Lint notebooks with black, nbqa, and pre-commit

mosdef-hub · Sep 15, 2021 · f78c437 · f78c437
1 parent 6a83fb6
commit f78c437
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Showing 11 changed files with 436 additions and 293 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,15 @@
+ci:
+  autoupdate_schedule: quarterly
+repos:
+- repo: https://github.com/psf/black
+  rev: 21.9b0
+  hooks:
+  - id: black
+  - id: black-jupyter
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 1.1.1
+  hooks:
+    - id: nbqa-isort
+    - id: nbqa-pyupgrade
+      args:
+        - --py36-plus
diff --git a/charmm-gui-gmx/charmm-gui-gmx.ipynb b/charmm-gui-gmx/charmm-gui-gmx.ipynb
@@ -58,9 +58,9 @@
    "source": [
     "class charmm_ethane(mb.Compound):\n",
     "    def __init__(self):\n",
-    "        super(charmm_ethane, self).__init__()\n",
-    "        mb.load('files/ethane.mol2', compound=self)\n",
-    "        self.name='ETHA'"
+    "        super().__init__()\n",
+    "        mb.load(\"files/ethane.mol2\", compound=self)\n",
+    "        self.name = \"ETHA\""
    ]
   },
   {
@@ -97,7 +97,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ethane_box.save('box.gro', residues=['ETHA'], overwrite=True)"
+    "ethane_box.save(\"box.gro\", residues=[\"ETHA\"], overwrite=True)"
    ]
   },
   {
@@ -118,13 +118,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with open('box.top', 'w') as f:\n",
-    "    f.write(\"#include \\\"files/charmm36.itp\\\" \\n\")\n",
-    "    f.write(\"#include \\\"files/ETHA.itp\\\" \\n\")\n",
+    "with open(\"box.top\", \"w\") as f:\n",
+    "    f.write('#include \"files/charmm36.itp\" \\n')\n",
+    "    f.write('#include \"files/ETHA.itp\" \\n')\n",
     "    f.write(\"[ System ] \\n\")\n",
-    "    f.write('mBuild box of ethane\\n')\n",
+    "    f.write(\"mBuild box of ethane\\n\")\n",
     "    f.write(\"[ Molecules ] \\n\")\n",
-    "    f.write(\"{} {}\".format(prototype.name, n_ethane))"
+    "    f.write(f\"{prototype.name} {n_ethane}\")"
    ]
   },
   {
@@ -189,7 +189,8 @@
    "outputs": [],
    "source": [
     "import mdtraj\n",
-    "traj = mdtraj.load('npt.xtc', top='npt.gro')\n",
+    "\n",
+    "traj = mdtraj.load(\"npt.xtc\", top=\"npt.gro\")\n",
     "rho = mdtraj.density(traj)"
    ]
   },
@@ -209,14 +210,15 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "%matplotlib inline\n",
     "import matplotlib\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "ref = np.loadtxt('ref/rho.dat')\n",
-    "fig, ax = plt.subplots(1,1)\n",
-    "ax.scatter(traj.time, rho, label='Simulated', alpha=0.6)\n",
-    "ax.scatter(ref[:,0], ref[:,1], label='Reference', alpha=0.6)\n",
+    "ref = np.loadtxt(\"ref/rho.dat\")\n",
+    "fig, ax = plt.subplots(1, 1)\n",
+    "ax.scatter(traj.time, rho, label=\"Simulated\", alpha=0.6)\n",
+    "ax.scatter(ref[:, 0], ref[:, 1], label=\"Reference\", alpha=0.6)\n",
     "ax.legend()\n",
     "ax.set_ylabel(r\"Density (kg m$^{{-3}}$)\")\n",
     "ax.set_xlabel(\"Time (ps)\")"