Added isort to tox (#221)

* setting isort with tox

* running isort (with tox) on the repo

* specifying isort to use Black

* running isort again

* removed unnecessary dep from travis + set up linting

* fix review notes

* removed pylint comment

* ran lint one more time

* ran pylint again

.github/workflows/linting.yml

@@ -12,6 +12,15 @@ jobs:
         run: pip install tox
       - name: Run black through tox
         run: tox -e black
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - name: Install tox
+        run: pip install tox
+      - name: Run isort through tox
+        run: tox -e isort
   pylint:
     runs-on: ubuntu-latest
     steps:

benchmarks/benchmark_utils.py

@@ -2,7 +2,6 @@
 
 import numpy as np
 
-
 SPD_MATRIX_5x5 = np.array(
     [
         [2.3, -2.3, 3.5, 4.2, 1.8],

benchmarks/ivpsolve.py

@@ -2,6 +2,7 @@
 Benchmarks for probabilistic ivp solvers
 """
 import numpy as np
+
 from probnum.diffeq import lotkavolterra, probsolve_ivp
 from probnum.random_variables import Dirac
 

benchmarks/linearsolvers.py

@@ -3,11 +3,12 @@
 """
 
 import os
+
 import numpy as np
 import scipy.sparse
 
-from probnum.linalg import problinsolve
 from benchmarks.benchmark_utils import SPD_MATRIX_5x5
+from probnum.linalg import problinsolve
 
 
 def load_poisson_linear_system():

benchmarks/random_variables.py

@@ -4,10 +4,9 @@
 
 import numpy as np
 
-from probnum import random_variables as rvs
 import probnum.linalg.linops as linops
-
 from benchmarks.benchmark_utils import SPD_MATRIX_5x5
+from probnum import random_variables as rvs
 
 # Module level variables
 RV_NAMES = [

docs/source/conf.py

@@ -17,9 +17,9 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
-from datetime import datetime
 import os
 import sys
+from datetime import datetime
 
 from pkg_resources import get_distribution
 

src/probnum/__init__.py

@@ -22,19 +22,11 @@
 diffeq
     Probabilistic solvers for ordinary differential equations.
 """
-# pylint: disable=wrong-import-order
-
-from . import diffeq
-from . import filtsmooth
-from . import linalg
-from . import quad
-from . import random_variables
-from . import utils
-
-from .random_variables import asrandvar, RandomVariable
-
 # -*- coding: utf-8 -*-
-from pkg_resources import get_distribution, DistributionNotFound
+from pkg_resources import DistributionNotFound, get_distribution
+
+from . import diffeq, filtsmooth, linalg, quad, random_variables, utils
+from .random_variables import RandomVariable, asrandvar
 
 try:
     # Change here if project is renamed and does not equal the package name

src/probnum/_randomvariablelist.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import probnum.random_variables as pnrvs
 
 

src/probnum/diffeq/__init__.py

@@ -1,9 +1,8 @@
 from .ode import *
 from .odefiltsmooth import *
-from .steprule import *
-from .odesolver import *
 from .odesolution import ODESolution
-
+from .odesolver import *
+from .steprule import *
 
 # Public classes and functions. Order is reflected in documentation.
 __all__ = [

src/probnum/diffeq/ode/ivp.py

@@ -10,7 +10,6 @@
 
 from probnum.diffeq.ode.ode import ODE
 
-
 __all__ = ["logistic", "fitzhughnagumo", "lotkavolterra", "IVP"]
 
 

src/probnum/diffeq/odefiltsmooth/ivp2filter.py

@@ -5,9 +5,9 @@
 
 import numpy as np
 
+from probnum import random_variables as rvs
 from probnum.filtsmooth import ExtendedKalman, UnscentedKalman
 from probnum.filtsmooth.statespace.discrete import DiscreteGaussianModel
-from probnum import random_variables as rvs
 
 
 def ivp2ekf0(ivp, prior, evlvar):

src/probnum/diffeq/odefiltsmooth/ivpfiltsmooth.py

@@ -1,9 +1,9 @@
 import numpy as np
 
-from probnum.random_variables import Normal
 from probnum.diffeq import odesolver
 from probnum.diffeq.odefiltsmooth.prior import ODEPrior
 from probnum.diffeq.odesolution import ODESolution
+from probnum.random_variables import Normal
 
 
 class GaussianIVPFilter(odesolver.ODESolver):

src/probnum/diffeq/odefiltsmooth/odefiltsmooth.py

@@ -20,7 +20,7 @@
 """
 
 from probnum.diffeq import steprule
-from probnum.diffeq.odefiltsmooth import prior, ivp2filter
+from probnum.diffeq.odefiltsmooth import ivp2filter, prior
 from probnum.diffeq.odefiltsmooth.ivpfiltsmooth import GaussianIVPFilter
 
 

src/probnum/diffeq/odefiltsmooth/prior.py

@@ -9,6 +9,7 @@
 provided by IOUP and change parameters
 """
 import warnings
+
 import numpy as np
 from scipy.special import binom  # for Matern
 from scipy.special import factorial  # vectorised factorial for IBM-Q(h)

src/probnum/diffeq/odesolution.py

@@ -7,11 +7,11 @@
 """
 import numpy as np
 
-from probnum.random_variables import Normal
+from probnum import utils
 from probnum._randomvariablelist import _RandomVariableList
-from probnum.filtsmooth.filtsmoothposterior import FiltSmoothPosterior
 from probnum.filtsmooth import KalmanPosterior
-from probnum import utils
+from probnum.filtsmooth.filtsmoothposterior import FiltSmoothPosterior
+from probnum.random_variables import Normal
 
 
 class ODESolution(FiltSmoothPosterior):

src/probnum/diffeq/odesolver.py

@@ -2,8 +2,8 @@
 Abstract ODESolver class. Interface for Runge-Kutta, ODEFilter.
 """
 
-from abc import ABC, abstractmethod
 import warnings
+from abc import ABC, abstractmethod
 
 from probnum.diffeq.odesolution import ODESolution
 

src/probnum/filtsmooth/__init__.py

@@ -2,10 +2,10 @@
 Bayesian filtering and smoothing.
 """
 
-from .statespace import *
-from .gaussfiltsmooth import *
 from .bayesfiltsmooth import *
 from .filtsmoothposterior import FiltSmoothPosterior
+from .gaussfiltsmooth import *
+from .statespace import *
 
 # Public classes and functions. Order is reflected in documentation.
 __all__ = [

src/probnum/filtsmooth/gaussfiltsmooth/__init__.py

@@ -1,6 +1,6 @@
 from .extendedkalman import *
 from .gaussfiltsmooth import *
 from .kalman import *
+from .kalmanposterior import KalmanPosterior
 from .unscentedkalman import *
 from .unscentedtransform import *
-from .kalmanposterior import KalmanPosterior

src/probnum/filtsmooth/gaussfiltsmooth/extendedkalman.py

@@ -4,14 +4,13 @@
 """
 import numpy as np
 
+from probnum.filtsmooth.gaussfiltsmooth._utils import is_cont_disc, is_disc_disc
 from probnum.filtsmooth.gaussfiltsmooth.gaussfiltsmooth import (
     GaussFiltSmooth,
     linear_discrete_update,
 )
+from probnum.filtsmooth.statespace import DiscreteGaussianModel, LinearSDEModel
 from probnum.random_variables import Normal
-from probnum.filtsmooth.statespace import LinearSDEModel, DiscreteGaussianModel
-
-from probnum.filtsmooth.gaussfiltsmooth._utils import is_cont_disc, is_disc_disc
 
 
 class ExtendedKalman(GaussFiltSmooth):

src/probnum/filtsmooth/gaussfiltsmooth/gaussfiltsmooth.py

@@ -6,10 +6,9 @@
 import numpy as np
 
 from probnum._randomvariablelist import _RandomVariableList
-
-from probnum.random_variables import Normal
 from probnum.filtsmooth.bayesfiltsmooth import BayesFiltSmooth
 from probnum.filtsmooth.gaussfiltsmooth.kalmanposterior import KalmanPosterior
+from probnum.random_variables import Normal
 
 
 class GaussFiltSmooth(BayesFiltSmooth, ABC):

src/probnum/filtsmooth/gaussfiltsmooth/kalman.py

@@ -4,14 +4,14 @@
 """
 
 import numpy as np
+
+from probnum.filtsmooth.gaussfiltsmooth._utils import is_cont_disc, is_disc_disc
 from probnum.filtsmooth.gaussfiltsmooth.gaussfiltsmooth import (
     GaussFiltSmooth,
     linear_discrete_update,
 )
+from probnum.filtsmooth.statespace import DiscreteGaussianLinearModel, LinearSDEModel
 from probnum.random_variables import Normal
-from probnum.filtsmooth.statespace import LinearSDEModel, DiscreteGaussianLinearModel
-
-from probnum.filtsmooth.gaussfiltsmooth._utils import is_cont_disc, is_disc_disc
 
 
 class Kalman(GaussFiltSmooth):

src/probnum/filtsmooth/gaussfiltsmooth/kalmanposterior.py

@@ -9,10 +9,10 @@
 
 import numpy as np
 
-from probnum._randomvariablelist import _RandomVariableList
-from probnum.filtsmooth.filtsmoothposterior import FiltSmoothPosterior
 import probnum.random_variables as rvs
 from probnum import utils
+from probnum._randomvariablelist import _RandomVariableList
+from probnum.filtsmooth.filtsmoothposterior import FiltSmoothPosterior
 
 
 class KalmanPosterior(FiltSmoothPosterior):

src/probnum/filtsmooth/gaussfiltsmooth/unscentedkalman.py

@@ -11,15 +11,15 @@
     GaussFiltSmooth,
     linear_discrete_update,
 )
-from probnum.random_variables import Normal
 from probnum.filtsmooth.gaussfiltsmooth.unscentedtransform import UnscentedTransform
 from probnum.filtsmooth.statespace import (
     ContinuousModel,
+    DiscreteGaussianLinearModel,
+    DiscreteGaussianModel,
     DiscreteModel,
     LinearSDEModel,
-    DiscreteGaussianModel,
-    DiscreteGaussianLinearModel,
 )
+from probnum.random_variables import Normal
 
 
 class UnscentedKalman(GaussFiltSmooth):

src/probnum/filtsmooth/gaussfiltsmooth/unscentedtransform.py

@@ -5,7 +5,6 @@
 
 import numpy as np
 
-
 __all__ = ["UnscentedTransform"]
 
 

src/probnum/filtsmooth/statespace/continuous/__init__.py

@@ -7,7 +7,7 @@
 Local import, because with a global import this does not seem
 to work.
 """
-from .linearsdemodel import *
 from .continuousmodel import *
+from .linearsdemodel import *
 
 __all__ = ["ContinuousModel", "LinearSDEModel", "LTISDEModel"]

src/probnum/filtsmooth/statespace/continuous/linearsdemodel.py

@@ -9,6 +9,7 @@
 
 import numpy as np
 import scipy.linalg
+
 from probnum.filtsmooth.statespace.continuous import continuousmodel
 from probnum.random_variables import Normal
 

src/probnum/filtsmooth/statespace/discrete/__init__.py

@@ -7,9 +7,8 @@
 Local import, because with a global import this does not seem
 to work.
 """
-from .discretemodel import *
 from .discretegaussianmodel import *
-
+from .discretemodel import *
 
 __all__ = [
     "DiscreteModel",

src/probnum/filtsmooth/statespace/discrete/discretegaussianmodel.py

@@ -3,9 +3,8 @@
 x_{i+1} = N(g(i, x_i), S(i))
 """
 
-from probnum.random_variables import Normal
 from probnum.filtsmooth.statespace.discrete import discretemodel
-
+from probnum.random_variables import Normal
 
 __all__ = [
     "DiscreteGaussianModel",

src/probnum/filtsmooth/statespace/transition.py

@@ -1,13 +1,12 @@
 """Markov transition rules: continuous and discrete."""
 
 import abc
-from typing import Union, Dict
+from typing import Dict, Union
 
 import numpy as np
 
 from probnum.random_variables import RandomVariable
 
-
 __all__ = ["Transition"]
 
 

src/probnum/linalg/linearsolvers/linearsolvers.py

@@ -13,8 +13,8 @@
 import scipy.sparse
 
 import probnum
-from probnum.linalg import linops
 from probnum import utils
+from probnum.linalg import linops
 from probnum.linalg.linearsolvers.matrixbased import (
     AsymmetricMatrixBasedSolver,
     NoisySymmetricMatrixBasedSolver,

src/probnum/linalg/linearsolvers/matrixbased.py

@@ -4,11 +4,11 @@
 Implementations of matrix-based linear solvers which perform inference on the matrix or
 its inverse given linear observations.
 """
-import warnings
 import abc
+import warnings
 
-import numpy as np
 import GPy
+import numpy as np
 
 import probnum
 from probnum import random_variables as rvs

src/probnum/linalg/linearsolvers/solutionbased.py

@@ -6,6 +6,7 @@
 """
 
 import warnings
+
 import numpy as np
 
 from probnum.linalg.linearsolvers.matrixbased import ProbabilisticLinearSolver

src/probnum/linalg/linops/__init__.py

@@ -6,8 +6,8 @@
 linear operator as a matrix in memory.
 """
 
-from probnum.linalg.linops.linearoperators import *
 from probnum.linalg.linops.kronecker import *
+from probnum.linalg.linops.linearoperators import *
 
 # Public classes and functions. Order is reflected in documentation.
 __all__ = [

src/probnum/quad/__init__.py

@@ -8,9 +8,9 @@
 model and using its predictions to adaptively choose points to evaluate the integrand.
 """
 
-from probnum.quad.quadrature import *
 from probnum.quad.bayesian import *
 from probnum.quad.polynomial import *
+from probnum.quad.quadrature import *
 
 # Public classes and functions. Order is reflected in documentation.
 __all__ = [