Ruff conforming entirely

examples/autoIgnition.py

@@ -5,7 +5,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 import peregrinepy as pg
 import cantera as ct
 import matplotlib.pyplot as plt

examples/coProcess.py

@@ -5,7 +5,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/couetteFlow.py

@@ -5,7 +5,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/detonationProfile.py

@@ -6,7 +6,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 from pathlib import Path
 
 import cantera as ct

examples/normalShock.py

@@ -6,7 +6,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 
 import matplotlib.pyplot as plt

examples/oneDAdvection.py

@@ -11,7 +11,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/oneDDiffusion.py

@@ -5,7 +5,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/realGasProperties.py

@@ -5,7 +5,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 import peregrinepy as pg
 import numpy as np
 import matplotlib.pyplot as plt

examples/shockCapture.py

@@ -15,7 +15,7 @@
 for more.
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/threeDTaylorGreen.py

@@ -11,7 +11,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/threeDTaylorGreenSkewed.py

@@ -17,7 +17,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 import peregrinepy as pg
 import numpy as np

examples/twoDEulerVortex.py

@@ -11,7 +11,7 @@
 
 """
 
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 import peregrinepy as pg
 import numpy as np
 from time import perf_counter
@@ -91,9 +91,7 @@ def simulate():
     r = np.sqrt(((xc - x0) ** 2 + (yc - y0) ** 2) / Rc**2)
 
     # u
-    blk.array["q"][:, :, :, 1] = uInf - (C0 * (yc - y0) / Rc**2) * np.exp(
-        -(r**2) / 2.0
-    )
+    blk.array["q"][:, :, :, 1] = uInf - (C0 * (yc - y0) / Rc**2) * np.exp(-(r**2) / 2.0)
     # v
     blk.array["q"][:, :, :, 2] = (C0 * (xc - x0) / Rc**2) * np.exp(-(r**2) / 2.0)
 

runPeregrine.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env -S python -m mpi4py
 import sys
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 from time import perf_counter
 
 import numpy as np

src/peregrinepy/__init__.py

@@ -1,28 +1,47 @@
-from ast import Import
+# For pytests to work, we cannot not initialize here
+# since each test needs to initialize and finalize each
+# time. Also for scripting, we dont need MPI.
+#
+# So for running real cases, we initialize in runPeregrine
+# which I think makes more sense anyway.
 import mpi4py.rc
 
 mpi4py.rc.initialize = False
 
-from ._version import __version__
-from . import grid
-from . import writers
-from . import readers
-
-from . import multiBlock
-
-from .bootstrapCase import bootstrapCase
-from .consistify import consistify
-from .RHS import RHS
-from . import bcs
-from . import thermoTransport
-
-from . import coproc
-
-from . import interpolation
-
-from . import files
-
-try:
-    from . import compute
-except ImportError:
-    pass
+from ._version import __version__  # noqa: E402
+from . import grid  # noqa: E402
+from . import writers  # noqa: E402
+from . import readers  # noqa: E402
+
+from . import multiBlock  # noqa: E402
+
+from .bootstrapCase import bootstrapCase  # noqa: E402
+from .consistify import consistify  # noqa: E402
+from .RHS import RHS  # noqa: E402
+from . import bcs  # noqa: E402
+from . import thermoTransport  # noqa: E402
+
+from . import coproc  # noqa: E402
+
+from . import interpolation  # noqa: E402
+
+from . import files  # noqa: E402
+
+from . import compute  # noqa: E402
+
+__all__ = [
+    "__version__",
+    "grid",
+    "writers",
+    "readers",
+    "multiBlock",
+    "bootstrapCase",
+    "consistify",
+    "RHS",
+    "bcs",
+    "thermoTransport",
+    "coproc",
+    "interpolation",
+    "files",
+    "compute",
+]

src/peregrinepy/bcs/__init__.py

@@ -1,3 +1,5 @@
 from . import prepInlets
 from . import prepExits
 from . import prepWalls
+
+__all__ = ["prepInlets", "prepExits", "prepWalls"]

src/peregrinepy/coproc/__init__.py

@@ -1 +1,3 @@
 from .pgCoprocessor import coprocessor
+
+__all__ = ["coprocessor"]

src/peregrinepy/files/__init__.py

@@ -1 +1,3 @@
 from .configFile import configFile
+
+__all__ = ["configFile"]

src/peregrinepy/grid/__init__.py

@@ -2,3 +2,5 @@
 from .generateHalo import generateHalo
 from .metrics import metrics
 from .unifySolverGrid import unifySolverGrid
+
+__all__ = ["create", "generateHalo", "metrics", "unifySolverGrid"]

src/peregrinepy/integrators/dualTime.py

@@ -1,7 +1,7 @@
 from abc import ABCMeta
 
 import numpy as np
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 
 from ..compute.timeIntegration import (
     DTrk3s1,

src/peregrinepy/integrators/rk2.py

@@ -1,7 +1,6 @@
 from abc import ABCMeta
 from ..RHS import RHS
 from ..consistify import consistify
-from ..compute.utils import AEQB
 from ..compute.timeIntegration import rk2s1, rk2s2
 
 

src/peregrinepy/integrators/rk3.py

@@ -1,7 +1,6 @@
 from abc import ABCMeta
 from ..RHS import RHS
 from ..consistify import consistify
-from ..compute.utils import AEQB
 from ..compute.timeIntegration import rk3s1, rk3s2, rk3s3
 
 

src/peregrinepy/integrators/rk34.py

@@ -1,7 +1,6 @@
 from abc import ABCMeta
 from ..RHS import RHS
 from ..consistify import consistify
-from ..compute.utils import AEQB
 from ..compute.timeIntegration import rk34s1, rk34s2, rk34s3, rk34s4
 
 

src/peregrinepy/integrators/rk4.py

@@ -1,7 +1,6 @@
 from abc import ABCMeta
 from ..RHS import RHS
 from ..consistify import consistify
-from ..compute.utils import AEQB
 from ..compute.timeIntegration import rk4s1, rk4s2, rk4s3, rk4s4
 
 

src/peregrinepy/integrators/strang.py

@@ -3,7 +3,6 @@
 from ..consistify import consistify
 from scipy.integrate import ode
 from itertools import product
-from ..compute.utils import AEQB
 from ..compute.timeIntegration import rk3s1, rk3s2, rk3s3
 
 

src/peregrinepy/interpolation/__init__.py

@@ -1,2 +1,4 @@
 from . import bounds
 from .blocksToBlock import blocksToBlock
+
+__all__ = ["bounds", "blocksToBlock"]

src/peregrinepy/misc/__init__.py

@@ -2,3 +2,5 @@
 from .progressBar import progressBar
 from .null import null
 from .createViewMirrorArray import createViewMirrorArray
+
+__all__ = ["frozenDict", "progressBar", "null", "createViewMirrorArray"]

src/peregrinepy/misc/createViewMirrorArray.py

@@ -23,7 +23,7 @@ def createViewMirrorArray(obj, names, shape):
 
     """
 
-    if type(names) != list:
+    if not isinstance(names, list):
         names = [names]
 
     view = getattr(pgkokkos, f"view{len(shape)}")

src/peregrinepy/mpiComm/__init__.py

@@ -1,2 +1,4 @@
 from . import mpiUtils
 from .communicate import communicate
+
+__all__ = ["mpiUtils", "communicate"]

src/peregrinepy/mpiComm/communicate.py

@@ -5,7 +5,7 @@
 
 
 def communicate(mb, varis):
-    if type(varis) is not list:
+    if not isinstance(varis, list):
         varis = [varis]
     comm, rank, size = getCommRankSize()
 
@@ -41,7 +41,7 @@ def communicate(mb, varis):
                     sliceS = face.nodeSendSlices
 
                 # Get the indices of the send slices from the numpy slice object
-                sliceIndxs = [s for f in sliceS for s in f if type(s) is int]
+                sliceIndxs = [s for f in sliceS for s in f if isinstance(s, int)]
                 # populate the temp recv array with the unoriented send data, since its
                 # the correct size and shape
                 extractSendBuffer(
@@ -74,7 +74,7 @@ def communicate(mb, varis):
                 # Push back up the device
                 face.updateDeviceView(recvName)
                 # Get the indices of the recv slices from the numpy slice object
-                sliceIndxs = [s for f in sliceR for s in f if type(s) is int]
+                sliceIndxs = [s for f in sliceR for s in f if isinstance(s, int)]
                 # Place the recv in the view
                 placeRecvBuffer(
                     getattr(blk, var), getattr(face, recvName), face, sliceIndxs

src/peregrinepy/mpiComm/mpiUtils.py

@@ -1,4 +1,4 @@
-from mpi4py import MPI
+from mpi4py import MPI  # noqa: F401
 from ..compute.utils import CFLmax, checkNan
 import numpy as np
 

src/peregrinepy/multiBlock/__init__.py

@@ -1,6 +1,3 @@
-from .topology import topology
-from .grid import grid
-from .restart import restart
 from .solver import solver
 
 from ..integrators import getIntegrator
@@ -111,7 +108,7 @@ def setRHS(cls, config):
 
     # spatial derivatives, subgrid mode, diffusive fluxes
     if config["RHS"]["diffusion"]:
-        cls.dqdxyz = getattr(compute.utils, f"dq2FD")
+        cls.dqdxyz = getattr(compute.utils, "dq2FD")
 
         # Subgrid models
         if config["RHS"]["subgrid"] is not None:

src/peregrinepy/multiBlock/solver.py

@@ -27,7 +27,7 @@ class solver(restart):
     mbType = "solver"
 
     def __init__(self, nblks, spNames, ng):
-        assert type(spNames) is list, f"spNames must me a list not {type(spNames)}"
+        assert isinstance(spNames, list), f"spNames must me a list not {type(spNames)}"
 
         temp = [solverBlock(i, spNames, ng) for i in range(nblks)]
         super().__init__(nblks, spNames, temp)

src/peregrinepy/multiBlock/solverBlock.py

@@ -244,13 +244,13 @@ def setBlockCommunication(self):
             face._setCommBuffers(self.ni, self.nj, self.nk, self.ne, self.nblki)
 
     def updateDeviceView(self, vars):
-        if type(vars) == str:
+        if isinstance(vars, str):
             vars = [vars]
         for var in vars:
             deep_copy(getattr(self, var), self.mirror[var])
 
     def updateHostView(self, vars):
-        if type(vars) == str:
+        if isinstance(vars, str):
             vars = [vars]
         for var in vars:
             deep_copy(self.mirror[var], getattr(self, var))

src/peregrinepy/multiBlock/solverFace.py

@@ -381,13 +381,13 @@ def ng(self):
         return self._ng
 
     def updateDeviceView(self, vars):
-        if type(vars) == str:
+        if isinstance(vars, str):
             vars = [vars]
         for var in vars:
             deep_copy(getattr(self, var), self.mirror[var])
 
     def updateHostView(self, vars):
-        if type(vars) == str:
+        if isinstance(vars, str):
             vars = [vars]
         for var in vars:
             deep_copy(self.mirror[var], getattr(self, var))

src/peregrinepy/multiBlock/topologyFace.py

@@ -22,7 +22,7 @@ def nface(self):
 
     @nface.setter
     def nface(self, value):
-        assert type(value) is int, f"nface must be an integer not {type(value)}"
+        assert isinstance(value, int), f"nface must be an integer not {type(value)}"
         assert 1 <= value <= 6, "nface must be between (1,6)"
         self._nface = value