run ruff via nbqa on notebooks

.pre-commit-config.yaml

@@ -8,7 +8,20 @@ repos:
       - id: ruff
         args:
           - "--fix"
+        exclude_types:
+          - jupyter
       - id: ruff-format
+        exclude_types:
+          - jupyter
+  # run ruff via nbqa, which has better and configurable handling of cell magics
+  # than ruff itself
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.0
+    hooks:
+      - id: nbqa-ruff-format
+      - id: nbqa-ruff-check
+        args:
+          - --fix
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:

docs/source/examples/Futures.ipynb

@@ -67,6 +67,7 @@
     "%%px --local --block\n",
     "import os\n",
     "import time\n",
+    "\n",
     "import numpy as np\n",
     "from numpy.linalg import norm"
    ]
@@ -186,8 +187,6 @@
     }
    ],
    "source": [
-    "import os\n",
-    "\n",
     "f = rc[-1].apply(os.getpid)\n",
     "f.add_done_callback(lambda _: print(\"I got PID: %i\" % _.result()))\n",
     "f.result()"

docs/source/examples/Monitoring an MPI Simulation - 1.ipynb

@@ -119,15 +119,15 @@
    "source": [
     "%%px --block\n",
     "# MPI initialization, library imports and sanity checks on all engines\n",
-    "from mpi4py import MPI\n",
-    "import numpy as np\n",
     "import time\n",
     "\n",
+    "from mpi4py import MPI\n",
+    "\n",
     "mpi = MPI.COMM_WORLD\n",
     "bcast = mpi.bcast\n",
     "barrier = mpi.barrier\n",
     "rank = mpi.rank\n",
-    "print(\"MPI rank: %i/%i\" % (mpi.rank,mpi.size))"
+    "print(\"MPI rank: %i/%i\" % (mpi.rank, mpi.size))"
    ]
   },
   {
@@ -229,7 +229,7 @@
     "        )\n",
     "        X, Y = np.meshgrid(Xax, Yax)\n",
     "        f = freqs[j]\n",
-    "        Z = np.cos(f * (X ** 2 + Y ** 2))\n",
+    "        Z = np.cos(f * (X**2 + Y**2))\n",
     "        # We add a small delay to simulate that a real-world computation\n",
     "        # would take much longer, and we ensure all nodes are synchronized\n",
     "        time.sleep(delay)\n",
@@ -533,7 +533,9 @@
    ],
    "source": [
     "%%px --target 0 --block\n",
-    "from ipyparallel import bind_kernel; bind_kernel()\n",
+    "from ipyparallel import bind_kernel\n",
+    "\n",
+    "bind_kernel()\n",
     "%connect_info"
    ]
   },
@@ -564,7 +566,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.11.9"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

docs/source/examples/Monitoring an MPI Simulation - 2.ipynb

@@ -108,17 +108,18 @@
    "source": [
     "%%px --block\n",
     "# MPI initialization, library imports and sanity checks on all engines\n",
+    "import time\n",
+    "\n",
     "from mpi4py import MPI\n",
+    "\n",
     "# Load data publication API so engines can send data to notebook client\n",
     "from ipyparallel.datapub import publish_data\n",
-    "import numpy as np\n",
-    "import time\n",
     "\n",
     "mpi = MPI.COMM_WORLD\n",
     "bcast = mpi.bcast\n",
     "barrier = mpi.barrier\n",
     "rank = mpi.rank\n",
-    "print(\"MPI rank: %i/%i\" % (mpi.rank,mpi.size))"
+    "print(\"MPI rank: %i/%i\" % (mpi.rank, mpi.size))"
    ]
   },
   {
@@ -196,7 +197,7 @@
     "        )\n",
     "        X, Y = np.meshgrid(Xax, Yax)\n",
     "        f = freqs[j]\n",
-    "        Z = np.cos(f * (X ** 2 + Y ** 2))\n",
+    "        Z = np.cos(f * (X**2 + Y**2))\n",
     "\n",
     "        # We are now going to publish data to the clients. We take advantage of fast\n",
     "        # MPI communications and gather the Z mesh at the rank 0 node in the Zcat variable:\n",
@@ -419,7 +420,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.11.9"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

docs/source/examples/Parallel Magics.ipynb

@@ -568,6 +568,7 @@
    "source": [
     "%%px\n",
     "import psutil\n",
+    "\n",
     "psutil.Process().nice(20 if psutil.POSIX else psutil.IDLE_PRIORITY_CLASS)"
    ]
   },
@@ -578,8 +579,8 @@
    "outputs": [],
    "source": [
     "%%px\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np"
    ]
   },
   {
@@ -619,10 +620,10 @@
    ],
    "source": [
     "%%px --noblock\n",
-    "x = np.linspace(0,np.pi,1000)\n",
-    "for n in range(id,12, stride):\n",
+    "x = np.linspace(0, np.pi, 1000)\n",
+    "for n in range(id, 12, stride):\n",
     "    print(n)\n",
-    "    plt.plot(x,np.sin(n*x))\n",
+    "    plt.plot(x, np.sin(n * x))\n",
     "plt.title(\"Plot %i\" % id)"
    ]
   },
@@ -1318,11 +1319,11 @@
    ],
    "source": [
     "%%px --group-outputs=engine\n",
-    "x = np.linspace(0,np.pi,1000)\n",
-    "for n in range(id+1,12, stride):\n",
+    "x = np.linspace(0, np.pi, 1000)\n",
+    "for n in range(id + 1, 12, stride):\n",
     "    print(n)\n",
     "    plt.figure()\n",
-    "    plt.plot(x,np.sin(n*x))\n",
+    "    plt.plot(x, np.sin(n * x))\n",
     "    plt.title(\"Plot %i\" % n)"
    ]
   },
@@ -3261,6 +3262,7 @@
    "source": [
     "%%px\n",
     "from numpy.random import random\n",
+    "\n",
     "A = random((100, 100, 'invalid shape'))"
    ]
   },
@@ -3343,10 +3345,10 @@
    "source": [
     "%%px\n",
     "import time\n",
+    "\n",
     "if rank == 0:\n",
     "    raise RuntimeError(\"rank 0 failed!\")\n",
-    "time.sleep(10)\n",
-    "    "
+    "time.sleep(10)"
    ]
   },
   {
@@ -3469,6 +3471,7 @@
    "source": [
     "%%px --local\n",
     "import os\n",
+    "\n",
     "thispid = os.getpid()\n",
     "print(thispid)"
    ]

docs/source/examples/Using MPI with IPython Parallel.ipynb

@@ -181,12 +181,12 @@
     "rank = comm.Get_rank()\n",
     "\n",
     "if rank == 0:\n",
-    "   data = [(i+1)**2 for i in range(size)]\n",
+    "    data = [(i + 1) ** 2 for i in range(size)]\n",
     "else:\n",
-    "   data = None\n",
+    "    data = None\n",
     "data = comm.scatter(data, root=0)\n",
     "\n",
-    "assert data == (rank+1)**2, 'data=%s, rank=%s' % (data, rank)\n",
+    "assert data == (rank + 1) ** 2, f'data={data}, rank={rank}'\n",
     "{\n",
     "    'data': data,\n",
     "    'rank': rank,\n",

docs/source/examples/broadcast/MPI Broadcast.ipynb

@@ -248,7 +248,7 @@
     }
    ],
    "source": [
-    "%%time \n",
+    "%%time\n",
     "ar = eall.push({'data': data}, block=False)\n",
     "ar.wait_interactive()"
    ]
@@ -2568,7 +2568,8 @@
    "source": [
     "%%px\n",
     "import numpy as np\n",
-    "np.linalg.norm(data, 2)\n"
+    "\n",
+    "np.linalg.norm(data, 2)"
    ]
   }
  ],
@@ -2588,7 +2589,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.11.9"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

docs/source/examples/progress.ipynb

@@ -353,19 +353,22 @@
     "n_steps = 10\n",
     "\n",
     "progress = W.IntProgress(max=n_steps, description=f\"rank {rank}: 0\")\n",
+    "\n",
+    "\n",
     "def _set_color(change):\n",
     "    if change.new == progress.max:\n",
     "        progress.bar_style = \"success\"\n",
     "    else:\n",
     "        progress.bar_style = \"\"\n",
+    "\n",
+    "\n",
     "progress.observe(_set_color, \"value\")\n",
     "display(progress)\n",
     "\n",
     "for i in range(n_steps):\n",
     "    time.sleep(random.random())\n",
     "    progress.value += 1\n",
-    "    progress.description = f\"rank {rank}: {progress.value}/{progress.max}\"\n",
-    "\n"
+    "    progress.description = f\"rank {rank}: {progress.value}/{progress.max}\""
    ]
   },
   {
@@ -448,11 +451,13 @@
     "\n",
     "if rank == 0:\n",
     "    progress = W.IntProgress(max=n_steps, description=\"Step 0\")\n",
+    "\n",
     "    def _set_color(change):\n",
     "        if change.new == progress.max:\n",
     "            progress.bar_style = \"success\"\n",
     "        else:\n",
     "            progress.bar_style = \"\"\n",
+    "\n",
     "    progress.observe(_set_color, \"value\")\n",
     "    display(progress)\n",
     "\n",
@@ -585,7 +590,7 @@
    ],
    "source": [
     "%%px\n",
-    "button = W.Button(description=f\"step\")\n",
+    "button = W.Button(description=\"step\")\n",
     "progress = W.IntProgress(max=5, description=\"0 / 5\")\n",
     "count = 0\n",
     "\n",