Replace flake8 and autopep8 with ruff

.github/workflows/linting.yml

@@ -19,13 +19,6 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install python dependencies
-      run: |
-        pip install flake8
+    - name: Run ruff
+      uses: chartboost/ruff-action@v1
 
-    - name: Run linting tests
-      run: |
-        export EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
-        flake8  --ignore $EXCLUDE src/
-        flake8  --ignore $EXCLUDE tests/
-        flake8  --ignore $EXCLUDE examples/

pyproject.toml

@@ -3,3 +3,13 @@ requires = ["setuptools>=45", "wheel", "oldest-supported-numpy", "cmake", "ninja
 build-backend = "setuptools.build_meta"
 
 [tools.setuptools_scm]
+
+[tool.ruff]
+src = ["src/simsopt"] 
+ignore = ["E226","E265","E266","E4","E501","E701","E702","E712","E722","E731","E741","F403","F405","F406","W5"]
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402","F401"]
+"tests/verify_MPI_not_initialized.py" = ["F401"]
+"tests/geo/test_plot.py" = ["F401"]
+"tests/geo/test_curve.py" = ["F401"]
+

run_autopep

@@ -2,7 +2,8 @@
 # https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
 set -ex
 
-EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
+# EXCLUDE="E226,E265,E266,E4,E5,E7,W,F"
+EXCLUDE="E226,E265,E266,E4,E501,E722,F403,F405,F406,W5"
 flake8  --ignore $EXCLUDE src/ || (exit 0)
 flake8  --ignore $EXCLUDE tests/ || (exit 0)
 flake8  --ignore $EXCLUDE examples/ || (exit 0)

run_ruff

@@ -0,0 +1,7 @@
+#!/bin/bash
+# https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
+set -ex
+
+ruff check . || (exit 0)
+ruff check --fix .
+ruff check .

tests/geo/test_curve.py

@@ -19,9 +19,8 @@
 
 try:
     import pyevtk
-    pyevtk_found = True
 except ImportError:
-    pyevtk_found = False
+    pyevtk = None
 
 logger = logging.getLogger(__name__)
 #logging.basicConfig(level=logging.INFO)
@@ -386,7 +385,7 @@ def test_curve_dkappa_by_dphi_derivative(self):
                 with self.subTest(curvetype=curvetype, rotated=rotated):
                     self.subtest_curve_dkappa_by_dphi_derivative(curvetype, rotated)
 
-    @unittest.skipIf(not pyevtk_found, "pyevtk not found")
+    @unittest.skipIf(pyevtk is None, "pyevtk not found")
     def test_curve_to_vtk(self):
         curve0 = get_curve(self.curvetypes[0], False)
         curve1 = get_curve(self.curvetypes[1], True)

tests/mhd/test_spec.py

@@ -8,16 +8,14 @@
 from monty.tempfile import ScratchDir
 
 try:
-    import spec
-    spec_found = True
+    import spec as spec_mod
 except ImportError:
-    spec_found = False
+    spec_mod = None
 
 try:
     import pyoculus
-    pyoculus_found = True
 except ImportError:
-    pyoculus_found = False
+    pyoculus = None
 
 try:
     from mpi4py import MPI
@@ -29,7 +27,7 @@
 from simsopt.objectives import LeastSquaresProblem
 from simsopt.solve import least_squares_serial_solve
 
-if (MPI is not None) and spec_found:
+if (MPI is not None) and (spec_mod is not None):
     from simsopt.mhd import Spec, Residue
 
 from . import TEST_DIR
@@ -38,7 +36,7 @@
 # logging.basicConfig(level=logging.DEBUG)
 
 
-@unittest.skipIf(not spec_found, "SPEC python module not found")
+@unittest.skipIf(spec_mod is None, "SPEC python module not found")
 class SpecTests(unittest.TestCase):
     def test_init_defaults(self):
         """
@@ -439,7 +437,7 @@ def test_integrated_stellopt_scenarios_2dof(self):
             self.assertAlmostEqual(equil.iota(), -0.4114567, places=3)
             self.assertAlmostEqual(prob.objective(), 7.912501330E-04, places=3)
 
-    @unittest.skipIf((not spec_found) or (not pyoculus_found),
+    @unittest.skipIf((spec_mod is None) or (pyoculus is None),
                      "SPEC python module or pyoculus not found")
     def test_residue(self):
         """

tests/mhd/test_vmec.py

@@ -11,10 +11,9 @@
     MPI = None
 
 try:
-    import vmec
-    vmec_found = True
+    import vmec as vmec_mod
 except ImportError:
-    vmec_found = False
+    vmec_mod = None
 
 from simsopt._core.optimizable import make_optimizable
 from simsopt.objectives.least_squares import LeastSquaresProblem
@@ -159,7 +158,7 @@ def test_error_on_rerun(self):
             iota2 = vmec.mean_iota()
 
 
-@unittest.skipIf((MPI is not None) and (vmec_found), "Interface to MPI and VMEC found")
+@unittest.skipIf((MPI is not None) and (vmec_mod is not None), "Interface to MPI and VMEC found")
 class VmecTestsWithoutMPIorvmec(unittest.TestCase):
     def test_runnable_raises(self):
         """
@@ -171,7 +170,7 @@ def test_runnable_raises(self):
             v = Vmec()
 
 
-@unittest.skipIf((MPI is None) or (not vmec_found), "Valid Python interface to VMEC not found")
+@unittest.skipIf((MPI is None) or (vmec_mod is None), "Valid Python interface to VMEC not found")
 class VmecTests(unittest.TestCase):
     def test_init_defaults(self):
         """