MNT: upgrade ruff pre-commit hook, move its configuration out of pre-commit-config.yaml and fix lints

.pre-commit-config.yaml

@@ -23,21 +23,10 @@ repos:
 
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.15.8
     hooks:
-      - id: ruff
-        args:
-        - --quiet
-        - --fix
-        - --select
-        - F # pyflakes
-        - B # flake8-bugbear
-        - I # isort
-        - NPY # numpy-specific rules
-        - --ignore
-        - F405
-        - --ignore
-        - F403 # ignore import *
+      - id: ruff-check
+        args: [--quiet, --fix, --show-fixes]
 
   - repo: https://github.com/neutrinoceros/inifix
     rev: v6.1.2

doc/source/plot_idefix_bench.py

@@ -1,6 +1,8 @@
-import matplotlib.pyplot as plt
 import json
 
+import matplotlib.pyplot as plt
+
+
 def do_plot(title, bench_file, gpumodels):
     with open(bench_file, 'r') as f:
         benches = json.load(f)

pytools/dump_io.py

@@ -59,7 +59,7 @@ def __init__(self, fh, byteorder="little"):
         self.ndims = int.from_bytes(fh.read(INT_SIZE), byteorder)
         dims = []
         ntot = 1
-        for dim in range(self.ndims):
+        for _ in range(self.ndims):
             dims.append(int.from_bytes(fh.read(INT_SIZE), byteorder))
             ntot = ntot * dims[-1]
         raw = struct.unpack(str(ntot) + stringchar, fh.read(mysize * ntot))

pytools/idfx_io.py

@@ -2,7 +2,6 @@
 
 import numpy as np
 
-
 __all__ = ["readIdfxFile"]
 # Read .idfx files which are created
 # for debug purposes by DataBlock.DumpToFile(std::string&)
@@ -27,7 +26,7 @@ def __init__(self, fh, byteorder="little"):
             return
         self.ndims = int.from_bytes(fh.read(INT_SIZE), byteorder)
         dims = []
-        for dim in range(self.ndims):
+        for _ in range(self.ndims):
             dims.append(int.from_bytes(fh.read(INT_SIZE), byteorder))
         ntot = int(np.prod(dims))
         raw = struct.unpack(str(ntot) + "d", fh.read(DOUBLE_SIZE * ntot))

pytools/idfx_test.py

@@ -1,15 +1,16 @@
 import argparse
 import os
+import re
 import shutil
 import subprocess
 import sys
-import re
 
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
 
 from .dump_io import readDump
 
+
 class bcolors:
     HEADER = '\033[95m'
     OKBLUE = '\033[94m'

pytools/sod.py

@@ -264,7 +264,7 @@ def solve(left_state, right_state, geometry, t, gamma=1.4, npts=500,
 
     pos_description = ('Head of Rarefaction', 'Foot of Rarefaction',
                        'Contact Discontinuity', 'Shock')
-    positions = dict(zip(pos_description, x_positions))
+    positions = dict(zip(pos_description, x_positions, strict=True))
 
     # create arrays
     x, p, rho, u = create_arrays(pl, pr, xl, xr, x_positions,

pytools/vtk_io.py

@@ -4,10 +4,11 @@
 @author: glesur
 """
 
-import warnings
-import numpy as np
 import os
 import re
+import warnings
+
+import numpy as np
 
 # restrict what's included with `import *` to public API
 __all__ = [
@@ -98,7 +99,7 @@ def _load_header(self, fh, geometry=None):
                     native_name, _ncomp, native_dim, _dtype = d.split()
                     self.native_coordinates[native_name] = np.fromfile(fh, dtype=dt, count=int(native_dim))
                 else:
-                    warnings.warn("Found unknown field %s" % d)
+                    warnings.warn("Found unknown field %s" % d, stacklevel=3)
                 fh.readline()  # skip extra linefeed (empty line)
 
         if self.geometry is None:

ruff.toml

@@ -0,0 +1,14 @@
+target-version = "py310"
+
+[lint]
+select = [
+    "F",    # pyflakes
+    "B",    # flake8-bugbear
+    "I",    # isort
+    "NPY",  # numpy-specific rules
+]
+ignore = [
+    # allow `import *`
+    "F403", # undefined-local-with-import-star
+    "F405", # undefined-local-with-import-star-usage
+]

test/Dust/DustEnergy/python/testidefix.py

@@ -5,10 +5,11 @@
 
 @author: lesurg
 """
-import sys
-import numpy as np
 import argparse
+import sys
+
 import matplotlib.pyplot as plt
+import numpy as np
 
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",

test/Dust/DustEnergy/testme.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst

test/Dust/DustyShock/python/testidefix.py

@@ -8,13 +8,16 @@
 
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
-from pytools.vtk_io import readVTK
 import argparse
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy.integrate import solve_ivp
 
+from pytools.vtk_io import readVTK
+
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",
                     default=False,

test/Dust/DustyShock/testme.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst

test/Dust/DustyWave/python/testidefix.py

@@ -5,10 +5,11 @@
 
 @author: lesurg
 """
-import sys
-import numpy as np
 import argparse
+import sys
+
 import matplotlib.pyplot as plt
+import numpy as np
 
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",

test/Dust/DustyWave/testme.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst

test/HD/FargoPlanet/testme.py

@@ -6,9 +6,11 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst
+
 tolerance=1e-13
 def testMe(test):
   test.configure()

test/HD/MachReflection/testme.py

@@ -6,10 +6,12 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst
 
+
 def testMe(test):
   test.configure()
   test.compile()

test/HD/SedovBlastWave/python/testidefix.py

@@ -8,13 +8,16 @@
 
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
-from pytools.vtk_io import readVTK
 import argparse
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy.interpolate import interp1d
 
+from pytools.vtk_io import readVTK
+
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",
                     default=False,

test/HD/SedovBlastWave/testme.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst

test/HD/ShearingBox/python/testidefix.py

@@ -5,11 +5,13 @@
 
 @author: lesurg
 """
+import argparse
 import sys
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy.integrate import solve_ivp
-import argparse
+
 
 #compute theoretical solution (from Balbus & Hawley 2006, using notations from Lesur 2021)
 def rhs(t, y, Omega, q, k0x, k0y, k0z):

test/HD/ShearingBox/testme.py

@@ -6,9 +6,11 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst
+
 tolerance=1e-15
 def testMe(test):
   test.configure()

test/HD/ViscousDisk/python/testidefix.py

@@ -8,11 +8,14 @@
 
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
-from pytools.vtk_io import readVTK
-import numpy as np
 import argparse
+
 import matplotlib.pyplot as plt
+import numpy as np
+
+from pytools.vtk_io import readVTK
 
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",

test/HD/ViscousDisk/testme.py

@@ -6,9 +6,11 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst
+
 tolerance=3e-15
 def testMe(test):
   test.configure()

test/HD/ViscousFlowPastCylinder/testme.py

@@ -6,9 +6,11 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst
+
 tolerance=3e-14
 def testMe(test):
   test.configure()

test/HD/sod-iso/python/testidefix.py

@@ -8,14 +8,17 @@
 
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
-from pytools.vtk_io import readVTK
-from pytools import sod
 import argparse
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy.interpolate import interp1d
 
+from pytools import sod
+from pytools.vtk_io import readVTK
+
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",
                     default=False,

test/HD/sod-iso/testme.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst

test/HD/sod/pydefix_example.py

@@ -1,6 +1,7 @@
-import pydefix as pdfx
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+import pydefix as pdfx
+
 
 def output(data):
 

test/HD/sod/python/testidefix.py

@@ -8,14 +8,17 @@
 
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
-from pytools.vtk_io import readVTK
-from pytools import sod
 import argparse
-import numpy as np
+
 import matplotlib.pyplot as plt
+import numpy as np
 from scipy.interpolate import interp1d
 
+from pytools import sod
+from pytools.vtk_io import readVTK
+
 parser = argparse.ArgumentParser()
 parser.add_argument("-noplot",
                     default=False,

test/HD/sod/testme.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+
 sys.path.append(os.getenv("IDEFIX_DIR"))
 
 import pytools.idfx_test as tst