Merge pull request #3287 from cphyc/lint-ipynb

CI: Pre-commit to apply black/isort/flake8 on ipython notebooks
yt-project · Oct 19, 2021 · 8c94e16 · 8c94e16
2 parents bc7c44a + e37ab0b
commit 8c94e16
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -38,3 +38,6 @@ cae222aec845d0b400e2aa2804e75b2adef17ccd
 ef783151bfd7c6777fa25e9e06f95fe47653b3aa
 063e2fb630932cbdcbbbdba603c100a37e7e40f6
 279b0551ccc9d9d4c114904b94bc705381c61105
+
+# apply linting to ipynb files
+ec8bb45ea1603f3862041fa9e8ec274afd9bbbfd
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -38,8 +38,8 @@ repos:
 -   repo: https://github.com/psf/black
     rev: 21.9b0
     hooks:
-    - id: black
-      language_version: python3
+    - id: black-jupyter
+
 -   repo: https://github.com/PyCQA/isort
     rev: '5.9.3'
     hooks:
@@ -66,3 +66,16 @@ repos:
     rev: v1.9.0
     hooks:
     -   id: rst-backticks
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 0.10.0
+  hooks:
+    - id: nbqa-pyupgrade
+      args: [--nbqa-mutate, --py36-plus]
+    - id: nbqa-isort
+      args: [--nbqa-mutate]
+    - id: nbqa-flake8
+      args: [--extend-ignore=E402]
+      additional_dependencies: [
+        flake8-bugbear>=20.3.2, # GH PR 2851
+        flake8-logging-format
+      ]
diff --git a/doc/source/analyzing/Particle_Trajectories.ipynb b/doc/source/analyzing/Particle_Trajectories.ipynb
@@ -18,11 +18,12 @@
     "%matplotlib inline\n",
     "import glob\n",
     "from os.path import join\n",
+    "\n",
     "import yt\n",
     "from yt.config import ytcfg\n",
+    "\n",
     "path = ytcfg.get(\"yt\", \"test_data_dir\")\n",
-    "import matplotlib.pyplot as plt\n",
-    "from mpl_toolkits.mplot3d import Axes3D"
+    "import matplotlib.pyplot as plt"
    ]
   },
   {
@@ -80,7 +81,7 @@
     "ds = yt.load(my_fns[0])\n",
     "dd = ds.all_data()\n",
     "indices = dd[\"all\", \"particle_index\"].astype(\"int\")\n",
-    "print (indices)"
+    "print(indices)"
    ]
   },
   {
@@ -118,8 +119,8 @@
    },
    "outputs": [],
    "source": [
-    "print (trajs[\"all\", \"particle_position_x\"])\n",
-    "print (trajs[\"all\", \"particle_position_x\"].shape)"
+    "print(trajs[\"all\", \"particle_position_x\"])\n",
+    "print(trajs[\"all\", \"particle_position_x\"].shape)"
    ]
   },
   {
@@ -219,7 +220,13 @@
    "outputs": [],
    "source": [
     "ds = yt.load(\"enzo_tiny_cosmology/DD0046/DD0046\")\n",
-    "slc = yt.SlicePlot(ds, \"x\", [(\"gas\", \"density\"), (\"gas\", \"dark_matter_density\")], center=\"max\", width=(3.0, \"Mpc\"))\n",
+    "slc = yt.SlicePlot(\n",
+    "    ds,\n",
+    "    \"x\",\n",
+    "    [(\"gas\", \"density\"), (\"gas\", \"dark_matter_density\")],\n",
+    "    center=\"max\",\n",
+    "    width=(3.0, \"Mpc\"),\n",
+    ")\n",
     "slc.show()"
    ]
   },
@@ -279,10 +286,22 @@
    "outputs": [],
    "source": [
     "fig = plt.figure(figsize=(8.0, 8.0))\n",
-    "ax = fig.add_subplot(111, projection='3d')\n",
-    "ax.plot(trajs[\"all\", \"particle_position_x\"][100], trajs[\"all\", \"particle_position_y\"][100], trajs[\"all\", \"particle_position_z\"][100])\n",
-    "ax.plot(trajs[\"all\", \"particle_position_x\"][8], trajs[\"all\", \"particle_position_y\"][8], trajs[\"all\", \"particle_position_z\"][8])\n",
-    "ax.plot(trajs[\"all\", \"particle_position_x\"][25], trajs[\"all\", \"particle_position_y\"][25], trajs[\"all\", \"particle_position_z\"][25])"
+    "ax = fig.add_subplot(111, projection=\"3d\")\n",
+    "ax.plot(\n",
+    "    trajs[\"all\", \"particle_position_x\"][100],\n",
+    "    trajs[\"all\", \"particle_position_y\"][100],\n",
+    "    trajs[\"all\", \"particle_position_z\"][100],\n",
+    ")\n",
+    "ax.plot(\n",
+    "    trajs[\"all\", \"particle_position_x\"][8],\n",
+    "    trajs[\"all\", \"particle_position_y\"][8],\n",
+    "    trajs[\"all\", \"particle_position_z\"][8],\n",
+    ")\n",
+    "ax.plot(\n",
+    "    trajs[\"all\", \"particle_position_x\"][25],\n",
+    "    trajs[\"all\", \"particle_position_y\"][25],\n",
+    "    trajs[\"all\", \"particle_position_z\"][25],\n",
+    ")"
    ]
   },
   {
@@ -300,7 +319,7 @@
    },
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(6,6))\n",
+    "plt.figure(figsize=(6, 6))\n",
     "plt.plot(trajs[\"all\", \"particle_time\"], trajs[\"all\", \"particle_position_x\"][100])\n",
     "plt.plot(trajs[\"all\", \"particle_time\"], trajs[\"all\", \"particle_position_x\"][8])\n",
     "plt.plot(trajs[\"all\", \"particle_time\"], trajs[\"all\", \"particle_position_x\"][25])"
@@ -339,7 +358,7 @@
    },
    "outputs": [],
    "source": [
-    "plt.figure(figsize=(6,6))\n",
+    "plt.figure(figsize=(6, 6))\n",
     "plt.plot(trajs[\"all\", \"particle_time\"], trajs[\"gas\", \"density\"][100])\n",
     "plt.plot(trajs[\"all\", \"particle_time\"], trajs[\"gas\", \"density\"][8])\n",
     "plt.plot(trajs[\"all\", \"particle_time\"], trajs[\"gas\", \"density\"][25])\n",
@@ -361,8 +380,12 @@
    },
    "outputs": [],
    "source": [
-    "trajs.write_out(\"halo_trajectories\") # This will write a separate file for each trajectory\n",
-    "trajs.write_out_h5(\"halo_trajectories.h5\") # This will write all trajectories to a single file"
+    "trajs.write_out(\n",
+    "    \"halo_trajectories\"\n",
+    ")  # This will write a separate file for each trajectory\n",
+    "trajs.write_out_h5(\n",
+    "    \"halo_trajectories.h5\"\n",
+    ")  # This will write all trajectories to a single file"
    ]
   }
  ],

diff --git a/doc/source/analyzing/domain_analysis/XrayEmissionFields.ipynb b/doc/source/analyzing/domain_analysis/XrayEmissionFields.ipynb
@@ -41,9 +41,13 @@
    "source": [
     "import yt\n",
     "\n",
-    "ds = yt.load(\"GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150\", default_species_fields=\"ionized\")\n",
+    "ds = yt.load(\n",
+    "    \"GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150\", default_species_fields=\"ionized\"\n",
+    ")\n",
     "\n",
-    "xray_fields = yt.add_xray_emissivity_field(ds, 0.5, 7.0, table_type='apec', metallicity=0.3)"
+    "xray_fields = yt.add_xray_emissivity_field(\n",
+    "    ds, 0.5, 7.0, table_type=\"apec\", metallicity=0.3\n",
+    ")"
    ]
   },
   {
@@ -69,7 +73,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print (xray_fields)"
+    "print(xray_fields)"
    ]
   },
   {
@@ -86,7 +90,7 @@
    "outputs": [],
    "source": [
     "sp = ds.sphere(\"c\", (2.0, \"Mpc\"))\n",
-    "print (sp.quantities.total_quantity((\"gas\",\"xray_luminosity_0.5_7.0_keV\")))"
+    "print(sp.quantities.total_quantity((\"gas\", \"xray_luminosity_0.5_7.0_keV\")))"
    ]
   },
   {
@@ -104,9 +108,15 @@
    },
    "outputs": [],
    "source": [
-    "slc = yt.SlicePlot(ds, 'z', [('gas', 'xray_emissivity_0.5_7.0_keV'),\n",
-    "                             ('gas', 'xray_photon_emissivity_0.5_7.0_keV')],\n",
-    "                   width=(0.75, \"Mpc\"))\n",
+    "slc = yt.SlicePlot(\n",
+    "    ds,\n",
+    "    \"z\",\n",
+    "    [\n",
+    "        (\"gas\", \"xray_emissivity_0.5_7.0_keV\"),\n",
+    "        (\"gas\", \"xray_photon_emissivity_0.5_7.0_keV\"),\n",
+    "    ],\n",
+    "    width=(0.75, \"Mpc\"),\n",
+    ")\n",
     "slc.show()"
    ]
   },
@@ -129,10 +139,17 @@
    "source": [
     "ds2 = yt.load(\"D9p_500/10MpcBox_HartGal_csf_a0.500.d\", default_species_fields=\"ionized\")\n",
     "\n",
-    "# In this case, use the redshift and cosmology from the dataset, \n",
+    "# In this case, use the redshift and cosmology from the dataset,\n",
     "# but in theory you could put in something different\n",
-    "xray_fields2 = yt.add_xray_emissivity_field(ds2, 0.5, 2.0, redshift=ds2.current_redshift, cosmology=ds2.cosmology,\n",
-    "                                            metallicity=(\"gas\", \"metallicity\"), table_type='cloudy')"
+    "xray_fields2 = yt.add_xray_emissivity_field(\n",
+    "    ds2,\n",
+    "    0.5,\n",
+    "    2.0,\n",
+    "    redshift=ds2.current_redshift,\n",
+    "    cosmology=ds2.cosmology,\n",
+    "    metallicity=(\"gas\", \"metallicity\"),\n",
+    "    table_type=\"cloudy\",\n",
+    ")"
    ]
   },
   {
@@ -148,7 +165,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print (xray_fields2)"
+    "print(xray_fields2)"
    ]
   },
   {
@@ -166,8 +183,9 @@
    },
    "outputs": [],
    "source": [
-    "prj = yt.ProjectionPlot(ds2, \"x\", (\"gas\",\"xray_intensity_0.5_2.0_keV\"),\n",
-    "                        center=\"max\", width=(40, \"kpc\"))\n",
+    "prj = yt.ProjectionPlot(\n",
+    "    ds2, \"x\", (\"gas\", \"xray_intensity_0.5_2.0_keV\"), center=\"max\", width=(40, \"kpc\")\n",
+    ")\n",
     "prj.set_zlim(\"xray_intensity_0.5_2.0_keV\", 1.0e-32, 5.0e-24)\n",
     "prj.show()"
    ]
@@ -197,8 +215,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "xray_fields3 = yt.add_xray_emissivity_field(ds2, 0.5, 2.0, dist=(1.0,\"Mpc\"), metallicity=(\"gas\", \"metallicity\"), \n",
-    "                                           table_type='cloudy')"
+    "xray_fields3 = yt.add_xray_emissivity_field(\n",
+    "    ds2,\n",
+    "    0.5,\n",
+    "    2.0,\n",
+    "    dist=(1.0, \"Mpc\"),\n",
+    "    metallicity=(\"gas\", \"metallicity\"),\n",
+    "    table_type=\"cloudy\",\n",
+    ")"
    ]
   },
   {
@@ -209,8 +233,13 @@
    },
    "outputs": [],
    "source": [
-    "prj = yt.ProjectionPlot(ds2, \"x\", (\"gas\", \"xray_photon_intensity_0.5_2.0_keV\"),\n",
-    "                        center=\"max\", width=(40, \"kpc\"))\n",
+    "prj = yt.ProjectionPlot(\n",
+    "    ds2,\n",
+    "    \"x\",\n",
+    "    (\"gas\", \"xray_photon_intensity_0.5_2.0_keV\"),\n",
+    "    center=\"max\",\n",
+    "    width=(40, \"kpc\"),\n",
+    ")\n",
     "prj.set_zlim(\"xray_photon_intensity_0.5_2.0_keV\", 1.0e-24, 5.0e-16)\n",
     "prj.show()"
    ]