz"
 
         if outfile.exists():
             print(f"Golden record {outfile} exists.")
diff --git a/tests/libneo/python/test_mgrid.py b/tests/libneo/python/test_mgrid.py
index 1aaa904..6407afb 100644
--- a/tests/libneo/python/test_mgrid.py
+++ b/tests/libneo/python/test_mgrid.py
@@ -3,17 +3,18 @@
 import numpy as np
 
 from libneo.mgrid import MgridFile
-from paths import data_path
 
-testfile_path = data_path / "LHD/VMEC/makegrid_alternative/mgrid_lhd_nfp10.nc"
+@pytest.fixture
+def testfile_path(data_path):
+    return data_path / "LHD/VMEC/makegrid_alternative/mgrid_lhd_nfp10.nc"
 
 
 @pytest.fixture
-def mgrid():
+def mgrid(testfile_path):
     return MgridFile.from_file(testfile_path)
 
 
-def test_mgrid_read():
+def test_mgrid_read(testfile_path):
     f = MgridFile.from_file(testfile_path)
     print(f)
 

From 791ef97eff0b4e17286a31378c3e3e1788fe7f3a Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 14:38:59 +0100
Subject: [PATCH 09/13] Fix paths

---
 requirements.txt                              |   1 +
 .../NEO-2/python/test_get_fluxsurface_area.py |   7 +-
 .../benchmark_with_NEO_2.ipynb                |   2 +-
 tests/efit_to_boozer/python/convexwall.dat    |   5 -
 ...fit2boozer.cpython-311-x86_64-linux-gnu.so |   1 -
 .../efit_to_boozer/python/efit_to_boozer.inp  |   7 -
 tests/efit_to_boozer/python/field_divB0.inp   |  36 ----
 tests/efit_to_boozer/python/gfile             |   1 -
 .../python/test_q_profile_eqdsk.py            |  62 -------
 tests/libneo/python/test_efit_to_boozer.py    |  49 +++++
 tests/libneo/python/test_eqdsk.py             |   1 +
 .../ntv-demo/python/test_vary_vrot_omegae.py  | 174 ------------------
 tests/pytest.ini                              |   3 +
 13 files changed, 59 insertions(+), 290 deletions(-)
 delete mode 100644 tests/efit_to_boozer/python/convexwall.dat
 delete mode 120000 tests/efit_to_boozer/python/efit2boozer.cpython-311-x86_64-linux-gnu.so
 delete mode 100644 tests/efit_to_boozer/python/efit_to_boozer.inp
 delete mode 100644 tests/efit_to_boozer/python/field_divB0.inp
 delete mode 120000 tests/efit_to_boozer/python/gfile
 delete mode 100644 tests/efit_to_boozer/python/test_q_profile_eqdsk.py
 delete mode 100644 tests/ntv-demo/python/test_vary_vrot_omegae.py
 create mode 100644 tests/pytest.ini

diff --git a/requirements.txt b/requirements.txt
index 1b2c418..d00c4eb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -63,6 +63,7 @@ fortls
 # Misc
 tqdm
 pytest
+pytest-time
 mpi4py
 meson
 meson-python
diff --git a/tests/NEO-2/python/test_get_fluxsurface_area.py b/tests/NEO-2/python/test_get_fluxsurface_area.py
index eb1a191..ab2fa13 100644
--- a/tests/NEO-2/python/test_get_fluxsurface_area.py
+++ b/tests/NEO-2/python/test_get_fluxsurface_area.py
@@ -4,15 +4,16 @@
 
 
 @pytest.fixture
-def run_files():
+def run_files(data_path):
     from libneo import read_eqdsk
 
-    filename_eqdsk = "/proj/plasma/DATA/AUG/EQUILIRBRIUM/QCE_discharge_Neon_shot_39561/eqdsk_39461_5.38s"
+    filename_eqdsk = data_path / "AUG/EQUILIRBRIUM/QCE_discharge_Neon_shot_39561/eqdsk_39461_5.38s"
     eqdsk = read_eqdsk(filename_eqdsk)
     neo2_output = "/temp/grassl_g/Neon_discharge_axisymmetric_gleiter/RUN_lag8/neon_discharge.out"
     yield eqdsk, neo2_output
 
 
+@pytest.mark.xfail(reason="TODO: Update paths")
 def test_get_fluxsurface_area_visual_check(run_files):
     from neo2_ql import get_fluxsurface_area
     from libneo import plot_fluxsurfaces, FluxConverter
@@ -38,4 +39,4 @@ def test_get_fluxsurface_area_visual_check(run_files):
 
 
 if __name__ == "__main__":
-    pytest.main()
+    pytest.main([__file__, "-s"])
diff --git a/tests/NEO-RT/benchmark_with_NEO_2/benchmark_with_NEO_2.ipynb b/tests/NEO-RT/benchmark_with_NEO_2/benchmark_with_NEO_2.ipynb
index 811620d..64f93f2 100644
--- a/tests/NEO-RT/benchmark_with_NEO_2/benchmark_with_NEO_2.ipynb
+++ b/tests/NEO-RT/benchmark_with_NEO_2/benchmark_with_NEO_2.ipynb
@@ -49,7 +49,7 @@
    "source": [
     "## Load NEO-2 output\n",
     "\n",
-    "neo2_dir = '/proj/plasma/DATA/DEMO/NEO-2/rerun_DEMO_MARS_PERTURBATION_N1_NEGATIVE_new_pert/'\n",
+    "neo2_dir = os.path.expandvars('$DATA/DEMO/NEO-2/rerun_DEMO_MARS_PERTURBATION_N1_NEGATIVE_new_pert/')\n",
     "neo_input = f90nml.read(os.path.join(neo2_dir, 'neo.in'))\n",
     "neo2_input = f90nml.read(os.path.join(neo2_dir, 'neo2.in'))\n",
     "neo2_output_file = os.path.join(neo2_dir, 'neo2_multispecies_out.h5')\n",
diff --git a/tests/efit_to_boozer/python/convexwall.dat b/tests/efit_to_boozer/python/convexwall.dat
deleted file mode 100644
index b855e27..0000000
--- a/tests/efit_to_boozer/python/convexwall.dat
+++ /dev/null
@@ -1,5 +0,0 @@
-580d0   -620d0
-1220d0  -620d0
-1220d0   640d0
-580d0    640d0
-580d0   -620d0
\ No newline at end of file
diff --git a/tests/efit_to_boozer/python/efit2boozer.cpython-311-x86_64-linux-gnu.so b/tests/efit_to_boozer/python/efit2boozer.cpython-311-x86_64-linux-gnu.so
deleted file mode 120000
index b2d12b6..0000000
--- a/tests/efit_to_boozer/python/efit2boozer.cpython-311-x86_64-linux-gnu.so
+++ /dev/null
@@ -1 +0,0 @@
-../../../efit_to_boozer/python/efit2boozer.cpython-311-x86_64-linux-gnu.so
\ No newline at end of file
diff --git a/tests/efit_to_boozer/python/efit_to_boozer.inp b/tests/efit_to_boozer/python/efit_to_boozer.inp
deleted file mode 100644
index 974ed82..0000000
--- a/tests/efit_to_boozer/python/efit_to_boozer.inp
+++ /dev/null
@@ -1,7 +0,0 @@
-3600      nstep    - number of integration steps
-500       nlabel   - grid size over radial variable 
-500       ntheta   - grid size over poloidal angle
-10000     nsurfmax - number of starting points for separarix search
-2000      nsurf    - number of flux surfaces in Boozer file
-12        mpol     - number of poloidal modes in Boozer file
-2119063900.d0 psimax - psi of plasma boundary
\ No newline at end of file
diff --git a/tests/efit_to_boozer/python/field_divB0.inp b/tests/efit_to_boozer/python/field_divB0.inp
deleted file mode 100644
index 7c4a2ec..0000000
--- a/tests/efit_to_boozer/python/field_divB0.inp
+++ /dev/null
@@ -1,36 +0,0 @@
-0                                 ipert        ! 0=eq only, 1=vac, 2,3=vac+plas
-1                                 iequil       ! 0=pert. alone, 1=with equil.
-1.00                              ampl         ! amplitude of perturbation, a.u.
-72                                ntor         ! number of toroidal harmonics
-0.99                              cutoff       ! inner cutoff in psi/psi_a units
-4                                 icftype      ! type of coil file
-'gfile'          gfile        ! equilibrium file
-''  !'DATA/ASDEX/MESH3D_30835/field.dat'    pfile        ! coil        file
-'convexwall.dat'            convexfile   ! convex file for stretchcoords
-''                  fluxdatapath ! directory with data in flux coord.
-0                                 window size for filtering of psi array over R
-0                                 window size for filtering of psi array over Z
-
-
-
-
-
-More detailed comments on switches.
-Axisymmetric equilibrium is called in all cases. If some routines are not 
-called, their data is not required.
-
-Perturbation switch "ipert": 
-0 - axisymmetric equilibrium is called alone (can be run withot coild data
-    and resonance plasma response data)
-1 - cylindrical routine is called in addition to equilibrium (plasma response
-    data is not required
-2 - both, cylindrical and flux coordinate routine modelling plasma response
-    are called, all data is required. Derivatives are not computed
-3 - the same as 2 with computation of derivatives (7 times slower)
-
-Equilibrium switch "iequil":
-0 - equilibrium field is not added to the output (needed for computing the 
-    perturbation field alone). The equilibrium routine is called - its
-    data is needed for plasma response field. For future: this call can be
-    disabled for stellarator modelling.
-1 - normal mode, perturbation is added to the output field
\ No newline at end of file
diff --git a/tests/efit_to_boozer/python/gfile b/tests/efit_to_boozer/python/gfile
deleted file mode 120000
index 44bb0a1..0000000
--- a/tests/efit_to_boozer/python/gfile
+++ /dev/null
@@ -1 +0,0 @@
-/proj/plasma/DATA/DEMO/teams/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT
\ No newline at end of file
diff --git a/tests/efit_to_boozer/python/test_q_profile_eqdsk.py b/tests/efit_to_boozer/python/test_q_profile_eqdsk.py
deleted file mode 100644
index 8dc15dc..0000000
--- a/tests/efit_to_boozer/python/test_q_profile_eqdsk.py
+++ /dev/null
@@ -1,62 +0,0 @@
-"""
-Tests for efit_2_boozer and eqdsk_base
-"""
-
-import pytest
-
-# Import standard modules
-import numpy as np
-import os
-
-# Import modules to be tested
-import efit2boozer
-
-from numpy.testing import assert_allclose
-from libneo import read_eqdsk, FluxLabelConverter
-
-
-def test_q_profile_eqdsk():
-
-    # Read data from EQDSK file
-    basedir_eqdsk = "/proj/plasma/DATA/DEMO/teams/Equilibrium_DEMO2019_CHEASE"
-    eqfile_eqdsk = "MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT"
-
-    eqdsk_data = read_eqdsk(os.path.join(basedir_eqdsk, eqfile_eqdsk))
-
-    # The data in EQDSK is writting in poloidal flux label,
-    # but efit2boozer uses toroidal flux label. Therefore, we need a mapping
-    q_profile_eqdsk = eqdsk_data["qprof"]
-    spol_eqdsk = np.linspace(0.0, 1.0, q_profile_eqdsk.shape[0])
-    converter = FluxLabelConverter(q_profile_eqdsk)
-    stor_eqdsk = converter.spol2stor(spol_eqdsk)
-
-    # The safety factor can be calculated alternatively using field line integration
-    # this is done as part of the symmetry flux transformation and given as output here
-
-    q_profile_field_line_integration = []
-
-    # inp_label = 1 makes it that efit2boozer.magdata_in_symfluxcoord_ext uses the
-    # flux label si instead of the actual flux psi to determine which
-    # flux surface one is on. Therefore psi is just set as a dummy variable here.
-    inp_label = 1
-    psi = np.array(0.0)
-    theta = np.array(0.0)
-
-    # current_directory = os.path.dirname(os.path.realpath(__file__))
-    current_directory = os.getcwd()
-    test_directory = os.path.join(current_directory, "tests/efit_to_boozer/python")
-    os.chdir(test_directory)
-
-    efit2boozer.efit_to_boozer.init()
-    for si in stor_eqdsk:
-        (q, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _) = (
-            efit2boozer.magdata_in_symfluxcoord_ext(inp_label, si, psi, theta)
-        )
-        q_profile_field_line_integration.append(q)
-
-    q_profile_field_line_integration = np.array(q_profile_field_line_integration)
-
-    os.chdir(current_directory)
-
-    assert_allclose(q_profile_field_line_integration, q_profile_eqdsk, rtol=1e-2)
-    print("Alternative safety factor calculation agrees with EQDSK file within 1%")
diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
index 74b43bf..fdc7cd9 100644
--- a/tests/libneo/python/test_efit_to_boozer.py
+++ b/tests/libneo/python/test_efit_to_boozer.py
@@ -4,10 +4,12 @@
 import tempfile
 from pathlib import Path
 import numpy as np
+from numpy.testing import assert_allclose
 import matplotlib.pyplot as plt
 
 import _efit_to_boozer as efit_to_boozer
 from libneo.boozer import get_angles_and_transformation
+from libneo import read_eqdsk, FluxConverter
 
 efit_to_boozer_input = """3600      nstep    - number of integration steps
 500       nlabel   - grid size over radial variable 
@@ -44,6 +46,7 @@ def test_files(code_path, data_path):
     }
 
 
+@pytest.mark.slow
 def test_angles_and_transformation(test_files):
     stor = 0.4
     num_theta = 64
@@ -59,6 +62,52 @@ def test_angles_and_transformation(test_files):
         plt.plot(th_boozers, th_geoms)
 
 
+@pytest.mark.slow
+def test_q_profile_eqdsk(data_path):
+
+    # Read data from EQDSK file
+    basedir_eqdsk = data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE"
+    eqfile_path = basedir_eqdsk / "MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT"
+
+    eqdsk_data = read_eqdsk(str(eqfile_path))
+
+    # The data in EQDSK is writting in poloidal flux label,
+    # but efit_to_boozer uses toroidal flux label. Therefore, we need a mapping
+    q_profile_eqdsk = eqdsk_data["qprof"]
+    spol_eqdsk = np.linspace(0.0, 1.0, q_profile_eqdsk.shape[0])
+    converter = FluxConverter(q_profile_eqdsk)
+    stor_eqdsk = converter.spol2stor(spol_eqdsk)
+
+    # The safety factor can be calculated alternatively using field line integration
+    # this is done as part of the symmetry flux transformation and given as output here
+
+    q_profile_field_line_integration = []
+
+    # inp_label = 1 makes it that efit_to_boozer.magdata_in_symfluxcoord_ext uses the
+    # flux label si instead of the actual flux psi to determine which
+    # flux surface one is on. Therefore psi is just set as a dummy variable here.
+    inp_label = 1
+    psi = np.array(0.0)
+    theta = np.array(0.0)
+
+    print(f"Testing EQDSK file: {eqfile_path}")
+    tmp_path = init_run_path(eqfile_path)
+    print(f"Running in {tmp_path}")
+    os.chdir(tmp_path)
+
+    efit_to_boozer.efit_to_boozer.init()
+    for si in stor_eqdsk:
+        (q, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _) = (
+            efit_to_boozer.magdata_in_symfluxcoord_ext(inp_label, si, psi, theta)
+        )
+        q_profile_field_line_integration.append(q)
+
+    q_profile_field_line_integration = np.array(q_profile_field_line_integration)
+
+    assert_allclose(q_profile_field_line_integration, q_profile_eqdsk, rtol=1e-2)
+    print("Alternative safety factor calculation agrees with EQDSK file within 1%")
+
+
 def init_run_path(gfile):
     tmp_path = Path(tempfile.mkdtemp())
     write_input_files(tmp_path, gfile)
diff --git a/tests/libneo/python/test_eqdsk.py b/tests/libneo/python/test_eqdsk.py
index fe54c25..8272d83 100644
--- a/tests/libneo/python/test_eqdsk.py
+++ b/tests/libneo/python/test_eqdsk.py
@@ -28,6 +28,7 @@ def test_eqdsk_read(test_files):
         _ = eqdsk.eqdsk_file(test_file)
 
 
+@pytest.mark.slow
 def test_eqdsk_golden_records(data_path, test_files):
     golden_record_path = data_path / "TESTS/libneo/eqdsk"
     store_golden_records(test_files.values(), golden_record_path)
diff --git a/tests/ntv-demo/python/test_vary_vrot_omegae.py b/tests/ntv-demo/python/test_vary_vrot_omegae.py
deleted file mode 100644
index 65d9a79..0000000
--- a/tests/ntv-demo/python/test_vary_vrot_omegae.py
+++ /dev/null
@@ -1,174 +0,0 @@
-# %% Standard imports
-import matplotlib.pyplot as plt
-import os
-import numpy as np
-
-# Custom imports
-from neo2_mars import generate_vrot_for_mars
-from neo2_mars import generate_omega_e_for_mars
-from neo2_mars import generate_nu_for_mars
-
-# Import to test
-from ntv_demo_parameter_study import read_profiles
-from ntv_demo_parameter_study import calculate_omegae, read_omegae_and_vrot
-from ntv_demo_parameter_study import get_omegae_linear_coefs
-
-base_dir = "/proj/plasma/DATA/DEMO/MARS/BASE_INPUT_PROFILES"
-negative_vrot_case = "/proj/plasma/DATA/DEMO/MARS/PROFWE/negative_vrot_case"
-positive_vrot_case = "/proj/plasma/DATA/DEMO/MARS/PROFWE/positive_vrot_case"
-
-def test_get_omegae_linear_coefs_visual_check():
-    fontsize = 24
-    profiles = read_profiles(base_dir)
-    vrot = profiles["vrot"][1:,1]
-    sqrtspol = profiles["vrot"][1:,0]
-    offset, slope = get_omegae_linear_coefs(negative_vrot_case, positive_vrot_case)
-    omegae_calculated = offset + slope * vrot
-    fig, ax_left = plt.subplots(1, 1, figsize=(10, 8))
-    ax_left.plot(sqrtspol, offset, '--k', label=r'offset $\delta$')
-    ax_left.plot([],[], '--r', label=r'slope $\kappa$')
-    ax_left.set_ylabel(r'$\delta$ [rad/s]', color='k', fontsize=fontsize)
-    ax_left.tick_params(axis='y', labelcolor='k', color='k', labelsize=fontsize)
-    ax_left.tick_params(axis='x', labelsize=fontsize)
-
-    ax_right = ax_left.twinx()
-    ax_right.plot(sqrtspol, slope, '--r')
-    ax_right.set_ylabel(r'$\kappa$ [1]', color='r', fontsize=fontsize)
-    ax_right.tick_params(axis='y', labelcolor='r', color='r', labelsize=fontsize)
-    ax_right.spines['right'].set_color('r')
-
-    ax_left.set_xlabel(r'$\rho_\mathrm{pol}$ [1]', fontsize=fontsize)
-    ax_left.set_ylim([-4e3, 1e4])
-    plt.show()
-
-def test_calculate_omegae_visual_check():
-    profiles = read_profiles(base_dir)
-    vrot = profiles["vrot"][1:,1]
-    sqrtspol = profiles["vrot"][1:,0]
-    omegae = calculate_omegae(vrot/2)
-    half_vrot_case = "/proj/plasma/DATA/DEMO/MARS/PROFWE/half_positive_vrot_case"
-    omegae_negative_vrot, _ = read_omegae_and_vrot(negative_vrot_case)
-    omegae_positive_vrot, _ = read_omegae_and_vrot(positive_vrot_case)
-    omegae_half_vrot, _ = read_omegae_and_vrot(half_vrot_case)
-    fig, ax = plt.subplots(1, 1, figsize=(10, 8))
-    ax.plot(sqrtspol, omegae_negative_vrot, '-b', label='negative vrot')
-    ax.plot(sqrtspol, omegae_positive_vrot, '-r', label='positive vrot')
-    ax.plot(sqrtspol, omegae, '--g', label='calculated')
-    ax.plot(sqrtspol, omegae_half_vrot, '.k', label='control')
-    ax.set_ylabel(r'$\omega_{e}$ [rad/s]')
-    ax.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax.set_ylim([-1.2e4, 1e4])
-    ax.set_xlim([0.01, 1])
-    plt.legend()
-    plt.show()
-
-def test_profit_runs_visual_check():
-    study = "/proj/plasma/DATA/DEMO/teams/parameter_study_profiles_MARS/vary_vrot_omegae_and_coilwidth/"
-    base_run = "/proj/plasma/DATA/DEMO/MARS/BASE_INPUT_PROFILES"
-    runs_color = (0.8, 0.8, 0.8)
-    base_color = (0.6, 0.2, 0.2)
-    fig, ax = plt.subplots(4, 2, figsize=(10, 8))
-    ax_Te = ax[0, 0]
-    ax_Ti = ax[0, 1]
-    ax_n = ax[1, 0]
-    ax_nue = ax[2, 0]
-    ax_nui = ax[2, 1]
-    ax_vrot = ax[3, 0]
-    ax_omegae = ax[3, 1]
-    number_of_ploted_runs = 0
-    max_number_of_runs = 20
-    for folder in os.listdir(study):
-        if number_of_ploted_runs >= max_number_of_runs:
-            break
-        if folder.startswith('run_'):
-            number_of_ploted_runs += 1
-            profiles = read_profiles(os.path.join(study, folder))
-            
-            ax_Te.plot(profiles["Te"][1:,0], profiles["Te"][1:,1]/1000, color=runs_color)
-            ax_Te.set_ylabel(r'$T_\mathrm{e}$ [keV]')
-            ax_Te.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_Te.set_xlim([0.01, 1])
-            
-            ax_Ti.plot(profiles["Ti"][1:,0], profiles["Ti"][1:,1]/1000, color=runs_color)
-            ax_Ti.set_ylabel(r'$T_\mathrm{i}$ [keV]')
-            ax_Ti.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_Ti.set_xlim([0.01, 1])
-            
-            ax_n.plot(profiles["n"][1:,0], profiles["n"][1:,1], color=runs_color)
-            ax_n.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_n.set_ylabel(r'$n$ [$\mathrm{m}^{-3}$]')
-            ax_n.set_xlim([0.01, 1])
-
-            ax_nue.plot(profiles["nue"][1:,0], profiles["nue"][1:,1], color=runs_color)
-            ax_nue.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_nue.set_ylabel(r'$\nu_{e}$ [s$^{-1}$]')
-            ax_nue.set_yscale('log')
-            ax_nue.set_xlim([0.01, 1])
-
-            ax_nui.plot(profiles["nui"][1:,0], profiles["nui"][1:,1], color=runs_color)
-            ax_nui.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_nui.set_ylabel(r'$\nu_{i}$ [s$^{-1}$]')
-            ax_nui.set_yscale('log')
-            ax_nui.set_xlim([0.01, 1])
-
-            ax_vrot.plot(profiles["vrot"][1:,0], profiles["vrot"][1:,1], color=runs_color)
-            ax_vrot.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_vrot.set_ylabel(r'$V^\varphi$ [rad/s]')
-            ax_vrot.set_ylim([-3e3, 1.6e4])
-            ax_vrot.set_xlim([0.01, 1])
-
-            ax_omegae.plot(profiles["omegae"][1:,0], profiles["omegae"][1:,1], color=runs_color)
-            ax_omegae.set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-            ax_omegae.set_ylabel(r'$\Omega_{e}$ [rad/s]')
-            ax_omegae.set_ylim([-3e3, 1.6e4])
-            ax_omegae.set_xlim([0.01, 1])
-
-    profiles = read_profiles(base_dir)
-    ax_Te.plot(profiles["Te"][1:,0], profiles["Te"][1:,1]/1000, color=base_color, label='base run')
-    ax_Ti.plot(profiles["Ti"][1:,0], profiles["Ti"][1:,1]/1000, color=base_color, label='base run')
-    ax_n.plot(profiles["n"][1:,0], profiles["n"][1:,1], color=base_color, label='base run')
-    ax_nue.plot(profiles["nue"][1:,0], profiles["nue"][1:,1], color=base_color, label='base run')
-    ax_nui.plot(profiles["nui"][1:,0], profiles["nui"][1:,1], color=base_color, label='base run')
-    ax_vrot.plot(profiles["vrot"][1:,0], profiles["vrot"][1:,1], color=base_color, label='base run')
-    ax_omegae.plot(profiles["omegae"][1:,0], profiles["omegae"][1:,1], color=base_color, label='base run')
-    ax_Te.legend()
-    ax_Ti.legend()
-    ax_n.legend()
-    ax_nue.legend()
-    ax_nui.legend()
-    ax_vrot.legend()
-    ax_omegae.legend()
-    fig.suptitle('run profiles', fontsize=16)
-    plt.tight_layout()
-    plt.show()
-
-def test_read_profiles_visual_check():
-    profiles = read_profiles(base_dir)
-    fig, ax = plt.subplots(3, 2, figsize=(10, 8 ))
-    ax[0, 0].plot(profiles["Te"][1:,0], profiles["Te"][1:,1]/1000)
-    ax[0, 0].set_ylabel(r'$T_\mathrm{e}$ [keV]')
-    ax[0, 0].set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax[0, 1].plot(profiles["Ti"][1:,0], profiles["Ti"][1:,1]/1000)
-    ax[0, 1].set_ylabel(r'$T_\mathrm{i}$ [keV]')
-    ax[0, 1].set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax[1, 0].plot(profiles["n"][1:,0], profiles["n"][1:,1])
-    ax[1, 0].set_ylabel(r'$n$ [$\mathrm{m}^{-3}$]')
-    ax[1, 0].set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax[1, 1].plot(profiles["vrot"][1:,0], profiles["vrot"][1:,1])
-    ax[1, 1].set_ylabel(r'$v_\mathrm{rot}$ [rad/s]')
-    ax[1, 1].set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax[2, 0].plot(profiles["nue"][1:,0], profiles["nue"][1:,1])
-    ax[2, 0].set_ylabel(r'$\nu_{e}$ [s$^{-1}$]')
-    ax[2, 0].set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax[2, 0].set_yscale('log')
-    ax[2, 1].plot(profiles["nui"][1:,0], profiles["nui"][1:,1])
-    ax[2, 1].set_ylabel(r'$\nu_{i}$ [s$^{-1}$]')
-    ax[2, 1].set_xlabel(r'$\rho_\mathrm{pol}$ [1]')
-    ax[2, 1].set_yscale('log')
-    plt.show()
-
-if __name__ == "__main__":
-    test_calculate_omegae_visual_check()    
-    test_profit_runs_visual_check()
-    test_get_omegae_linear_coefs_visual_check()
-    test_read_profiles_visual_check()
\ No newline at end of file
diff --git a/tests/pytest.ini b/tests/pytest.ini
new file mode 100644
index 0000000..7617853
--- /dev/null
+++ b/tests/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')

From 619bdbb5bd7dc680e4de5f2c454f15d54e2f6b0e Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 15:51:24 +0100
Subject: [PATCH 10/13] Trim trailing whitespaces

---
 .vscode/settings.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 4245d76..645a1f9 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -41,5 +41,6 @@
     "github.codespaces.devcontainerChangedNotificationStyle": "none",
     "mesonbuild.selectRootDir": false,
     "testing.automaticallyOpenTestResults": "neverOpen",
-    "files.insertFinalNewline": true
+    "files.insertFinalNewline": true,
+    "files.trimTrailingWhitespace": true
 }

From cbeef6c96dc9dbe384d85035d5e8e173273280ef Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 16:50:49 +0100
Subject: [PATCH 11/13] Testing efit_to_boozer

---
 tests/libneo/python/test_efit_to_boozer.py | 76 +++++++++++-----------
 1 file changed, 37 insertions(+), 39 deletions(-)

diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
index fdc7cd9..287e262 100644
--- a/tests/libneo/python/test_efit_to_boozer.py
+++ b/tests/libneo/python/test_efit_to_boozer.py
@@ -12,7 +12,7 @@
 from libneo import read_eqdsk, FluxConverter
 
 efit_to_boozer_input = """3600      nstep    - number of integration steps
-500       nlabel   - grid size over radial variable 
+500       nlabel   - grid size over radial variable
 500       ntheta   - grid size over poloidal angle
 10000     nsurfmax - number of starting points for separarix search
 2000      nsurf    - number of flux surfaces in Boozer file
@@ -37,12 +37,12 @@
 @pytest.fixture
 def test_files(code_path, data_path):
     return {
+        "local": code_path / "libneo/test/resources/input_efit_file.dat",
         "CHEASE": data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
         "AUG": data_path / "AUG/EQDSK/g30835.3200_ed6",
         "MASTU": data_path / "MASTU/EQDSK/MAST_47051_450ms.geqdsk",
-        "local": code_path / "libneo/test/resources/input_efit_file.dat",
-        "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
-        "standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
+        # TODO: "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
+        # TODO: "standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
     }
 
 
@@ -63,49 +63,47 @@ def test_angles_and_transformation(test_files):
 
 
 @pytest.mark.slow
-def test_q_profile_eqdsk(data_path):
-
-    # Read data from EQDSK file
-    basedir_eqdsk = data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE"
-    eqfile_path = basedir_eqdsk / "MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT"
+def test_q_profile_eqdsk(test_files):
 
-    eqdsk_data = read_eqdsk(str(eqfile_path))
-
-    # The data in EQDSK is writting in poloidal flux label,
-    # but efit_to_boozer uses toroidal flux label. Therefore, we need a mapping
-    q_profile_eqdsk = eqdsk_data["qprof"]
-    spol_eqdsk = np.linspace(0.0, 1.0, q_profile_eqdsk.shape[0])
-    converter = FluxConverter(q_profile_eqdsk)
-    stor_eqdsk = converter.spol2stor(spol_eqdsk)
+    for key in ["CHEASE"]:
+        # TODO: local, AUG, MASTU, PROCESS, standardized
+        test_file = test_files[key]
+        print(f"Testing {key} EQDSK file: {test_file}")
+        tmp_path = init_run_path(test_file)
+        print(f"Running in {tmp_path}")
+        os.chdir(tmp_path)
+        eqdsk_data = read_eqdsk(str(test_file))
 
-    # The safety factor can be calculated alternatively using field line integration
-    # this is done as part of the symmetry flux transformation and given as output here
+        # The data in EQDSK is writting in poloidal flux label,
+        # but efit_to_boozer uses toroidal flux label. Therefore, we need a mapping
+        q_profile_eqdsk = eqdsk_data["qprof"]
+        spol_eqdsk = np.linspace(0.0, 1.0, q_profile_eqdsk.shape[0])
+        converter = FluxConverter(q_profile_eqdsk)
+        stor_eqdsk = converter.spol2stor(spol_eqdsk)
 
-    q_profile_field_line_integration = []
+        # The safety factor can be calculated alternatively using field line integration
+        # this is done as part of the symmetry flux transformation and given as output here
 
-    # inp_label = 1 makes it that efit_to_boozer.magdata_in_symfluxcoord_ext uses the
-    # flux label si instead of the actual flux psi to determine which
-    # flux surface one is on. Therefore psi is just set as a dummy variable here.
-    inp_label = 1
-    psi = np.array(0.0)
-    theta = np.array(0.0)
+        q_profile_field_line_integration = []
 
-    print(f"Testing EQDSK file: {eqfile_path}")
-    tmp_path = init_run_path(eqfile_path)
-    print(f"Running in {tmp_path}")
-    os.chdir(tmp_path)
+        # inp_label = 1 makes it that efit_to_boozer.magdata_in_symfluxcoord_ext uses the
+        # flux label si instead of the actual flux psi to determine which
+        # flux surface one is on. Therefore psi is just set as a dummy variable here.
+        inp_label = 1
+        psi = np.array(0.0)
+        theta = np.array(0.0)
 
-    efit_to_boozer.efit_to_boozer.init()
-    for si in stor_eqdsk:
-        (q, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _) = (
-            efit_to_boozer.magdata_in_symfluxcoord_ext(inp_label, si, psi, theta)
-        )
-        q_profile_field_line_integration.append(q)
+        efit_to_boozer.efit_to_boozer.init()
+        for si in stor_eqdsk:
+            (q, _, _, _, _, _, _, _, _, _, _, _, _, _, _, _) = (
+                efit_to_boozer.magdata_in_symfluxcoord_ext(inp_label, si, psi, theta)
+            )
+            q_profile_field_line_integration.append(q)
 
-    q_profile_field_line_integration = np.array(q_profile_field_line_integration)
+        q_profile_field_line_integration = np.array(q_profile_field_line_integration)
 
-    assert_allclose(q_profile_field_line_integration, q_profile_eqdsk, rtol=1e-2)
-    print("Alternative safety factor calculation agrees with EQDSK file within 1%")
+        assert_allclose(q_profile_field_line_integration, q_profile_eqdsk, rtol=1e-2)
+        print("Alternative safety factor calculation agrees with EQDSK file within 1%")
 
 
 def init_run_path(gfile):

From 782face2657c7c01e9f2466872444b837e043a76 Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 16:55:43 +0100
Subject: [PATCH 12/13] Failing test with MASTU

---
 tests/libneo/python/test_efit_to_boozer.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
index 287e262..cc8326b 100644
--- a/tests/libneo/python/test_efit_to_boozer.py
+++ b/tests/libneo/python/test_efit_to_boozer.py
@@ -65,7 +65,7 @@ def test_angles_and_transformation(test_files):
 @pytest.mark.slow
 def test_q_profile_eqdsk(test_files):
 
-    for key in ["CHEASE"]:
+    for key in ["CHEASE", "MASTU"]:
         # TODO: local, AUG, MASTU, PROCESS, standardized
         test_file = test_files[key]
         print(f"Testing {key} EQDSK file: {test_file}")
@@ -102,6 +102,11 @@ def test_q_profile_eqdsk(test_files):
 
         q_profile_field_line_integration = np.array(q_profile_field_line_integration)
 
+        plt.figure()
+        plt.plot(spol_eqdsk, q_profile_eqdsk, "-r", label=r"q profile from EQDSK")
+        plt.plot(spol_eqdsk, q_profile_field_line_integration, "--b", label=r"q profile from field line integration")
+        plt.legend()
+
         assert_allclose(q_profile_field_line_integration, q_profile_eqdsk, rtol=1e-2)
         print("Alternative safety factor calculation agrees with EQDSK file within 1%")
 
@@ -121,5 +126,7 @@ def write_input_files(tmp_path, gfile):
 
 
 if __name__ == "__main__":
-    pytest.main([__file__, "-s"])
-    plt.show()
+    try:
+        pytest.main([__file__, "-s"])
+    finally:
+        plt.show()

From 304f05ea68ef45573d4259e57a5d4e2842f2d4b2 Mon Sep 17 00:00:00 2001
From: Christopher Albert <albert@tugraz.at>
Date: Sat, 14 Dec 2024 17:18:10 +0100
Subject: [PATCH 13/13] Beautify plots

---
 tests/libneo/python/test_efit_to_boozer.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/tests/libneo/python/test_efit_to_boozer.py b/tests/libneo/python/test_efit_to_boozer.py
index cc8326b..96bde3f 100644
--- a/tests/libneo/python/test_efit_to_boozer.py
+++ b/tests/libneo/python/test_efit_to_boozer.py
@@ -38,11 +38,11 @@
 def test_files(code_path, data_path):
     return {
         "local": code_path / "libneo/test/resources/input_efit_file.dat",
-        "CHEASE": data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
+        "DEMO CHEASE": data_path / "DEMO/EQDSK/Equilibrium_DEMO2019_CHEASE/MOD_Qprof_Test/EQDSK_DEMO2019_q1_COCOS_02.OUT",
         "AUG": data_path / "AUG/EQDSK/g30835.3200_ed6",
         "MASTU": data_path / "MASTU/EQDSK/MAST_47051_450ms.geqdsk",
-        # TODO: "PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
-        # TODO: "standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
+        # TODO: "DEMO PROCESS": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF.eqdsk",
+        # TODO: "DEMO standardized": data_path / "DEMO/EQDSK/Equil_2021_PMI_QH_mode_betap_1d04_li_1d02_Ip_18d27MA_SOF_std.eqdsk",
     }
 
 
@@ -60,12 +60,14 @@ def test_angles_and_transformation(test_files):
 
         plt.figure()
         plt.plot(th_boozers, th_geoms)
+        plt.xlabel(r"$\theta_{\mathrm{Boozer}}$")
+        plt.ylabel(r"$\theta_{\mathrm{geom}}$")
+        plt.title(f"{key}")
 
 
 @pytest.mark.slow
 def test_q_profile_eqdsk(test_files):
-
-    for key in ["CHEASE", "MASTU"]:
+    for key in ["DEMO CHEASE", "MASTU"]:
         # TODO: local, AUG, MASTU, PROCESS, standardized
         test_file = test_files[key]
         print(f"Testing {key} EQDSK file: {test_file}")
@@ -105,6 +107,7 @@ def test_q_profile_eqdsk(test_files):
         plt.figure()
         plt.plot(spol_eqdsk, q_profile_eqdsk, "-r", label=r"q profile from EQDSK")
         plt.plot(spol_eqdsk, q_profile_field_line_integration, "--b", label=r"q profile from field line integration")
+        plt.title(f"{key}")
         plt.legend()
 
         assert_allclose(q_profile_field_line_integration, q_profile_eqdsk, rtol=1e-2)