diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 080bc9ac3..b897bfb16 100644 --- a/.pre-commit-config.yaml +++ b/.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 diff --git a/doc/source/plot_idefix_bench.py b/doc/source/plot_idefix_bench.py index 43482eb04..baa74ac89 100644 --- a/doc/source/plot_idefix_bench.py +++ b/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) diff --git a/pytools/dump_io.py b/pytools/dump_io.py index 4b258336f..7d0ec580b 100644 --- a/pytools/dump_io.py +++ b/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)) diff --git a/pytools/idfx_io.py b/pytools/idfx_io.py index 17dc62725..0e53a39aa 100644 --- a/pytools/idfx_io.py +++ b/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)) diff --git a/pytools/idfx_test.py b/pytools/idfx_test.py index fed74a22e..bb4aa4588 100644 --- a/pytools/idfx_test.py +++ b/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' diff --git a/pytools/sod.py b/pytools/sod.py index 07a60d2cc..ba0e16314 100644 --- a/pytools/sod.py +++ b/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, diff --git a/pytools/vtk_io.py b/pytools/vtk_io.py index eb5cf4125..ac4551b2f 100644 --- a/pytools/vtk_io.py +++ b/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: diff --git a/ruff.toml b/ruff.toml new file mode 100644 index 000000000..9b6b6c620 --- /dev/null +++ b/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 +] diff --git a/test/Dust/DustEnergy/python/testidefix.py b/test/Dust/DustEnergy/python/testidefix.py index d7d766a15..14b64e002 100755 --- a/test/Dust/DustEnergy/python/testidefix.py +++ b/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", diff --git a/test/Dust/DustEnergy/testme.py b/test/Dust/DustEnergy/testme.py index 7187d299b..4aa246430 100755 --- a/test/Dust/DustEnergy/testme.py +++ b/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 diff --git a/test/Dust/DustyShock/python/testidefix.py b/test/Dust/DustyShock/python/testidefix.py index 8fca15a3f..df575bfe2 100755 --- a/test/Dust/DustyShock/python/testidefix.py +++ b/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, diff --git a/test/Dust/DustyShock/testme.py b/test/Dust/DustyShock/testme.py index 2b03d1636..9ae7acb20 100755 --- a/test/Dust/DustyShock/testme.py +++ b/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 diff --git a/test/Dust/DustyWave/python/testidefix.py b/test/Dust/DustyWave/python/testidefix.py index ad52d3306..1c386e6bf 100755 --- a/test/Dust/DustyWave/python/testidefix.py +++ b/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", diff --git a/test/Dust/DustyWave/testme.py b/test/Dust/DustyWave/testme.py index 2b03d1636..9ae7acb20 100755 --- a/test/Dust/DustyWave/testme.py +++ b/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 diff --git a/test/HD/FargoPlanet/testme.py b/test/HD/FargoPlanet/testme.py index 5890d010f..e90e83028 100755 --- a/test/HD/FargoPlanet/testme.py +++ b/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() diff --git a/test/HD/MachReflection/testme.py b/test/HD/MachReflection/testme.py index ce87f3923..1249f593a 100755 --- a/test/HD/MachReflection/testme.py +++ b/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() diff --git a/test/HD/SedovBlastWave/python/testidefix.py b/test/HD/SedovBlastWave/python/testidefix.py index a78bc88e5..40d39a79a 100755 --- a/test/HD/SedovBlastWave/python/testidefix.py +++ b/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, diff --git a/test/HD/SedovBlastWave/testme.py b/test/HD/SedovBlastWave/testme.py index 95fdd030a..63d381f33 100755 --- a/test/HD/SedovBlastWave/testme.py +++ b/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 diff --git a/test/HD/ShearingBox/python/testidefix.py b/test/HD/ShearingBox/python/testidefix.py index 1a0c2509a..d76561875 100755 --- a/test/HD/ShearingBox/python/testidefix.py +++ b/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): diff --git a/test/HD/ShearingBox/testme.py b/test/HD/ShearingBox/testme.py index 3739910a0..521af004e 100755 --- a/test/HD/ShearingBox/testme.py +++ b/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() diff --git a/test/HD/ViscousDisk/python/testidefix.py b/test/HD/ViscousDisk/python/testidefix.py index 39e3666e1..8ee0d3491 100755 --- a/test/HD/ViscousDisk/python/testidefix.py +++ b/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", diff --git a/test/HD/ViscousDisk/testme.py b/test/HD/ViscousDisk/testme.py index 1e8ad742b..421ec90f3 100755 --- a/test/HD/ViscousDisk/testme.py +++ b/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() diff --git a/test/HD/ViscousFlowPastCylinder/testme.py b/test/HD/ViscousFlowPastCylinder/testme.py index c831e8093..a13eaa856 100755 --- a/test/HD/ViscousFlowPastCylinder/testme.py +++ b/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() diff --git a/test/HD/sod-iso/python/testidefix.py b/test/HD/sod-iso/python/testidefix.py index ec91c63eb..94b06c0f4 100755 --- a/test/HD/sod-iso/python/testidefix.py +++ b/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, diff --git a/test/HD/sod-iso/testme.py b/test/HD/sod-iso/testme.py index e8f0f9ae2..53c938492 100755 --- a/test/HD/sod-iso/testme.py +++ b/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 diff --git a/test/HD/sod/pydefix_example.py b/test/HD/sod/pydefix_example.py index 58d73642b..937159f80 100644 --- a/test/HD/sod/pydefix_example.py +++ b/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): diff --git a/test/HD/sod/python/testidefix.py b/test/HD/sod/python/testidefix.py index 899218b17..3ba7a000c 100755 --- a/test/HD/sod/python/testidefix.py +++ b/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, diff --git a/test/HD/sod/testme.py b/test/HD/sod/testme.py index e8f0f9ae2..53c938492 100755 --- a/test/HD/sod/testme.py +++ b/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 diff --git a/test/HD/thermalDiffusion/python/testidefix.py b/test/HD/thermalDiffusion/python/testidefix.py index 126c0be06..e032a5327 100755 --- a/test/HD/thermalDiffusion/python/testidefix.py +++ b/test/HD/thermalDiffusion/python/testidefix.py @@ -1,10 +1,11 @@ #!/usr/bin/env python3 # -*- coding: utf-8 -*- -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", diff --git a/test/HD/thermalDiffusion/testme.py b/test/HD/thermalDiffusion/testme.py index 3806293d0..a4ab9e186 100755 --- a/test/HD/thermalDiffusion/testme.py +++ b/test/HD/thermalDiffusion/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() diff --git a/test/IO/dump/testme.py b/test/IO/dump/testme.py index 35affdba2..95304defb 100755 --- a/test/IO/dump/testme.py +++ b/test/IO/dump/testme.py @@ -5,6 +5,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/IO/pydefix/pydefix_example.py b/test/IO/pydefix/pydefix_example.py index a08e86464..788518b26 100644 --- a/test/IO/pydefix/pydefix_example.py +++ b/test/IO/pydefix/pydefix_example.py @@ -1,6 +1,7 @@ -from pydefix import * -import numpy as np import matplotlib.pyplot as plt +import numpy as np +from pydefix import * + # The output function # the only argument is dataBlockHost python object, wrapping a dataBlockHost Idefix object diff --git a/test/IO/pydefix/testme.py b/test/IO/pydefix/testme.py index 0a3ad0432..0df789ce6 100755 --- a/test/IO/pydefix/testme.py +++ b/test/IO/pydefix/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-12 def testMe(test): test.configure() diff --git a/test/IO/xdmf/testme.py b/test/IO/xdmf/testme.py index a1e333430..d6b013a23 100755 --- a/test/IO/xdmf/testme.py +++ b/test/IO/xdmf/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst @@ -30,10 +31,7 @@ def check_xdmf_exists(): if not test.dec: test.dec=['2','2','2'] -if test.check: - check_xdmf_exists() - -else: +if not test.check: test.vectPot=False test.single=False test.reconstruction=2 @@ -42,4 +40,5 @@ def check_xdmf_exists(): test.configure(definitionFile="definitions.hpp") test.compile() test.run(inputFile="idefix.ini") - check_xdmf_exists + +check_xdmf_exists() diff --git a/test/MHD/AmbipolarCshock/python/testidefix.py b/test/MHD/AmbipolarCshock/python/testidefix.py index 8c95dbb1a..fe780c816 100755 --- a/test/MHD/AmbipolarCshock/python/testidefix.py +++ b/test/MHD/AmbipolarCshock/python/testidefix.py @@ -5,15 +5,18 @@ @author: lesurg """ -import numpy as np -from scipy.integrate import ode -import matplotlib.pyplot as plt import os import sys + +import matplotlib.pyplot as plt +import numpy as np +from scipy.integrate import ode + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK import argparse +from pytools.vtk_io import readVTK + parser = argparse.ArgumentParser() parser.add_argument("-noplot", default=False, diff --git a/test/MHD/AmbipolarCshock/testme.py b/test/MHD/AmbipolarCshock/testme.py index 675958a7b..7bc1df9d2 100755 --- a/test/MHD/AmbipolarCshock/testme.py +++ b/test/MHD/AmbipolarCshock/testme.py @@ -6,9 +6,11 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst + tolerance=0 def testMe(test): diff --git a/test/MHD/AmbipolarCshock3D/python/testidefix.py b/test/MHD/AmbipolarCshock3D/python/testidefix.py index a7354fbaa..c151dd789 100755 --- a/test/MHD/AmbipolarCshock3D/python/testidefix.py +++ b/test/MHD/AmbipolarCshock3D/python/testidefix.py @@ -5,15 +5,18 @@ @author: lesurg """ -import numpy as np -from scipy.integrate import ode -import matplotlib.pyplot as plt import os import sys + +import matplotlib.pyplot as plt +import numpy as np +from scipy.integrate import ode + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK import argparse +from pytools.vtk_io import readVTK + parser = argparse.ArgumentParser() parser.add_argument("-noplot", default=False, diff --git a/test/MHD/AmbipolarCshock3D/testme.py b/test/MHD/AmbipolarCshock3D/testme.py index 964224854..a928ab553 100755 --- a/test/MHD/AmbipolarCshock3D/testme.py +++ b/test/MHD/AmbipolarCshock3D/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() diff --git a/test/MHD/AmbipolarShearingBox/python/testidefix.py b/test/MHD/AmbipolarShearingBox/python/testidefix.py index 1d1ccb281..6aec86a64 100755 --- a/test/MHD/AmbipolarShearingBox/python/testidefix.py +++ b/test/MHD/AmbipolarShearingBox/python/testidefix.py @@ -5,10 +5,12 @@ @author: lesurg """ -import numpy as np -import matplotlib.pyplot as plt import os import sys + +import matplotlib.pyplot as plt +import numpy as np + sys.path.append(os.getenv("IDEFIX_DIR")) from pytools.vtk_io import readVTK diff --git a/test/MHD/AxisFluxTube/python/checkAxisBounds.py b/test/MHD/AxisFluxTube/python/checkAxisBounds.py index 44eec58e2..774069886 100755 --- a/test/MHD/AxisFluxTube/python/checkAxisBounds.py +++ b/test/MHD/AxisFluxTube/python/checkAxisBounds.py @@ -7,10 +7,12 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.idfx_io import readIdfxFile import matplotlib.pyplot as plt +from pytools.idfx_io import readIdfxFile + rep="../" idfx=readIdfxFile(rep+"analysis.99.0.idfx") diff --git a/test/MHD/AxisFluxTube/testme.py b/test/MHD/AxisFluxTube/testme.py index 44a53dc28..4e40d9ca6 100755 --- a/test/MHD/AxisFluxTube/testme.py +++ b/test/MHD/AxisFluxTube/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/Coarsening/python/testidefix.py b/test/MHD/Coarsening/python/testidefix.py index e3ea0cd0a..206c01600 100755 --- a/test/MHD/Coarsening/python/testidefix.py +++ b/test/MHD/Coarsening/python/testidefix.py @@ -8,12 +8,15 @@ 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 inifix +import matplotlib.pyplot as plt +import numpy as np + +from pytools.vtk_io import readVTK parser = argparse.ArgumentParser() parser.add_argument("-noplot", diff --git a/test/MHD/Coarsening/testme.py b/test/MHD/Coarsening/testme.py index 52a083bd2..d5d6398db 100755 --- a/test/MHD/Coarsening/testme.py +++ b/test/MHD/Coarsening/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/FargoMHDSpherical/testme.py b/test/MHD/FargoMHDSpherical/testme.py index 7ee3100b2..193fecaab 100755 --- a/test/MHD/FargoMHDSpherical/testme.py +++ b/test/MHD/FargoMHDSpherical/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/HallWhistler/python/testidefix.py b/test/MHD/HallWhistler/python/testidefix.py index 3d3eab2d3..2ca5d6bf8 100755 --- a/test/MHD/HallWhistler/python/testidefix.py +++ b/test/MHD/HallWhistler/python/testidefix.py @@ -12,10 +12,11 @@ @author: lesurg """ -import sys -import numpy as np import argparse +import sys + import matplotlib.pyplot as plt +import numpy as np from scipy.signal import argrelextrema parser = argparse.ArgumentParser() diff --git a/test/MHD/HallWhistler/testme.py b/test/MHD/HallWhistler/testme.py index f8d633840..33a1cfa2e 100755 --- a/test/MHD/HallWhistler/testme.py +++ b/test/MHD/HallWhistler/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/LinearWaveTest/python/testidefix.py b/test/MHD/LinearWaveTest/python/testidefix.py index be82269a6..8603ee8ed 100755 --- a/test/MHD/LinearWaveTest/python/testidefix.py +++ b/test/MHD/LinearWaveTest/python/testidefix.py @@ -1,15 +1,19 @@ #!/usr/bin/env python3 # -*- coding: utf-8 -*- -import numpy as np +import math import os import sys -import math + +import numpy as np + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.dump_io import readDump -import matplotlib.pyplot as plt import argparse +import matplotlib.pyplot as plt + +from pytools.dump_io import readDump + parser = argparse.ArgumentParser() parser.add_argument("-noplot", default=False, diff --git a/test/MHD/LinearWaveTest/testme.py b/test/MHD/LinearWaveTest/testme.py index 390a5759b..6b9804fd0 100755 --- a/test/MHD/LinearWaveTest/testme.py +++ b/test/MHD/LinearWaveTest/testme.py @@ -6,9 +6,11 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst + tolerance=2e-13 def testMe(test): test.configure() diff --git a/test/MHD/MTI/python/testidefix.py b/test/MHD/MTI/python/testidefix.py index 4b60cc8bd..18481692d 100644 --- a/test/MHD/MTI/python/testidefix.py +++ b/test/MHD/MTI/python/testidefix.py @@ -9,9 +9,10 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -import numpy as np import inifix +import numpy as np n = 1 # fondamental mode diff --git a/test/MHD/MTI/testme.py b/test/MHD/MTI/testme.py index 7975c8075..15166dc76 100755 --- a/test/MHD/MTI/testme.py +++ b/test/MHD/MTI/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/OrszagTang/testme.py b/test/MHD/OrszagTang/testme.py index 761505caa..7ccef02b3 100755 --- a/test/MHD/OrszagTang/testme.py +++ b/test/MHD/OrszagTang/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-12 def testMe(test): test.configure() diff --git a/test/MHD/OrszagTang3D/testme.py b/test/MHD/OrszagTang3D/testme.py index b9626f9cc..c0d9772ce 100755 --- a/test/MHD/OrszagTang3D/testme.py +++ b/test/MHD/OrszagTang3D/testme.py @@ -5,6 +5,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/ResistiveAlfvenWave/python/testidefix.py b/test/MHD/ResistiveAlfvenWave/python/testidefix.py index 89b0f136c..52b11c8c8 100644 --- a/test/MHD/ResistiveAlfvenWave/python/testidefix.py +++ b/test/MHD/ResistiveAlfvenWave/python/testidefix.py @@ -1,7 +1,8 @@ -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", diff --git a/test/MHD/ResistiveAlfvenWave/testme.py b/test/MHD/ResistiveAlfvenWave/testme.py index f9b8ae56f..f703db89b 100755 --- a/test/MHD/ResistiveAlfvenWave/testme.py +++ b/test/MHD/ResistiveAlfvenWave/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-14 def testMe(test): diff --git a/test/MHD/ShearingBox/python/testidefix.py b/test/MHD/ShearingBox/python/testidefix.py index e1a882229..1ab5b2935 100755 --- a/test/MHD/ShearingBox/python/testidefix.py +++ b/test/MHD/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, B0y, B0z, k0x, k0y, k0z): diff --git a/test/MHD/ShearingBox/testme.py b/test/MHD/ShearingBox/testme.py index 364adde9b..b50b48c31 100755 --- a/test/MHD/ShearingBox/testme.py +++ b/test/MHD/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-14 def testMe(test): diff --git a/test/MHD/clessTDiffusion/python/testidefix.py b/test/MHD/clessTDiffusion/python/testidefix.py index 9427aca82..f37cf5032 100644 --- a/test/MHD/clessTDiffusion/python/testidefix.py +++ b/test/MHD/clessTDiffusion/python/testidefix.py @@ -1,9 +1,11 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK -import numpy as np import inifix +import numpy as np + +from pytools.vtk_io import readVTK conf = inifix.load("../idefix.ini") gamma = conf["Hydro"]["gamma"] diff --git a/test/MHD/clessTDiffusion/testme.py b/test/MHD/clessTDiffusion/testme.py index 6ed5b1648..fcb6554b9 100755 --- a/test/MHD/clessTDiffusion/testme.py +++ b/test/MHD/clessTDiffusion/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/sod-iso/testme.py b/test/MHD/sod-iso/testme.py index 798aace57..f8bde96c4 100755 --- a/test/MHD/sod-iso/testme.py +++ b/test/MHD/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 diff --git a/test/MHD/sod/testme.py b/test/MHD/sod/testme.py index 798aace57..f8bde96c4 100755 --- a/test/MHD/sod/testme.py +++ b/test/MHD/sod/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/sphBragTDiffusion/python/testidefix.py b/test/MHD/sphBragTDiffusion/python/testidefix.py index 8bf639cb4..d42c8bc92 100644 --- a/test/MHD/sphBragTDiffusion/python/testidefix.py +++ b/test/MHD/sphBragTDiffusion/python/testidefix.py @@ -1,9 +1,11 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK -import numpy as np import inifix +import numpy as np + +from pytools.vtk_io import readVTK conf = inifix.load("../idefix.ini") amplitude = conf["Setup"]["amplitude"] diff --git a/test/MHD/sphBragTDiffusion/testme.py b/test/MHD/sphBragTDiffusion/testme.py index 6ed5b1648..fcb6554b9 100755 --- a/test/MHD/sphBragTDiffusion/testme.py +++ b/test/MHD/sphBragTDiffusion/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/MHD/sphBragViscosity/python/testidefix.py b/test/MHD/sphBragViscosity/python/testidefix.py index c016242d6..7369f636e 100644 --- a/test/MHD/sphBragViscosity/python/testidefix.py +++ b/test/MHD/sphBragViscosity/python/testidefix.py @@ -1,11 +1,13 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK -import numpy as np import inifix +import numpy as np from scipy.special import jn +from pytools.vtk_io import readVTK + conf = inifix.load("../idefix.ini") amplitude = conf["Setup"]["amplitude"] time_step = conf["Output"]["vtk"] diff --git a/test/MHD/sphBragViscosity/testme.py b/test/MHD/sphBragViscosity/testme.py index 254417f44..255d74556 100755 --- a/test/MHD/sphBragViscosity/testme.py +++ b/test/MHD/sphBragViscosity/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Planet/Planet3Body/python/testidefix.py b/test/Planet/Planet3Body/python/testidefix.py index a3b7f64d5..91a680d63 100755 --- a/test/Planet/Planet3Body/python/testidefix.py +++ b/test/Planet/Planet3Body/python/testidefix.py @@ -8,9 +8,11 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import numpy as np + def separation(resonance): a = int(resonance[-1]) b = int(resonance[0]) diff --git a/test/Planet/Planet3Body/testme.py b/test/Planet/Planet3Body/testme.py index c11d08963..b2de8eff4 100755 --- a/test/Planet/Planet3Body/testme.py +++ b/test/Planet/Planet3Body/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Planet/PlanetMigration2D/python/testidefix.py b/test/Planet/PlanetMigration2D/python/testidefix.py index 897d7b53f..0a47d24f7 100755 --- a/test/Planet/PlanetMigration2D/python/testidefix.py +++ b/test/Planet/PlanetMigration2D/python/testidefix.py @@ -8,9 +8,11 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import numpy as np + def datafile(filename): return np.loadtxt(filename, dtype="float64").T diff --git a/test/Planet/PlanetMigration2D/testme.py b/test/Planet/PlanetMigration2D/testme.py index 0921d4e62..9444c33a0 100755 --- a/test/Planet/PlanetMigration2D/testme.py +++ b/test/Planet/PlanetMigration2D/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Planet/PlanetPlanetRK42D/python/testidefix.py b/test/Planet/PlanetPlanetRK42D/python/testidefix.py index c3d4aa9b6..656e55c28 100755 --- a/test/Planet/PlanetPlanetRK42D/python/testidefix.py +++ b/test/Planet/PlanetPlanetRK42D/python/testidefix.py @@ -7,11 +7,13 @@ """ import os -import sys import re +import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import numpy as np + def filter_index(t): # get read of data previously generated (when the code was restarted) tref=t[-1] diff --git a/test/Planet/PlanetPlanetRK42D/testme.py b/test/Planet/PlanetPlanetRK42D/testme.py index 26cb8ee21..a91438c99 100755 --- a/test/Planet/PlanetPlanetRK42D/testme.py +++ b/test/Planet/PlanetPlanetRK42D/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Planet/PlanetSpiral2D/python/testidefix.py b/test/Planet/PlanetSpiral2D/python/testidefix.py index ee9f5acc2..0b7fafe59 100755 --- a/test/Planet/PlanetSpiral2D/python/testidefix.py +++ b/test/Planet/PlanetSpiral2D/python/testidefix.py @@ -1,13 +1,14 @@ #!/usr/bin/env python # coding: utf-8 -import sys import os -sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK +import sys -import numpy as np +sys.path.append(os.getenv("IDEFIX_DIR")) import matplotlib.pyplot as plt +import numpy as np + +from pytools.vtk_io import readVTK on = 3 ds = readVTK(f"../data.{on:04d}.vtk", geometry="polar") diff --git a/test/Planet/PlanetSpiral2D/testme.py b/test/Planet/PlanetSpiral2D/testme.py index 0921d4e62..9444c33a0 100755 --- a/test/Planet/PlanetSpiral2D/testme.py +++ b/test/Planet/PlanetSpiral2D/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Planet/PlanetTorque3D/python/testidefix.py b/test/Planet/PlanetTorque3D/python/testidefix.py index 47477f64b..f51b4974b 100755 --- a/test/Planet/PlanetTorque3D/python/testidefix.py +++ b/test/Planet/PlanetTorque3D/python/testidefix.py @@ -8,9 +8,11 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import numpy as np + def datafile(filename): return np.loadtxt(filename, dtype="float64").T diff --git a/test/Planet/PlanetTorque3D/testme.py b/test/Planet/PlanetTorque3D/testme.py index b4f04a507..edcb2c3a8 100755 --- a/test/Planet/PlanetTorque3D/testme.py +++ b/test/Planet/PlanetTorque3D/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Planet/PlanetsIsActiveRK52D/python/testidefix.py b/test/Planet/PlanetsIsActiveRK52D/python/testidefix.py index 0a5f91499..c39f51784 100755 --- a/test/Planet/PlanetsIsActiveRK52D/python/testidefix.py +++ b/test/Planet/PlanetsIsActiveRK52D/python/testidefix.py @@ -8,9 +8,11 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import numpy as np + def find_nearest(array, value): array = np.asarray(array) idx = (np.abs(array - value)).argmin() diff --git a/test/Planet/PlanetsIsActiveRK52D/testme.py b/test/Planet/PlanetsIsActiveRK52D/testme.py index ce0d405c0..ccde30c86 100755 --- a/test/Planet/PlanetsIsActiveRK52D/testme.py +++ b/test/Planet/PlanetsIsActiveRK52D/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/Pluto/HD/sod/python/idefixTools.py b/test/Pluto/HD/sod/python/idefixTools.py index a8d2dc86f..06e63afa8 100644 --- a/test/Pluto/HD/sod/python/idefixTools.py +++ b/test/Pluto/HD/sod/python/idefixTools.py @@ -7,6 +7,8 @@ import numpy as np + + class DataStructure: pass diff --git a/test/Pluto/HD/sod/python/sod.py b/test/Pluto/HD/sod/python/sod.py index 717c27ca6..90ad62fe0 100755 --- a/test/Pluto/HD/sod/python/sod.py +++ b/test/Pluto/HD/sod/python/sod.py @@ -266,7 +266,7 @@ 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, diff --git a/test/Pluto/HD/sod/python/testidefix.py b/test/Pluto/HD/sod/python/testidefix.py index d01db7bca..239bb1c86 100755 --- a/test/Pluto/HD/sod/python/testidefix.py +++ b/test/Pluto/HD/sod/python/testidefix.py @@ -6,12 +6,13 @@ @author: glesur """ -import idefixTools as idfx -import sod -import sys import argparse -import numpy as np +import sys + +import idefixTools as idfx import matplotlib.pyplot as plt +import numpy as np +import sod from scipy.interpolate import interp1d parser = argparse.ArgumentParser() diff --git a/test/SelfGravity/DustyCollapse/python/testidefix.py b/test/SelfGravity/DustyCollapse/python/testidefix.py index 370d89e77..83ec380ac 100644 --- a/test/SelfGravity/DustyCollapse/python/testidefix.py +++ b/test/SelfGravity/DustyCollapse/python/testidefix.py @@ -1,7 +1,8 @@ -import numpy as np import os import sys +import numpy as np + sys.path.append(os.getenv("IDEFIX_DIR")) from pytools.vtk_io import readVTK diff --git a/test/SelfGravity/DustyCollapse/testme.py b/test/SelfGravity/DustyCollapse/testme.py index 689038265..b686539bd 100755 --- a/test/SelfGravity/DustyCollapse/testme.py +++ b/test/SelfGravity/DustyCollapse/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/SelfGravity/JeansInstability/python/testidefix.py b/test/SelfGravity/JeansInstability/python/testidefix.py index 80d6ee620..34c52975c 100755 --- a/test/SelfGravity/JeansInstability/python/testidefix.py +++ b/test/SelfGravity/JeansInstability/python/testidefix.py @@ -8,11 +8,13 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK import numpy as np from scipy.fftpack import fft, fftfreq +from pytools.vtk_io import readVTK + # Arguments gravCst = np.pi # grav cst G=pi gamma = 5/3 diff --git a/test/SelfGravity/JeansInstability/testme.py b/test/SelfGravity/JeansInstability/testme.py index ff2f39a83..8f79b4258 100755 --- a/test/SelfGravity/JeansInstability/testme.py +++ b/test/SelfGravity/JeansInstability/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/SelfGravity/RandomSphere/python/testidefix.py b/test/SelfGravity/RandomSphere/python/testidefix.py index 444c3034d..65f3b8045 100755 --- a/test/SelfGravity/RandomSphere/python/testidefix.py +++ b/test/SelfGravity/RandomSphere/python/testidefix.py @@ -6,11 +6,12 @@ @author: glesur """ +import argparse import os import sys -import numpy as np + import matplotlib.pyplot as plt -import argparse +import numpy as np sys.path.append(os.getenv("IDEFIX_DIR")) diff --git a/test/SelfGravity/RandomSphere/testme.py b/test/SelfGravity/RandomSphere/testme.py index 38fc30d92..a9c43c43c 100755 --- a/test/SelfGravity/RandomSphere/testme.py +++ b/test/SelfGravity/RandomSphere/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() diff --git a/test/SelfGravity/RandomSphereCartesian/python/testidefix.py b/test/SelfGravity/RandomSphereCartesian/python/testidefix.py index 7367b3d9a..3f8983843 100755 --- a/test/SelfGravity/RandomSphereCartesian/python/testidefix.py +++ b/test/SelfGravity/RandomSphereCartesian/python/testidefix.py @@ -6,12 +6,13 @@ @author: glesur """ +import argparse import os import sys -import numpy as np + import matplotlib.pyplot as plt +import numpy as np import numpy.fft as fft -import argparse sys.path.append(os.getenv("IDEFIX_DIR")) diff --git a/test/SelfGravity/RandomSphereCartesian/testme.py b/test/SelfGravity/RandomSphereCartesian/testme.py index 64b4a9ba5..ef68e1c88 100755 --- a/test/SelfGravity/RandomSphereCartesian/testme.py +++ b/test/SelfGravity/RandomSphereCartesian/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() diff --git a/test/SelfGravity/UniformCollapse/python/testidefix.py b/test/SelfGravity/UniformCollapse/python/testidefix.py index e89a296a0..90dfacdac 100755 --- a/test/SelfGravity/UniformCollapse/python/testidefix.py +++ b/test/SelfGravity/UniformCollapse/python/testidefix.py @@ -8,10 +8,12 @@ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) -from pytools.vtk_io import readVTK import numpy as np +from pytools.vtk_io import readVTK + # Arguments gravCst = 1./(4.*np.pi) # grav cst 4piG rho0 = 1e-3 # initial density diff --git a/test/SelfGravity/UniformCollapse/testme.py b/test/SelfGravity/UniformCollapse/testme.py index 21debc0e0..1b0a3d7a2 100755 --- a/test/SelfGravity/UniformCollapse/testme.py +++ b/test/SelfGravity/UniformCollapse/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/utils/columnDensity/testme.py b/test/utils/columnDensity/testme.py index 6f017d7d8..648285cce 100755 --- a/test/utils/columnDensity/testme.py +++ b/test/utils/columnDensity/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/utils/dumpImage/testme.py b/test/utils/dumpImage/testme.py index 6f017d7d8..648285cce 100755 --- a/test/utils/dumpImage/testme.py +++ b/test/utils/dumpImage/testme.py @@ -6,6 +6,7 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import pytools.idfx_test as tst diff --git a/test/utils/lookupTable/testme.py b/test/utils/lookupTable/testme.py index d40884652..37fa208e9 100755 --- a/test/utils/lookupTable/testme.py +++ b/test/utils/lookupTable/testme.py @@ -6,11 +6,14 @@ """ import os import sys + sys.path.append(os.getenv("IDEFIX_DIR")) import numpy as np + #from scipy.interpolate import RegularGridInterpolator import pytools.idfx_test as tst + def MakeNumpyFile(): x=np.arange(1,10,1.0) y=np.arange(5,10,1.0)