Add precommit.yaml file

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+exclude: 'dev'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: check-merge-conflict  # checks for files that contain merge conflict strings
+  - id: check-toml  # checks toml files for parseable syntax
+  - id: debug-statements  # checks for debugger imports and py37+ `breakpoint()` calls in python source
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.2
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [python, pyi, jupyter]
+      args: 
+        - --fix
+        - --exit-non-zero-on-fix
+        - --per-file-ignores
+        - getting-started/python-basics.ipynb:E999
+
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [python, pyi, jupyter]
+      exclude: getting-started/python-basics.ipynb
+
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.1.0
+#   hooks:
+#   - id: codespell

examples/08-tutorial-standard-problem4.ipynb

@@ -96,7 +96,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "system = mm.System(name='stdprob4')"
+    "system = mm.System(name=\"stdprob4\")"
    ]
   },
   {
@@ -299,7 +299,7 @@
    ],
    "source": [
     "# x-component\n",
-    "system.m.x.sel('z').mpl()"
+    "system.m.x.sel(\"z\").mpl()"
    ]
   },
   {
@@ -320,7 +320,7 @@
    ],
    "source": [
     "# y-component\n",
-    "system.m.y.sel('z').mpl()"
+    "system.m.y.sel(\"z\").mpl()"
    ]
   },
   {
@@ -341,7 +341,7 @@
    ],
    "source": [
     "# vectors\n",
-    "system.m.sel('z').mpl()"
+    "system.m.sel(\"z\").mpl()"
    ]
   },
   {
@@ -375,10 +375,10 @@
     "fig, ax = plt.subplots(figsize=(20, 5))\n",
     "\n",
     "# plot vectors on grid of 20 x 5 over the numerical resulotion\n",
-    "system.m.sel('z').resample((20, 5)).mpl.vector(ax=ax)\n",
+    "system.m.sel(\"z\").resample((20, 5)).mpl.vector(ax=ax)\n",
     "\n",
     "# add colouring for mx-component to this plot\n",
-    "system.m.x.sel('z').mpl.scalar(ax=ax, cmap='magma')"
+    "system.m.x.sel(\"z\").mpl.scalar(ax=ax, cmap=\"magma\")"
    ]
   },
   {
@@ -408,10 +408,13 @@
     }
    ],
    "source": [
-    "print('The average magnetisation is {}.'.format(system.m.mean()))\n",
+    "print(\"The average magnetisation is {}.\".format(system.m.mean()))\n",
     "\n",
-    "print('The magnetisation at the mesh centre {}\\nis {}.'.format(\n",
-    "        system.m.mesh.region.centre, system.m(system.m.mesh.region.centre)))"
+    "print(\n",
+    "    \"The magnetisation at the mesh centre {}\\nis {}.\".format(\n",
+    "        system.m.mesh.region.centre, system.m(system.m.mesh.region.centre)\n",
+    "    )\n",
+    ")"
    ]
   },
   {
@@ -435,7 +438,7 @@
    "outputs": [],
    "source": [
     "# Add Zeeman energy term to the Hamiltonian\n",
-    "H1 = (-24.6e-3/mm.consts.mu0, 4.3e-3/mm.consts.mu0, 0.0)\n",
+    "H1 = (-24.6e-3 / mm.consts.mu0, 4.3e-3 / mm.consts.mu0, 0.0)\n",
     "system.energy += mm.Zeeman(H=H1)"
    ]
   },
@@ -749,7 +752,7 @@
     }
    ],
    "source": [
-    "myplot = system.table.data.plot('t', 'my')"
+    "myplot = system.table.data.plot(\"t\", \"my\")"
    ]
   },
   {
@@ -783,10 +786,10 @@
     "fig, ax = plt.subplots(figsize=(20, 5))\n",
     "\n",
     "# plot vectors on grid of 20 x 5 over the numerical resulotion\n",
-    "system.m.sel('z').resample((20, 5)).mpl.vector(ax=ax)\n",
+    "system.m.sel(\"z\").resample((20, 5)).mpl.vector(ax=ax)\n",
     "\n",
     "# add colouring for mx-component to this plot\n",
-    "system.m.x.sel('z').mpl.scalar(ax=ax, cmap='magma')"
+    "system.m.x.sel(\"z\").mpl.scalar(ax=ax, cmap=\"magma\")"
    ]
   },
   {

examples/09-tutorial-standard-problem5.ipynb

@@ -42,9 +42,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import oommfc as oc\n",
     "import discretisedfield as df\n",
-    "import micromagneticmodel as mm"
+    "import micromagneticmodel as mm\n",
+    "import oommfc as oc"
    ]
   },
   {
@@ -64,7 +64,7 @@
     "lx = 100e-9  # x dimension of the sample(m)\n",
     "ly = 100e-9  # y dimension of the sample (m)\n",
     "lz = 10e-9  # sample thickness (m)\n",
-    "dx = dy = dz = 5e-9  #discretisation cell (nm)\n",
+    "dx = dy = dz = 5e-9  # discretisation cell (nm)\n",
     "\n",
     "# Material (permalloy) parameters\n",
     "Ms = 8e5  # saturation magnetisation (A/m)\n",
@@ -90,7 +90,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "system = mm.System(name='stdprob5')"
+    "system = mm.System(name=\"stdprob5\")"
    ]
   },
   {
@@ -182,10 +182,11 @@
    ],
    "source": [
     "def m_vortex(pos):\n",
-    "    x, y, z = pos[0]/1e-9-50, pos[1]/1e-9-50, pos[2]/1e-9\n",
-    "    \n",
+    "    x, y, _ = pos[0] / 1e-9 - 50, pos[1] / 1e-9 - 50, pos[2] / 1e-9\n",
+    "\n",
     "    return (-y, x, 10)\n",
     "\n",
+    "\n",
     "system.m = df.Field(mesh, nvdim=3, value=m_vortex, norm=Ms)\n",
     "system.m.sel(z=0).mpl()"
    ]
@@ -271,7 +272,9 @@
     }
    ],
    "source": [
-    "system.dynamics += mm.Precession(gamma0=gamma0) + mm.Damping(alpha=alpha) + mm.ZhangLi(u=ux, beta=beta)\n",
+    "system.dynamics += (\n",
+    "    mm.Precession(gamma0=gamma0) + mm.Damping(alpha=alpha) + mm.ZhangLi(u=ux, beta=beta)\n",
+    ")\n",
     "system.dynamics"
    ]
   },
@@ -354,7 +357,7 @@
     }
    ],
    "source": [
-    "system.table.data.plot('t', 'mx')"
+    "system.table.data.plot(\"t\", \"mx\")"
    ]
   },
   {

examples/10-tutorial-standard-problem-fmr.ipynb

@@ -83,7 +83,7 @@
    "source": [
     "mesh = df.Mesh(p1=(0, 0, 0), p2=(lx, ly, lz), cell=(dx, dy, dz))\n",
     "\n",
-    "system = mm.System(name='stdprobfmr')\n",
+    "system = mm.System(name=\"stdprobfmr\")\n",
     "\n",
     "system.energy = mm.Exchange(A=A) + mm.Demag() + mm.Zeeman(H=H)\n",
     "system.dynamics = mm.Precession(gamma0=gamma0) + mm.Damping(alpha=alpha)\n",
@@ -139,7 +139,7 @@
     }
    ],
    "source": [
-    "system.m.sel('z').resample((10, 10)).mpl()"
+    "system.m.sel(\"z\").resample((10, 10)).mpl()"
    ]
   },
   {
@@ -228,14 +228,14 @@
    "source": [
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "t = system.table.data['t'].values\n",
-    "my = system.table.data['mx'].values\n",
+    "t = system.table.data[\"t\"].values\n",
+    "my = system.table.data[\"mx\"].values\n",
     "\n",
     "# Plot <my> time evolution.\n",
     "plt.figure(figsize=(8, 6))\n",
     "plt.plot(t, my)\n",
-    "plt.xlabel('t (ns)')\n",
-    "plt.ylabel('my average')\n",
+    "plt.xlabel(\"t (ns)\")\n",
+    "plt.ylabel(\"my average\")\n",
     "plt.grid()"
    ]
   },
@@ -265,13 +265,13 @@
    "source": [
     "import scipy.fft\n",
     "\n",
-    "psd = np.log10(np.abs(scipy.fft.fft(my))**2)\n",
-    "f_axis = scipy.fft.fftfreq(4000, d=20e-9/4000)\n",
+    "psd = np.log10(np.abs(scipy.fft.fft(my)) ** 2)\n",
+    "f_axis = scipy.fft.fftfreq(4000, d=20e-9 / 4000)\n",
     "\n",
-    "plt.plot(f_axis/1e9, psd)\n",
+    "plt.plot(f_axis / 1e9, psd)\n",
     "plt.xlim([6, 12])\n",
-    "plt.xlabel('f (GHz)')\n",
-    "plt.ylabel('Psa (a.u.)')\n",
+    "plt.xlabel(\"f (GHz)\")\n",
+    "plt.ylabel(\"Psa (a.u.)\")\n",
     "plt.grid()"
    ]
   },

examples/11-tutorial-deriving-fields.ipynb

@@ -89,16 +89,15 @@
     }
    ],
    "source": [
-    "system = mm.System(name='system')\n",
+    "system = mm.System(name=\"system\")\n",
     "\n",
     "A = 1e-11\n",
-    "H = (0.1/mm.consts.mu0, 0, 0)\n",
+    "H = (0.1 / mm.consts.mu0, 0, 0)\n",
     "K = 1e3\n",
     "u = (1, 1, 1)\n",
-    "system.energy = (mm.Exchange(A=A)\n",
-    "                 + mm.Demag()\n",
-    "                 + mm.Zeeman(H=H)\n",
-    "                 + mm.UniaxialAnisotropy(K=K, u=u))\n",
+    "system.energy = (\n",
+    "    mm.Exchange(A=A) + mm.Demag() + mm.Zeeman(H=H) + mm.UniaxialAnisotropy(K=K, u=u)\n",
+    ")\n",
     "\n",
     "system.energy"
    ]
@@ -158,7 +157,7 @@
     }
    ],
    "source": [
-    "oc.compute(system.energy.effective_field, system).sel('x').mpl()"
+    "oc.compute(system.energy.effective_field, system).sel(\"x\").mpl()"
    ]
   },
   {
@@ -244,7 +243,7 @@
    ],
    "source": [
     "w = oc.compute(system.energy.density, system)\n",
-    "w.sel('x').mpl()"
+    "w.sel(\"x\").mpl()"
    ]
   },
   {
@@ -270,7 +269,7 @@
    ],
    "source": [
     "E = oc.compute(system.energy.energy, system)\n",
-    "print(f'The energy of the system is {E} J.')"
+    "print(f\"The energy of the system is {E} J.\")"
    ]
   },
   {
@@ -333,7 +332,7 @@
     "E = oc.compute(system.energy.energy, system)\n",
     "print(\"The system's energy is {} J.\".format(E))\n",
     "\n",
-    "system.m.sel('x').mpl()"
+    "system.m.sel(\"x\").mpl()"
    ]
   },
   {
@@ -419,7 +418,7 @@
     "total_energy = 0\n",
     "for term in system.energy:\n",
     "    total_energy += oc.compute(term.energy, system)\n",
-    "    \n",
+    "\n",
     "print(\"The sum of energy terms is {} J.\".format(total_energy))\n",
     "print(\"The system's energy is {} J.\".format(oc.compute(system.energy.energy, system)))"
    ]

examples/12-tutorial-stray-field.ipynb

@@ -28,14 +28,16 @@
     "region = df.Region(p1=(-100e-9, -100e-9, -100e-9), p2=(100e-9, 100e-9, 100e-9))\n",
     "mesh = df.Mesh(region=region, cell=(5e-9, 5e-9, 5e-9))\n",
     "\n",
+    "\n",
     "def norm_fun(pos):\n",
     "    x, y, z = pos\n",
     "    if -50e-9 <= x <= 50e-9 and -50e-9 <= y <= 50e-9 and -50e-9 <= z <= 50e-9:\n",
     "        return 8e5\n",
     "    else:\n",
     "        return 0\n",
     "\n",
-    "system = mm.System(name='airbox_method')\n",
+    "\n",
+    "system = mm.System(name=\"airbox_method\")\n",
     "system.energy = mm.Exchange(A=1e-12) + mm.Demag()\n",
     "system.dynamics = mm.Precession(gamma0=mm.consts.gamma0) + mm.Damping(alpha=1)\n",
     "system.m = df.Field(mesh, nvdim=3, value=(0, 0, 1), norm=norm_fun, valid=\"norm\")"
@@ -65,7 +67,7 @@
     }
    ],
    "source": [
-    "system.m.norm.sel('z').mpl()"
+    "system.m.norm.sel(\"z\").mpl()"
    ]
   },
   {
@@ -102,7 +104,7 @@
     "md = oc.MinDriver()\n",
     "md.drive(system)\n",
     "\n",
-    "system.m.sel('z').mpl(figsize=(10, 10))"
+    "system.m.sel(\"z\").mpl(figsize=(10, 10))"
    ]
   },
   {
@@ -159,7 +161,7 @@
     }
    ],
    "source": [
-    "stray_field.sel('z').mpl(figsize=(8, 8), vector_kw={'scale': 1e6})"
+    "stray_field.sel(\"z\").mpl(figsize=(8, 8), vector_kw={\"scale\": 1e6})"
    ]
   }
  ],