Merge pull request #150 from nathanaelbosch/pylint

Code Linting with Pylint

.github/workflows/black.yml → .github/workflows/linting.yml

@@ -12,4 +12,12 @@ jobs:
         run: pip install tox
       - name: Run black through tox
         run: tox -e black
-
+  pylint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - name: Install tox
+        run: pip install tox
+      - name: Run pylint through tox
+        run: tox -e pylint

benchmarks/__init__.py

@@ -1 +0,0 @@
-

pyproject.toml

@@ -20,4 +20,36 @@ exclude = '''
   | build
   | dist
 )/
-'''
+'''
+
+
+[tool.pylint.messages_control]
+# Exceptions suggested from Black: bad-continuation, bad-whitespace
+disable = """
+bad-continuation,
+bad-whitespace,
+
+invalid-name,
+
+no-else-return,
+no-else-raise,
+"""
+# Many more `disable`s are defined in `./tox.ini` on a per-module basis!
+
+[tool.pylint.format]
+max-line-length = "88"
+
+[tool.pylint.master]
+extension-pkg-whitelist = "numpy"
+# Extensions that might be of interest in the future:
+# pylint.extensions.docstyle,
+# pylint.extensions.check_elif,
+# pylint.extensions.docparams,
+load-plugins = """
+pylint.extensions.mccabe,
+pylint.extensions.redefined_variable_type,
+pylint.extensions.overlapping_exceptions,
+"""
+
+[tool.pylint.design]
+max-complexity = "14"

src/probnum/__init__.py

@@ -22,6 +22,7 @@
 diffeq
     Probabilistic solvers for ordinary differential equations.
 """
+# pylint: disable=wrong-import-order
 
 from . import diffeq
 from . import filtsmooth

src/probnum/diffeq/__init__.py

@@ -1,6 +1,3 @@
-"""
-"""
-
 from .ode import *
 from .odefiltsmooth import *
 from .steprule import *
@@ -30,7 +27,8 @@
     "ODESolution",
 ]
 
-# Set correct module paths (for superclasses). Corrects links and module paths in documentation.
+# Set correct module paths (for superclasses).
+# Corrects links and module paths in documentation.
 ODE.__module__ = "probnum.diffeq"
 ODESolver.__module__ = "probnum.diffeq"
 StepRule.__module__ = "probnum.diffeq"

src/probnum/diffeq/ode/__init__.py

@@ -1,6 +1,3 @@
-"""
-"""
-
 from .ivp import *
 from .ode import *
 

src/probnum/diffeq/ode/ivp.py

@@ -4,6 +4,7 @@
 there might be more ode-based problems,
 such as bvp.
 """
+# pylint: disable=unused-variable
 
 import numpy as np
 
@@ -284,8 +285,7 @@ class IVP(ODE):
     """
 
     def __init__(self, timespan, initrv, rhs, jac=None, hess=None, sol=None):
-        """
-        """
+
         self.initrv = initrv
         super().__init__(timespan=timespan, rhs=rhs, jac=jac, hess=hess, sol=sol)
 

src/probnum/diffeq/ode/ode.py

@@ -102,7 +102,7 @@ def hessian(self, t, y, **kwargs):
         since for any directions :math:`v_1, v_2` the outcome of
         :math:`H_f(t_0, y_0) \\cdot v_1 \\cdot v_2` is expected to contain
         the incline of :math:`f_i` in direction :math:`(v_1, v_2)`.
-        """
+        """  # pylint: disable=line-too-long
         if self._hess is None:
             raise NotImplementedError
         else:

src/probnum/diffeq/odefiltsmooth/ivp2filter.py

@@ -4,7 +4,8 @@
 """
 
 import numpy as np
-from probnum.filtsmooth import *
+
+from probnum.filtsmooth import ExtendedKalman, UnscentedKalman
 from probnum.filtsmooth.statespace.discrete import DiscreteGaussianModel
 from probnum.prob import RandomVariable
 from probnum.prob.distributions import Normal, Dirac
@@ -14,19 +15,19 @@ def ivp2ekf0(ivp, prior, evlvar):
     """
     Computes measurement model and initial distribution
     for KF based on IVP and prior.
-    
+
     **Initialdistribution:**
 
     Conditions the initial distribution of the Gaussian filter
     onto the initial values.
 
     - If preconditioning is set to ``False``, it conditions
-      the initial distribution :math:`\mathcal{N}(0, I)`
+      the initial distribution :math:`\\mathcal{N}(0, I)`
       on the initial values :math:`(x_0, f(t_0, x_0), ...)` using
       as many available deri    vatives as possible.
 
     - If preconditioning is set to ``True``, it conditions
-      the initial distribution :math:`\mathcal{N}(0, P P^\\top)`
+      the initial distribution :math:`\\mathcal{N}(0, P P^\\top)`
       on the initial values :math:`(x_0, f(t_0, x_0), ...)` using
       as many available derivatives as possible.
       Note that the projection matrices :math:`H_0` and :math:`H_1`
@@ -35,7 +36,7 @@ def ivp2ekf0(ivp, prior, evlvar):
 
     **Measurement model:**
 
-    Returns a measurement model :math:`\mathcal{N}(g(m), R)`
+    Returns a measurement model :math:`\\mathcal{N}(g(m), R)`
     involving computing the discrepancy
 
     .. math:: g(m) = H_1 m(t) - f(t, H_0 m(t)).
@@ -51,7 +52,7 @@ def ivp2ekf0(ivp, prior, evlvar):
     model, :math:`H_0` and :math:`H_1`
     become :math:`H_0 P^{-1}` and :math:`H_1 P^{-1}` which has
     to be taken into account. In this case,
-    
+
     - EKF0 thinks :math:`J_g(m) = H_1 P^{-1}`
     - EKF1 thinks :math:`J_g(m) = H_1 P^{-1} - J_f(t, H_0  P^{-1} m(t)) (H_0 P^{-1})^\\top`
     - UKF again thinks: ''What is a Jacobian?''
@@ -65,7 +66,7 @@ def ivp2ekf0(ivp, prior, evlvar):
 
     evlvar : float,
         measurement variance; in the literature, this is "R"
-    """
+    """  # pylint: disable=line-too-long
     measmod = _measmod_ekf0(ivp, prior, evlvar)
     initrv = _initialdistribution(ivp, prior)
     return ExtendedKalman(prior, measmod, initrv)
@@ -143,8 +144,7 @@ def ivp2ukf(ivp, prior, evlvar):
 
 
 def _measmod_ukf(ivp, prior, measvar):
-    """
-    """
+
     spatialdim = prior.spatialdim
     h0 = prior.proj2coord(coord=0)
     h1 = prior.proj2coord(coord=1)
@@ -160,7 +160,7 @@ def diff(t, **kwargs):
 
 def _initialdistribution(ivp, prior):
     """
-    Conditions initialdistribution :math:`\mathcal{N}(0, P P^\\top)`
+    Conditions initialdistribution :math:`\\mathcal{N}(0, P P^\\top)`
     on the initial values :math:`(x_0, f(t_0, x_0), ...)` using
     as many available derivatives as possible.
 
@@ -203,7 +203,7 @@ def _initialdistribution(ivp, prior):
 
 
 def _initialdistribution_no_precond(ivp, prior):
-    """ """
+
     x0 = ivp.initialdistribution.mean()
     dx0 = ivp.rhs(ivp.t0, x0)
     ddx0 = _ddx(ivp.t0, x0, ivp)

src/probnum/diffeq/odefiltsmooth/ivpfiltsmooth.py

@@ -5,7 +5,6 @@
 from probnum.prob.distributions import Normal
 from probnum.diffeq import odesolver
 from probnum.diffeq.odefiltsmooth.prior import ODEPrior
-from probnum.filtsmooth import *
 from probnum.diffeq.odesolution import ODESolution
 
 
@@ -172,5 +171,4 @@ def _suggest_step(self, step, errorest):
 
     @property
     def prior(self):
-        """ """
         return self.gfilt.dynamicmodel

src/probnum/diffeq/odefiltsmooth/odefiltsmooth.py

@@ -255,7 +255,7 @@ def _create_solver_object(
 
 
 def _check_step_tol(step, tol):
-    """ """
+
     both_none = tol is None and step is None
     both_not_none = tol is not None and step is not None
     if both_none or both_not_none:
@@ -264,14 +264,13 @@ def _check_step_tol(step, tol):
 
 
 def _check_method(method):
-    """ """
+
     if method not in ["ekf0", "ekf1", "ukf", "eks0", "eks1", "uks"]:
         raise ValueError("Method not supported.")
 
 
 def _string2prior(ivp, which_prior, precond_step, **kwargs):
-    """
-    """
+
     ibm_family = ["ibm1", "ibm2", "ibm3", "ibm4"]
     ioup_family = ["ioup1", "ioup2", "ioup3", "ioup4"]
     matern_family = ["matern32", "matern52", "matern72", "matern92"]
@@ -286,8 +285,7 @@ def _string2prior(ivp, which_prior, precond_step, **kwargs):
 
 
 def _string2ibm(ivp, which_prior, precond_step, **kwargs):
-    """
-    """
+
     if "diffconst" in kwargs.keys():
         diffconst = kwargs["diffconst"]
     else:
@@ -305,8 +303,7 @@ def _string2ibm(ivp, which_prior, precond_step, **kwargs):
 
 
 def _string2ioup(ivp, which_prior, precond_step, **kwargs):
-    """
-    """
+
     if "diffconst" in kwargs.keys():
         diffconst = kwargs["diffconst"]
     else:
@@ -328,8 +325,7 @@ def _string2ioup(ivp, which_prior, precond_step, **kwargs):
 
 
 def _string2matern(ivp, which_prior, precond_step, **kwargs):
-    """
-    """
+
     if "diffconst" in kwargs.keys():
         diffconst = kwargs["diffconst"]
     else:
@@ -351,17 +347,16 @@ def _string2matern(ivp, which_prior, precond_step, **kwargs):
 
 
 def _string2filter(_ivp, _prior, _method, **kwargs):
-    """
-    """
+
     if "evlvar" in kwargs.keys():
         evlvar = kwargs["evlvar"]
     else:
         evlvar = 0.0
-    if _method == "ekf0" or _method == "eks0":
+    if _method in ("ekf0", "eks0"):
         return ivp2filter.ivp2ekf0(_ivp, _prior, evlvar)
-    elif _method == "ekf1" or _method == "eks1":
+    elif _method in ("ekf1", "eks1"):
         return ivp2filter.ivp2ekf1(_ivp, _prior, evlvar)
-    elif _method == "ukf" or _method == "uks":
+    elif _method in ("ukf", "uks"):
         return ivp2filter.ivp2ukf(_ivp, _prior, evlvar)
     else:
         raise ValueError("Type of filter not supported.")

src/probnum/diffeq/odefiltsmooth/prior.py

@@ -42,7 +42,7 @@ class ODEPrior(LTISDEModel):
     matrix that maps to filtering iteration to the Nordsieck vector,
 
     .. math:: P = \\text{diag }(1, h, h^2, ..., h^q).
-    
+
     Here, :math:`h` is some expected average step size. Note that we
     ignored the factorials in this matrix. Our setting makes it easy to
     recover "no preconditioning" by choosing :math:`h=1`.
@@ -78,7 +78,6 @@ class ODEPrior(LTISDEModel):
     """
 
     def __init__(self, driftmat, dispmat, ordint, spatialdim, precond_step=1.0):
-        """ """
         self.ordint = ordint
         self.spatialdim = spatialdim
         self.precond, self.invprecond = self.precond2nordsieck(precond_step)
@@ -283,7 +282,8 @@ def _trans_ibm(self, start, stop):
         step = stop - start
 
         # This seems like the faster solution compared to fully vectorising.
-        # I suspect it is because np.math.factorial is much faster than scipy.special.factorial
+        # I suspect it is because np.math.factorial is much faster than
+        # scipy.special.factorial
         ah_1d = np.diag(np.ones(self.ordint + 1), 0)
         for i in range(self.ordint):
             offdiagonal = (
@@ -394,7 +394,7 @@ def _driftmat_matern(ordint, spatialdim, lengthscale):
 
 def _dispmat(ordint, spatialdim, diffconst):
     """
-    Returns I_D \otimes L
+    Returns I_D \\otimes L
     diffconst = sigma**2
     """
     dispvec = diffconst * np.eye(ordint + 1)[:, -1]

src/probnum/diffeq/steprule.py

@@ -88,7 +88,4 @@ def suggest(self, laststep, errorest, **kwargs):
         return step
 
     def is_accepted(self, proposedstep, errorest, **kwargs):
-        if errorest * proposedstep < self.tol_per_step:
-            return True
-        else:
-            return False
+        return errorest * proposedstep < self.tol_per_step