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CI: Pre-commit to apply black/isort/flake8 on ipython notebooks #3287

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merged 12 commits into from Oct 19, 2021
Merged

CI: Pre-commit to apply black/isort/flake8 on ipython notebooks #3287

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99255a0
Apply black on ipynb
cphyc May 20, 2021
ca3a328
Use nbQA instead
cphyc May 20, 2021
669a284
Fix order
cphyc May 20, 2021
5b2103e
Update nbQA with @MarcoGorelli fixes
cphyc Jun 1, 2021
de17622
Fix syntax error in ipynb
cphyc Jun 1, 2021
60282ad
Fix flake8 errors in ipynb
cphyc Jun 1, 2021
ec8bb45
Automatic linting
Jul 26, 2021
c22fbd7
Add lint pass to ignore list
cphyc Jul 26, 2021
8e744a8
Merge branch 'main' into lint-ipynb
cphyc Sep 7, 2021
d96db08
Use black's pre-commit hook instead of nbqa's
cphyc Sep 7, 2021
167a67f
Take @MarcoGorelli comment into account
cphyc Sep 7, 2021
e37ab0b
Remove useless language_version stmt
cphyc Sep 7, 2021
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3 changes: 3 additions & 0 deletions .git-blame-ignore-revs
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Expand Up @@ -38,3 +38,6 @@ cae222aec845d0b400e2aa2804e75b2adef17ccd
ef783151bfd7c6777fa25e9e06f95fe47653b3aa
063e2fb630932cbdcbbbdba603c100a37e7e40f6
279b0551ccc9d9d4c114904b94bc705381c61105

# apply linting to ipynb files
ec8bb45ea1603f3862041fa9e8ec274afd9bbbfd
17 changes: 15 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -35,8 +35,8 @@ repos:
- repo: https://github.com/psf/black
rev: 21.8b0
hooks:
- id: black
language_version: python3
- id: black-jupyter

- repo: https://github.com/PyCQA/isort
rev: '5.9.3'
hooks:
Expand All @@ -63,3 +63,16 @@ 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]
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Note: deactivating E402 (https://www.flake8rules.com/rules/E402.html) as it seems to clash with adding some line magics in cells.

additional_dependencies: [
flake8-bugbear>=20.3.2, # GH PR 2851
flake8-logging-format
]
51 changes: 37 additions & 14 deletions doc/source/analyzing/Particle_Trajectories.ipynb
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Expand Up @@ -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"
]
},
{
Expand Down Expand Up @@ -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)"
]
},
{
Expand Down Expand Up @@ -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)"
]
},
{
Expand Down Expand Up @@ -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()"
]
},
Expand Down Expand Up @@ -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",
")"
]
},
{
Expand All @@ -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])"
Expand Down Expand Up @@ -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",
Expand All @@ -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"
]
}
],
Expand Down
63 changes: 46 additions & 17 deletions doc/source/analyzing/domain_analysis/XrayEmissionFields.ipynb
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Expand Up @@ -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",
")"
]
},
{
Expand All @@ -69,7 +73,7 @@
"metadata": {},
"outputs": [],
"source": [
"print (xray_fields)"
"print(xray_fields)"
]
},
{
Expand All @@ -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\")))"
]
},
{
Expand All @@ -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()"
]
},
Expand All @@ -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",
")"
]
},
{
Expand All @@ -148,7 +165,7 @@
"metadata": {},
"outputs": [],
"source": [
"print (xray_fields2)"
"print(xray_fields2)"
]
},
{
Expand All @@ -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()"
]
Expand Down Expand Up @@ -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",
")"
]
},
{
Expand All @@ -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()"
]
Expand Down