switch to ruff format

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
 # Clang-format whole repo
 d8f14fdddb5ca0fbb32d8e2bf5ac2960d6ac5ce6
 ed2117e6d6826a98b6988e2f18c0c34e408563b6
+# ruff format whole repo
+289205524393f52634346adcbcf74ea9d00257d5

.github/workflows/black-fix.yml

@@ -28,19 +28,19 @@ jobs:
       run: |
         sudo apt update -y
         sudo apt -y install python3-pip python3-setuptools python3-wheel
-        pip3 install black
+        pip3 install ruff
 
     - name: Version
       run: |
         python3 --version
-        $HOME/.local/bin/black --version
+        $HOME/.local/bin/ruff --version
 
     - name: Run black
       run: |
         pwd
         ls
-        $HOME/.local/bin/black tests/ tools/ $(grep -EIlr '^#!.*python.*$' bin/ tests/ tools/ src/ | grep -v _boutpp_build)
+        $HOME/.local/bin/ruff format .
 
     - uses: stefanzweifel/git-auto-commit-action@v5
       with:
-        commit_message: "Apply black changes"
+        commit_message: "Apply ruff format changes"

.github/workflows/python-package.yml

@@ -22,7 +22,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -62,7 +62,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -111,7 +111,7 @@ jobs:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&

.github/workflows/tests.yml

@@ -172,7 +172,7 @@ jobs:
         with:
           submodules: true
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.x'
 

bin/bout-v5-factory-upgrader.py

@@ -62,9 +62,7 @@ def find_factory_calls(factory, source):
         \s*=\s*
         {factory_name}::
         .*{create_method}.*
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -75,9 +73,7 @@ def find_type_pointers(factory, source):
         r"""
         \b{type_name}\s*\*\s*   # Type name and pointer
         ([\w_]+)\s*;            # Variable name
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -107,9 +103,7 @@ def fix_declarations(factory, variables, source):
             (.*?)(class\s*)?         # optional "class" keyword
             \b({type_name})\s*\*\s*  # Type-pointer
             ({variable_name})\s*;    # Variable
-            """.format(
-                type_name=factory["type_name"], variable_name=variable
-            ),
+            """.format(type_name=factory["type_name"], variable_name=variable),
             r"\1std::unique_ptr<\3> \4{nullptr};",
             source,
             flags=re.VERBOSE,
@@ -123,9 +117,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment from factory
             ({factory_name}::.*{create_method}.*);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1auto \4 = \5;",
             source,
             flags=re.VERBOSE,
@@ -139,9 +131,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment
             (0|nullptr|NULL);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1std::unique_ptr<\2> \3{nullptr};",
             source,
             flags=re.VERBOSE,

bin/bout-v5-xzinterpolation-upgrader.py

@@ -54,9 +54,7 @@ def fix_header_includes(old_header, new_header, source):
         (<|")
         ({header})              # Header name
         (>|")
-        """.format(
-            header=old_header
-        ),
+        """.format(header=old_header),
         r"\1\2{header}\4".format(header=new_header),
         source,
         flags=re.VERBOSE,
@@ -67,9 +65,7 @@ def fix_interpolations(old_interpolation, new_interpolation, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_interpolation
-        ),
+        """.format(old_interpolation),
         r"{}".format(new_interpolation),
         source,
         flags=re.VERBOSE,
@@ -120,9 +116,7 @@ def fix_factories(old_factory, new_factory, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_factory
-        ),
+        """.format(old_factory),
         r"{}".format(new_factory),
         source,
         flags=re.VERBOSE,

examples/blob2d/blob_velocity.py

@@ -3,96 +3,100 @@
 import pickle
 
 try:
-        from past.utils import old_div
+    from past.utils import old_div
 except ImportError:
-        def old_div(a,b):
-                return a/b
 
-
-def blob_velocity(n,**kwargs):
-
-        from boututils import calculus as Calc
-        # Calculate blob velocity in normalized time and normalized grid spacing
-        #
-        # Input: Blob density as a 3D vector in the form  n[t,x,z] where t is time and x,z are the perpendicular spatial coordinates
-        #
-        # Keywords:
-        #
-        #           type='peak' -> Calculate velocity of the peak density
-        #           type='COM' -> Calculate centre of mass velocity
-        #           Index=True -> return indices used to create velocity
-        #
-        # Default: Peak velocity with no index returning
-
-        size = n.shape
-
-        try:
-                v_type = kwargs['type']
-        except:
-                v_type = 'peak'         #Default to peak velocity calculation
-        try:
-                return_index = kwargs['Index']
-        except:
-                return_index = False    #Default to no index returning
-
-
-        if v_type == 'peak':
-                x = np.zeros(size[0])
-                z = np.zeros(size[0])
-                for i in np.arange(size[0]):
-                        nmax,nmin = np.amax((n[i,:,:])),np.amin((n[i,:,:]))
-                        xpos,zpos = np.where(n[i,:,:]==nmax)
-                        x[i] = xpos[0]
-                        z[i] = zpos[0]
-
-        if v_type == 'COM':
-                x = np.zeros(size[0])
-                z = np.zeros(size[0])
-                for i in np.arange(size[0]):
-                        data = n[i,:,:] - n[0,0,0]   #use corner cell rather than nmin
-                        ntot = np.sum(data[:,:])
-
-                        z[i] = old_div(np.sum(np.sum(data[:,:],axis=0)*(np.arange(size[2]))),ntot)
-                        x[i] = old_div(np.sum(np.sum(data[:,:],axis=1)*(np.arange(size[1]))),ntot)
-
-        vx = Calc.deriv(x)
-        vz = Calc.deriv(z)
-
-        if return_index:
-                return vx,vz,x,z
-        else:
-                return vx,vz
-
-
-
-data='data'
+    def old_div(a, b):
+        return a / b
+
+
+def blob_velocity(n, **kwargs):
+    from boututils import calculus as Calc
+    # Calculate blob velocity in normalized time and normalized grid spacing
+    #
+    # Input: Blob density as a 3D vector in the form  n[t,x,z] where t is time and x,z are the perpendicular spatial coordinates
+    #
+    # Keywords:
+    #
+    #           type='peak' -> Calculate velocity of the peak density
+    #           type='COM' -> Calculate centre of mass velocity
+    #           Index=True -> return indices used to create velocity
+    #
+    # Default: Peak velocity with no index returning
+
+    size = n.shape
+
+    try:
+        v_type = kwargs["type"]
+    except:
+        v_type = "peak"  # Default to peak velocity calculation
+    try:
+        return_index = kwargs["Index"]
+    except:
+        return_index = False  # Default to no index returning
+
+    if v_type == "peak":
+        x = np.zeros(size[0])
+        z = np.zeros(size[0])
+        for i in np.arange(size[0]):
+            nmax, nmin = np.amax((n[i, :, :])), np.amin((n[i, :, :]))
+            xpos, zpos = np.where(n[i, :, :] == nmax)
+            x[i] = xpos[0]
+            z[i] = zpos[0]
+
+    if v_type == "COM":
+        x = np.zeros(size[0])
+        z = np.zeros(size[0])
+        for i in np.arange(size[0]):
+            data = n[i, :, :] - n[0, 0, 0]  # use corner cell rather than nmin
+            ntot = np.sum(data[:, :])
+
+            z[i] = old_div(
+                np.sum(np.sum(data[:, :], axis=0) * (np.arange(size[2]))), ntot
+            )
+            x[i] = old_div(
+                np.sum(np.sum(data[:, :], axis=1) * (np.arange(size[1]))), ntot
+            )
+
+    vx = Calc.deriv(x)
+    vz = Calc.deriv(z)
+
+    if return_index:
+        return vx, vz, x, z
+    else:
+        return vx, vz
+
+
+data = "data"
 
 if True:
-        import sys
-        if len(sys.argv) > 1:
-                data=sys.argv[1]
+    import sys
+
+    if len(sys.argv) > 1:
+        data = sys.argv[1]
 
-n = collect('n', path=data, info=False)
+n = collect("n", path=data, info=False)
 
 
-vx,vy,xx,yy = blob_velocity(n[:,:,0,:],type='COM',Index=True)
+vx, vy, xx, yy = blob_velocity(n[:, :, 0, :], type="COM", Index=True)
 
-f = open('Velocity.dat','wb')
-pickle.dump(vx,f)
+f = open("Velocity.dat", "wb")
+pickle.dump(vx, f)
 f.close()
 
-f = open('Position.dat','wb')
-pickle.dump(xx,f)
+f = open("Position.dat", "wb")
+pickle.dump(xx, f)
 f.close()
 
 
-f = open('Velocity.dat','rb')
+f = open("Velocity.dat", "rb")
 vx = pickle.load(f)
 f.close()
 
 try:
-        import matplotlib.pyplot as plt
-        plt.plot(vx)
-        plt.show()
+    import matplotlib.pyplot as plt
+
+    plt.plot(vx)
+    plt.show()
 except ImportError:
-        pass
+    pass

examples/boutpp/simulation.py

@@ -3,12 +3,13 @@
 
 bc.init("mesh:n=48")
 
+
 class Model(bc.PhysicsModel):
-    def init(self,restart):
+    def init(self, restart):
         self.dens = bc.create3D("sin(x)")
         self.solve_for(n=self.dens)
 
-    def rhs(self,time):
+    def rhs(self, time):
         self.dens.ddt(bc.DDX(self.dens))
 
 

examples/conduction-snb/fit_temperature.py

@@ -3,23 +3,31 @@
 import matplotlib.pyplot as plt
 
 Te_ref = np.loadtxt("temperature.csv", delimiter=",")
-Te_ref[:,0] *= 1e-4 # Convert X axis to m
+Te_ref[:, 0] *= 1e-4  # Convert X axis to m
+
 
 def te_function(ypos, mid, wwid, w0, w1, w2, Tmax, Tmin, clip=False):
-    width = w0 + ((ypos - mid)*w1 + (ypos - mid)**2 * w2) * np.exp(-((ypos - mid)/wwid)**2)
+    width = w0 + ((ypos - mid) * w1 + (ypos - mid) ** 2 * w2) * np.exp(
+        -(((ypos - mid) / wwid) ** 2)
+    )
 
     if clip:
         width = np.clip(width, 1e-10, None)
 
-    return Tmax - 0.5 * (1 + np.tanh((ypos - mid)/width)) * (Tmax - Tmin)
+    return Tmax - 0.5 * (1 + np.tanh((ypos - mid) / width)) * (Tmax - Tmin)
+
 
-popt, pcov = optimize.curve_fit(te_function, Te_ref[:,0], Te_ref[:,1],
-                                p0 = [2.2e-4, 1e-4, 1e-4, 0.0, 0.0, 0.960, 0.190])
+popt, pcov = optimize.curve_fit(
+    te_function,
+    Te_ref[:, 0],
+    Te_ref[:, 1],
+    p0=[2.2e-4, 1e-4, 1e-4, 0.0, 0.0, 0.960, 0.190],
+)
 
 print(popt)
 
-xfit = np.linspace(Te_ref[0,0], Te_ref[-1,0], 100)
+xfit = np.linspace(Te_ref[0, 0], Te_ref[-1, 0], 100)
 
-plt.plot(xfit, te_function(xfit, *popt, clip=True), '-k')
-plt.plot(Te_ref[:,0], Te_ref[:,1], 'or')
+plt.plot(xfit, te_function(xfit, *popt, clip=True), "-k")
+plt.plot(Te_ref[:, 0], Te_ref[:, 1], "or")
 plt.show()