Migrate to ruff (#475)

* Switched from flakeheaven to ruff as linter

* Changed docs to now use ruff instead of flakeheaven

* Skip other jobs in CI (revert once change is finished)

* Corrected linting error about not chaning exceptions (B904)

* Corrected linting error about assigning names to lambdas (E731)

* Corrected issue with true-fals-comparisons

* Corrected tests if not member (E713)

* Corrected accessing attributes without assigning them (B018)

* Readded all Tests from CI

* Corrected empty lines with whitespaces (W293)

* Removed trailing whitespaces (W291)

* Corrected comparison to None (E711)

* Forgot to add linebreaks when corrected lambdas

.github/workflows/ci_pipeline.yml

@@ -25,13 +25,13 @@ jobs:
         with:
           environment-file: ${{ env.YML }}
           create-args: >-
-              python=3.10
+              python=3.12
       - name: Code reformatting with black
         run: |
           black pySDC  --check --diff --color
-      - name: Linting with flakeheaven
+      - name: Linting with ruff
         run: |
-          flakeheaven lint --benchmark pySDC
+          ruff check pySDC
 
   user_cpu_tests_linux:
     runs-on: ubuntu-latest

docs/contrib/02_continuous_integration.md

@@ -6,17 +6,17 @@ Finally, the CI also build artifacts that are used to generate the documentation
 
 ## Code linting
 
-Code style linting is performed using [black](https://black.readthedocs.io/en/stable/) and [flakeheaven](https://flakeheaven.readthedocs.io/en/latest/) for code syntax checking. In particular, `black` is used to check compliance with (most of) [PEP-8 guidelines](https://peps.python.org/pep-0008/).
+Code style linting is performed using [black](https://black.readthedocs.io/en/stable/) and [ruff](https://docs.astral.sh/ruff/) for code syntax checking. In particular, `black` is used to check compliance with (most of) [PEP-8 guidelines](https://peps.python.org/pep-0008/).
 
 Those tests are conducted for each commit (even for forks), but you can also run it locally in the root folder of `pySDC` before pushing any commit :
 
 ```bash
 # Install required packages (works also with conda/mamba)
-pip install black flakeheaven flake8-comprehensions flake8-bugbear
+pip install black ruff
 # First : test code style linting with black
 black pySDC --check --diff --color
-# Second : test code syntax with flakeheaven
-flakeheaven lint --benchmark pySDC
+# Second : test code syntax with ruff
+ruff check pySDC
 ```
 
 > :bell: To avoid any error about formatting (`black`), you can simply use this program to reformat your code directly using the command :
@@ -59,7 +59,7 @@ fi
 You may need to run `chmod +x` on the file to allow it to be executed.
 Be aware that the hook will alter files you may have opened in an editor whenever you make a commit, which may confuse you(r editor).
 
-To automate flakeheaven, we want to write a hook that alters the commit message in case any errors are detected. This gives us the choice of aborting the commit and fixing the issues, or we can go ahead and commit them and worry about flakeheaven only when the time comes to do a pull request.
+To automate ruff, we want to write a hook that alters the commit message in case any errors are detected. This gives us the choice of aborting the commit and fixing the issues, or we can go ahead and commit them and worry about ruff only when the time comes to do a pull request.
 To obtain this functionality, add the following to `<pySDC-root-directory>/.git/hooks/prepare-commit-msg`:
 
 ```bash
@@ -71,11 +71,11 @@ export files=$(git diff --staged --name-only HEAD | grep .py | sed -e "s,^,$(git
 
 if [[ $files != "" ]]
 then
-        export flakeheaven_output=$(flakeheaven lint --format default $files)
-        if [[ "$flakeheaven_output" != 0 ]]
+        export ruff_output=$(ruff check --quiet $files)
+        if [[ "$ruff_output" != 0 ]]
         then
-                git interpret-trailers --in-place --trailer "$(echo "$flakeheaven_output" | sed -e 's/^/#/')" "$COMMIT_MSG_FILE"
-                git interpret-trailers --in-place --trailer "#!!!!!!!!!! WARNING: FLAKEHEAVEN FAILED !!!!!!!!!!" "$COMMIT_MSG_FILE"
+                git interpret-trailers --in-place --trailer "$(echo "$ruff_output" | sed -e 's/^/#/')" "$COMMIT_MSG_FILE"
+                git interpret-trailers --in-place --trailer "#!!!!!!!!!! WARNING: RUFF FAILED !!!!!!!!!!" "$COMMIT_MSG_FILE"
         fi
 fi
 

etc/environment-lint.yml

@@ -6,6 +6,4 @@ channels:
   - defaults
 dependencies:
   - black
-  - flakeheaven
-  - flake8-comprehensions
-  - flake8-bugbear
+  - ruff

pySDC/core/collocation.py

@@ -65,7 +65,7 @@ def __init__(self, num_nodes=None, tleft=0, tright=1, node_type='LEGENDRE', quad
                 nNodes=num_nodes, nodeType=node_type, quadType=quad_type, tLeft=tleft, tRight=tright
             )
         except Exception as e:
-            raise CollocationError(f"could not instantiate qmat generator, got error: {e}")
+            raise CollocationError(f"could not instantiate qmat generator, got error: {e}") from e
 
         # Set base attributes
         self.num_nodes = num_nodes

pySDC/core/common.py

@@ -56,8 +56,8 @@ def _makeAttributeAndRegister(self, *names, localVars=None, readOnly=False):
         for name in names:
             try:
                 super().__setattr__(name, localVars[name])
-            except KeyError:  # pragma: no cover
-                raise ValueError(f'value for {name} not given in localVars')
+            except KeyError as e:  # pragma: no cover
+                raise ValueError(f'value for {name} not given in localVars') from e
         # Register as class parameter
         if readOnly:
             self._parNamesReadOnly = self._parNamesReadOnly.union(names)

pySDC/core/sweeper.py

@@ -104,7 +104,7 @@ def setupGenerator(self, qd_type):
                 tLeft=coll.tleft,
             )
         except Exception as e:
-            raise ValueError(f"could not generate {qd_type=!r} with qmat, got error : {e}")
+            raise ValueError(f"could not generate {qd_type=!r} with qmat, got error : {e}") from e
 
     def get_Qdelta_implicit(self, qd_type, k=None):
         QDmat = np.zeros_like(self.coll.Qmat)

pySDC/implementations/hooks/log_solution.py

@@ -84,7 +84,7 @@ class LogToFile(Hooks):
     index associated with individual files by giving a different lambda function ``format_index`` class attribute. This
     lambda should accept one index and return one string.
 
-    You can also give a custom ``logging_condition`` lambda, accepting the current level if you want to log selectively.
+    You can also give a custom ``logging_condition`` function, accepting the current level if you want to log selectively.
 
     Importantly, you may need to change ``process_solution``. By default, this will return a numpy view of the solution.
     Of course, if you are not using numpy, you need to change this. Again, this is a lambda accepting the level.
@@ -99,9 +99,15 @@ class LogToFile(Hooks):
 
     path = None
     file_name = 'solution'
-    logging_condition = lambda L: True
-    process_solution = lambda L: {'t': L.time + L.dt, 'u': L.uend.view(np.ndarray)}
-    format_index = lambda index: f'{index:06d}'
+
+    def logging_condition(L):
+        return True
+
+    def process_solution(L):
+        return {'t': L.time + L.dt, 'u': L.uend.view(np.ndarray)}
+
+    def format_index(index):
+        return f'{index:06d}'
 
     def __init__(self):
         super().__init__()

pySDC/implementations/problem_classes/Battery.py

@@ -163,7 +163,7 @@ def eval_f(self, u, t):
         else:
             # proof all switching conditions and find largest index where it drops below V_ref
             switch = [True if u[k] <= self.V_ref[k - 1] else False for k in range(1, len(u))]
-            max_index = max([k if switch[k] == True else -1 for k in range(len(switch))])
+            max_index = max([k if switch[k] else -1 for k in range(len(switch))])
 
             if max_index == -1:
                 f.expl[:] = self.switch_f[0]
@@ -200,7 +200,7 @@ def solve_system(self, rhs, factor, u0, t):
         else:
             # proof all switching conditions and find largest index where it drops below V_ref
             switch = [True if rhs[k] <= self.V_ref[k - 1] else False for k in range(1, len(rhs))]
-            max_index = max([k if switch[k] == True else -1 for k in range(len(switch))])
+            max_index = max([k if switch[k] else -1 for k in range(len(switch))])
             if max_index == -1:
                 self.A = self.switch_A[0]
 

pySDC/implementations/problem_classes/HeatEquation_ND_FD_CuPy.py

@@ -86,9 +86,9 @@ def __init__(
         """Initialization routine"""
 
         # make sure parameters have the correct types
-        if not type(nvars) in [int, tuple]:
+        if type(nvars) not in [int, tuple]:
             raise ProblemError('nvars should be either tuple or int')
-        if not type(freq) in [int, tuple]:
+        if type(freq) not in [int, tuple]:
             raise ProblemError('freq should be either tuple or int')
 
         # transforms nvars into a tuple

pySDC/implementations/problem_classes/PenningTrap_3D.py

@@ -172,7 +172,7 @@ def eval_f(self, part, t):
 
         self.work_counters['rhs']()
         try:
-            penningtrap.Harmonic_oscillator
+            _unused = penningtrap.Harmonic_oscillator
             Emat = np.diag([0, 0, -1])
         except AttributeError:
             Emat = np.diag([1, 1, -2])

pySDC/implementations/problem_classes/generic_ND_FD.py

@@ -95,9 +95,9 @@ def __init__(
         bcParams=None,
     ):
         # make sure parameters have the correct types
-        if not type(nvars) in [int, tuple]:
+        if type(nvars) not in [int, tuple]:
             raise ProblemError('nvars should be either tuple or int')
-        if not type(freq) in [int, tuple]:
+        if type(freq) not in [int, tuple]:
             raise ProblemError('freq should be either tuple or int')
 
         # transforms nvars into a tuple

pySDC/projects/DAE/sweepers/rungeKuttaDAE.py

@@ -15,7 +15,7 @@ class RungeKuttaDAE(RungeKutta):
 
     .. math::
         0 = F(u, u', t).
-    
+
     RK methods for general DAEs have the form
 
     .. math::

pySDC/projects/DAE/sweepers/semiImplicitDAE.py

@@ -26,7 +26,7 @@ class SemiImplicitDAE(FullyImplicitDAE):
         0 = g(\vec{U}_0 + \Delta t (\mathbf{Q} \otimes \mathbf{I}_{n_d}) \vec{U}, \vec{z}, \tau),
 
     where
-    
+
     - :math:`\tau=(\tau_1,..,\tau_M) in \mathbb{R}^M` the vector of collocation nodes,
     - :math:`\vec{U}_0 = (u_0,..,u_0) \in \mathbb{R}^{MN_d}` the vector of initial condition spread to each node,
     - spectral integration matrix :math:`\mathbf{Q} \in \mathbb{R}^{M \times M}`,

pySDC/projects/Monodomain/problem_classes/TestODE.py

@@ -6,9 +6,9 @@
 from pySDC.projects.Monodomain.datatype_classes.my_mesh import imexexp_mesh
 
 
-""" 
+"""
 Here we define the problems classes for the multirate Dahlquist test equation y'=lambda_I*y + lambda_E*y + lambda_e*y
-Things are done so that it is compatible witht the sweepers. 
+Things are done so that it is compatible witht the sweepers.
 """
 
 

pySDC/projects/Monodomain/run_scripts/run_TestODE.py

@@ -19,7 +19,7 @@
 )
 from pySDC.projects.Monodomain.sweeper_classes.runge_kutta.imexexp_1st_order import imexexp_1st_order
 
-""" 
+"""
 Run the multirate Dahlquist test equation and plot the stability domain of the method.
 We vary only the exponential term and the stiff term, while the non stiff term is kept constant (to allow 2D plots).
 """

pySDC/projects/PinTSimE/hardcoded_solutions.py

@@ -475,9 +475,9 @@ def testSolution(u_num, prob_cls_name, dt, use_adaptivity, use_detection):
         if key == 't_switches' or key == 'e_event':
             err_msg = f'{msg} Expected {key}={expected[key]}, got {key}={got[key]}'
             if len(expected[key]) == got[key]:
-                assert np.allclose(expected[key], got[key], atol=1e-4) == True, err_msg
+                assert np.allclose(expected[key], got[key], atol=1e-4), err_msg
             else:
-                assert np.isclose(expected[key][-1], got[key][-1], atol=1e-4) == True, err_msg
+                assert np.isclose(expected[key][-1], got[key][-1], atol=1e-4), err_msg
         else:
             err_msg = f'{msg} Expected {key}={expected[key]:.4e}, got {key}={got[key]:.4e}'
             assert np.isclose(expected[key], got[key], atol=1e-4), err_msg

pySDC/projects/PinTSimE/switch_estimator.py

@@ -297,7 +297,9 @@ def get_switch(t_interp, state_function, m_guess):
         """
 
         LagrangeInterpolation = LagrangeApproximation(points=t_interp, fValues=state_function)
-        p = lambda t: LagrangeInterpolation.__call__(t)
+
+        def p(t):
+            return LagrangeInterpolation.__call__(t)
 
         def fprime(t):
             r"""

pySDC/projects/Resilience/fault_injection.py

@@ -55,7 +55,7 @@ def __init__(self, params=None):
         for k, v in params.items():
             setattr(self, k, v)
 
-        self._freeze
+        self._freeze()
 
     @classmethod
     def random(cls, args, rnd_params, random_generator=None):

pySDC/projects/Second_orderSDC/penningtrap_HookClass.py

@@ -41,7 +41,7 @@ def post_step(self, step, level_number):
         #
 
         try:  # pragma: no cover
-            L.prob.Harmonic_oscillator
+            _unused = L.prob.Harmonic_oscillator
 
             # add up kinetic and potntial contributions to total energy
             epot = 0

pySDC/projects/Second_orderSDC/plot_helper.py

@@ -314,7 +314,7 @@ def organize_data(self, filename='data/dt_vs_local_errorSDC.csv', time_iter=None
             filename (string): data to find approximate order
             time_iter : in case it you used different time iterations
         """
-        if time_iter == None:
+        if time_iter is None:
             time_iter = self.time_iter
 
         items = np.genfromtxt(filename, delimiter=',', skip_header=1)

pySDC/tutorial/step_6/C_MPI_parallelization.py

@@ -14,8 +14,8 @@ def main(cwd):
         import mpi4py
 
         del mpi4py
-    except ImportError:
-        raise ImportError('petsc tests need mpi4py')
+    except ImportError as e:
+        raise ImportError('petsc tests need mpi4py') from e
 
     # Set python path once
     my_env = os.environ.copy()

pyproject.toml

@@ -47,9 +47,7 @@ apps = [
     'mpi4py-fft>=2.0.2'
     ]
 dev = [
-    'flakeheaven',
-    'flake8-comprehensions',
-    'flake8-bugbear',
+    'ruff',
     'pytest',
     'pytest-cov',
     'sphinx'
@@ -70,31 +68,35 @@ markers = [
     ]
 timeout = 300
 
-[tool.flakeheaven]
-max-line-length = 120
-per-file-ignores = [
-    'pySDC/tutorial/step_6/C_MPI_parallelization.py:F401',
-    'pySDC/projects/Hamiltonian/solar_system.py:F401'
-    ]
-exclude = [
+[tool.ruff]
+line-length = 120
+extend-exclude = [
     'playgrounds',
     'tests',
     '*/data/*'
     ]
-count = true
-show-source = true
-statistics = true
-
-# list of plugins and rules for them
-[tool.flakeheaven.plugins]
-# include everything in pyflakes except F401
-pyflakes = [
-    '+C*', '+E*', '+F*', '+W*', '+B*', '+B9*',
-    '-E203', '-E741', '-E402', '-W504', '-W605', '-F401'
-    ]
-#flake8-black = ["+*"]
-flake8-bugbear = ["+*", '-B023', '-B028']
-flake8-comprehensions = ["+*", '-C408', '-C417']
+
+[tool.ruff.lint]
+select = ["C", "E", "F", "W", "B"]
+ignore = ["E203", # Whitespace before punctuation
+          "E741", # Ambiguous variable name
+          "E402", # Module level import not at top of cell
+          "W605", # Invalid escape sequence
+          "F401", # unused import
+          "B023", # function uses loop variable
+          "B028", # No excplicit stackvariable
+          "C408", # Unnecessary collection call
+          "C417", # Unnecessary map usage
+          # Newly added
+          "C901", # Complex name
+          "E501", # Line length, as enforced by black, but black ignores comments
+          "E721" # Type comparison
+          ]
+# W504 is not supported by ruff and does not need to be excluded
+
+[tool.ruff.lint.per-file-ignores]
+"pySDC/tutorial/step_6/C_MPI_parallelization.py" = ["F401"]
+"pySDC/projects/Hamiltonian/solar_system.py" = ["F401"]
 
 [tool.black]
 line-length = 120