Merge remote-tracking branch 'origin/issue_0093-add-lint-at-the-actio…

…ns' into issue_0128-adapt-cells-per-wavelength-calculator-for-elastic-elements

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Run lint
+
+on:
+  # Push to master or PR
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  linter:
+    name: "Run linter"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+      - name: Setup flake8 annotations
+        uses: rbialon/flake8-annotations@v1
+      - name: Install linter
+        run: |
+          pip install flake8 pylint
+      - name: Lint codebase
+        run: |
+          make lint GITHUB_ACTIONS_FORMATTING=1

Makefile

@@ -25,13 +25,7 @@ clean:
 	@rm -rf dist/
 
 format:
-	isort -rc spyro/ test/*.py
-	black spyro/ test/*.py
-
-black:
-	black .
+	autopep8 --in-place --global-config setup.cfg --recursive .
 
 lint:
-	isort --check . spyro/ setup.py test/*.py
-	black --check spyro/ setup.py test/*.py
 	flake8 setup.py spyro/ test/*.py

demos/with_automatic_differentiation/run_forward_ad.py

@@ -1,7 +1,7 @@
 import firedrake as fire
 import spyro
 from demos.with_automatic_differentiation.utils import \
-      model_settings, make_c_camembert
+    model_settings, make_c_camembert
 import os
 os.environ["OMP_NUM_THREADS"] = "1"
 
@@ -16,7 +16,7 @@
 element = fire.FiniteElement(
     model["opts"]["method"], mesh.ufl_cell(), degree=model["opts"]["degree"],
     variant=model["opts"]["quadrature"]
-    )
+)
 V = fire.FunctionSpace(mesh, element)
 
 
@@ -43,4 +43,4 @@
     sol = forward_solver.solution
     fire.VTKFile(
         "solution_" + str(source_number) + ".pvd", comm=my_ensemble.comm
-        ).write(sol)
+    ).write(sol)

demos/with_automatic_differentiation/run_fwi_ad.py

@@ -65,7 +65,7 @@ def forward(
         sol = forward_solver.solution
         fire.VTKFile(
             "solution_" + str(source_number) + ".pvd", comm=my_ensemble.comm
-            ).write(sol)
+        ).write(sol)
 
     return receiver_data, J
 
@@ -77,7 +77,7 @@ def forward(
 element = fire.FiniteElement(
     model["opts"]["method"], mesh.ufl_cell(), degree=model["opts"]["degree"],
     variant=model["opts"]["quadrature"]
-    )
+)
 V = fire.FunctionSpace(mesh, element)
 
 
@@ -97,7 +97,7 @@ def forward(
 guess_rec, J = forward(
     c_guess, compute_functional=True, true_data_receivers=true_rec,
     annotate=True
-    )
+)
 
 # :class:`~.EnsembleReducedFunctional` is employed to recompute in
 # parallel the functional and its gradient associated with the multiple sources

demos/with_automatic_differentiation/utils.py

@@ -2,6 +2,7 @@
 import firedrake as fire
 import spyro
 
+
 def model_settings():
     """Model settings for forward and Full Waveform Inversion (FWI)
     simulations.
@@ -29,7 +30,7 @@ def model_settings():
         # None - no shots parallelism.
         "type": "shots_parallelism",
         "num_spacial_cores": 1,  # Number of cores to use in the spatial
-                                # parallelism.
+        # parallelism.
     }
 
     # Define the domain size without the ABL.

setup.cfg

@@ -3,5 +3,10 @@ ignore =
     E501,F403,F405,E226,E402,E721,E731,E741,W503,F999,
     N801,N802,N803,N806,N807,N811,N813,N814,N815,N816
 exclude = .git,__pycache__
+
 [coverage:run]
 omit=*/site-packages/*,*/test/*,*/.eggs/*,/home/alexandre/firedrake/*
+
+[pep8]
+ignore = E501,E226,E731,E741,W503
+exclude = .git,__pycache__

spyro/domains/space.py

@@ -40,6 +40,6 @@ def FE_method(mesh, method, degree, dim=1):
 
     if dim > 1:
         element = VectorElement(element, dim=dim)
-    
+
     function_space = FunctionSpace(mesh, element)
     return function_space

spyro/examples/camembert_elastic.py

@@ -6,33 +6,33 @@
 import numpy as np
 import spyro
 
-L = 500 # [m]
+L = 500  # [m]
 
 rho = 7850          # [kg/m3]
 lambda_in = 6.86e9  # [Pa]
-lambda_out = 9.88e9 # [Pa]
+lambda_out = 9.88e9  # [Pa]
 mu_in = 3.86e9      # [Pa]
 mu_out = 5.86e9     # [Pa]
 
 smag = 1e6
-freq = 2 # Central frequency of Ricker wavelet [Hz]
-hf =  90 # [m]
-hs = 100 # [m]
+freq = 2  # Central frequency of Ricker wavelet [Hz]
+hf = 90  # [m]
+hs = 100  # [m]
 source_locations = spyro.create_transect((-hf, 0.2*L), (-hf, 0.8*L), 3)
 receiver_locations = spyro.create_transect((-hs, 0), (-hs, L), 40)
 source_locations = [[-hf, 0.5*L]]
 
-time_step = 2e-4 # [s]
-final_time = 1.5 # [s]
+time_step = 2e-4  # [s]
+final_time = 1.5  # [s]
 out_freq = int(0.01/time_step)
 
 n = 20
 mesh = fire.RectangleMesh(n, n, 0, L, originX=-L, diagonal='crossed')
 z, x = fire.SpatialCoordinate(mesh)
 
-zc = 250 # [m]
-xc = 250 # [m]
-ri =  50 # [m]
+zc = 250  # [m]
+xc = 250  # [m]
+ri = 50  # [m]
 camembert = lambda v_inside, v_outside: fire.conditional(
     (z - zc) ** 2 + (x - xc) ** 2 < ri**2, v_inside, v_outside)
 
@@ -60,8 +60,8 @@
     "delay": 0,
     "delay_type": "time",
     "amplitude": np.array([0, smag]),
-    #"amplitude": smag * np.eye(2),
-    #"amplitude": smag * np.array([[0, 1], [-1, 0]]),
+    # "amplitude": smag * np.eye(2),
+    # "amplitude": smag * np.array([[0, 1], [-1, 0]]),
     "receiver_locations": receiver_locations,
 }
 

spyro/examples/cut_marmousi.py

@@ -114,6 +114,7 @@ class Cut_marmousi_acoustic(Example_model_acoustic):
         Dictionary with the parameters of the model that are different from
         the default model. The default is None.
     """
+
     def __init__(
         self,
         dictionary=None,

spyro/examples/elastic_cube_3D.py

@@ -9,11 +9,11 @@
 N = 5      # Number of elements in each direction
 h = L/N    # Element size [m]
 
-c_p = 5000 # P-wave velocity [m/s]
-c_s = 2500 # S-wave velocity [m/s]
-rho = 1000 # Density [kg/m3]
+c_p = 5000  # P-wave velocity [m/s]
+c_s = 2500  # S-wave velocity [m/s]
+rho = 1000  # Density [kg/m3]
 
-smag = 1e9 # Source magnitude
+smag = 1e9  # Source magnitude
 freq = 1   # Source frequency [Hz]
 
 final_time = 2

spyro/examples/marmousi.py

@@ -122,6 +122,7 @@ class Marmousi_acoustic(Example_model_acoustic):
         Dictionary with the parameters of the model that are different from
         the default model. The default is None.
     """
+
     def __init__(
         self,
         dictionary=None,

spyro/examples/rectangle.py

@@ -121,6 +121,7 @@ class Rectangle_acoustic(Example_model_acoustic):
         If True, the mesh will be periodic in all directions. The default is
         False.
     """
+
     def __init__(
         self,
         dictionary=None,

spyro/io/dictionaryio.py

@@ -526,7 +526,6 @@ def get_mesh_type(self):
 
     def _derive_mesh_type(self):
         dictionary = self.mesh_dictionary
-        user_mesh_in_dictionary = False
         if "user_mesh" not in dictionary:
             dictionary["user_mesh"] = None
 

spyro/io/field_logger.py

@@ -4,15 +4,17 @@
 
 from .basicio import parallel_print
 
+
 class Field:
     def __init__(self, name, file, callback):
         self.name = name
         self.file = file
         self.callback = callback
-    
+
     def write(self, t):
         self.file.write(self.callback(), time=t, name=self.name)
 
+
 class FieldLogger:
     def __init__(self, comm, vis_dict):
         self.comm = comm
@@ -21,14 +23,14 @@ def __init__(self, comm, vis_dict):
         self.__source_id = None
         self.__enabled_fields = []
         self.__wave_data = []
-    
+
     def add_field(self, key, name, callback):
         self.__wave_data.append((key, name, callback))
-    
+
     def start_logging(self, source_id):
-        if self.__source_id != None:
+        if self.__source_id is not None:
             warnings.warn("Started a new record without stopping the previous one")
-        
+
         self.__source_id = source_id
         self.__enabled_fields = []
         for key, name, callback in self.__wave_data:
@@ -42,10 +44,10 @@ def start_logging(self, source_id):
 
                 file = VTKFile(filename, comm=self.comm.comm)
                 self.__enabled_fields.append(Field(name, file, callback))
-    
+
     def stop_logging(self):
         self.__source_id = None
-    
+
     def log(self, t):
         for field in self.__enabled_fields:
-            field.write(t)
+            field.write(t)

spyro/io/model_parameters.py

@@ -570,9 +570,9 @@ def _sanitize_optimization_and_velocity(self):
             if "velocity_conditional" not in dictionary["synthetic_data"]:
                 self.velocity_model_type = None
                 warnings.warn(
-                    "No velocity model set initially. If using " \
-                        "user defined conditional or expression, please " \
-                            "input it in the Wave object."
+                    "No velocity model set initially. If using "
+                    "user defined conditional or expression, please "
+                    "input it in the Wave object."
                 )
 
         if "velocity_conditional" in dictionary["synthetic_data"]:
@@ -599,7 +599,7 @@ def _sanitize_optimization_and_velocity_for_fwi(self):
         else:
             default_optimization_parameters = {
                 "General": {"Secant": {"Type": "Limited-Memory BFGS",
-                    "Maximum Storage": 10}},
+                                       "Maximum Storage": 10}},
                 "Step": {
                     "Type": "Augmented Lagrangian",
                     "Augmented Lagrangian": {

spyro/meshing/__init__.py

@@ -1,6 +1,6 @@
-from .meshing_functions import RectangleMesh
-from .meshing_functions import PeriodicRectangleMesh, BoxMesh
-from .meshing_functions import AutomaticMesh
+from .meshing_functions import RectangleMesh  # noqa: F401
+from .meshing_functions import PeriodicRectangleMesh, BoxMesh  # noqa: F401
+from .meshing_functions import AutomaticMesh  # noqa: F401
 
 all = [
     "RectangleMesh",