Limit nb to 80 char. to display OK with PyData Sphinx Theme width

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
pyxem · Oct 26, 2022 · a319d76 · a319d76
1 parent b6c0032
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,4 +2,4 @@ repos:
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
-      - id: black-jupyter
+      - id: black
diff --git a/doc/tutorials/esteem2022_diffraction_workshop.ipynb b/doc/tutorials/esteem2022_diffraction_workshop.ipynb
@@ -91,7 +91,9 @@
     "from pyebsdindex import ebsd_index, pcopt\n",
     "\n",
     "\n",
-    "plt.rcParams.update({\"figure.facecolor\": \"w\", \"font.size\": 15, \"figure.dpi\": 75})"
+    "plt.rcParams.update(\n",
+    "    {\"figure.facecolor\": \"w\", \"font.size\": 15, \"figure.dpi\": 75}\n",
+    ")"
    ]
   },
   {
@@ -2484,7 +2486,9 @@
     }
    ],
    "source": [
-    "xmap_di = s.dictionary_indexing(s_dict, signal_mask=signal_mask, n_per_iteration=2000)"
+    "xmap_di = s.dictionary_indexing(\n",
+    "    s_dict, signal_mask=signal_mask, n_per_iteration=2000\n",
+    ")"
    ]
   },
   {
@@ -2570,7 +2574,10 @@
    ],
    "source": [
     "fig = xmap_di.plot(\n",
-    "    xmap_di.scores[:, 0], colorbar=True, colorbar_label=\"NCC\", return_figure=True\n",
+    "    xmap_di.scores[:, 0],\n",
+    "    colorbar=True,\n",
+    "    colorbar_label=\"NCC\",\n",
+    "    return_figure=True,\n",
     ")\n",
     "# fig.savefig(os.path.join(dir_data, \"maps_di_ncc.png\"))"
    ]

diff --git a/doc/tutorials/geometrical_ebsd_simulations.ipynb b/doc/tutorials/geometrical_ebsd_simulations.ipynb
@@ -134,7 +134,8 @@
     "phase = Phase(\n",
     "    space_group=225,\n",
     "    structure=Structure(\n",
-    "        atoms=[Atom(\"Ni\", [0, 0, 0])], lattice=Lattice(3.52, 3.52, 3.52, 90, 90, 90)\n",
+    "        atoms=[Atom(\"Ni\", [0, 0, 0])],\n",
+    "        lattice=Lattice(3.52, 3.52, 3.52, 90, 90, 90),\n",
     "    ),\n",
     ")\n",
     "\n",
@@ -209,7 +210,12 @@
     "hkl_colors = np.zeros((ref.size, 3))\n",
     "for idx, color in zip(\n",
     "    hkl_sets.values(),\n",
-    "    [[1, 0, 0], [0, 1, 0], [0, 0, 1], [0.75, 0, 0.75]],  # Red, green, blue, magenta\n",
+    "    [\n",
+    "        [1, 0, 0],\n",
+    "        [0, 1, 0],\n",
+    "        [0, 0, 1],\n",
+    "        [0.75, 0, 0.75],\n",
+    "    ],  # Red, green, blue, magenta\n",
     "):\n",
     "    hkl_colors[idx] = color"
    ]

diff --git a/doc/tutorials/hough_indexing.ipynb b/doc/tutorials/hough_indexing.ipynb
@@ -51,7 +51,12 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "from orix import plot\n",
-    "from orix.crystal_map import create_coordinate_arrays, CrystalMap, Phase, PhaseList\n",
+    "from orix.crystal_map import (\n",
+    "    create_coordinate_arrays,\n",
+    "    CrystalMap,\n",
+    "    Phase,\n",
+    "    PhaseList,\n",
+    ")\n",
     "from orix.quaternion import Rotation\n",
     "from orix.vector import Vector3d\n",
     "from pyebsdindex import ebsd_index, pcopt\n",
@@ -376,7 +381,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "detector = kp.detectors.EBSDDetector(shape=sig_shape, pc=pcs.mean(0), sample_tilt=70)\n",
+    "detector = kp.detectors.EBSDDetector(\n",
+    "    shape=sig_shape, pc=pcs.mean(0), sample_tilt=70\n",
+    ")\n",
     "detector"
    ]
   },
@@ -409,7 +416,9 @@
    },
    "outputs": [],
    "source": [
-    "data, *_ = indexer.index_pats(s.data.reshape(-1, *sig_shape), PC=detector.pc, verbose=2)"
+    "data, *_ = indexer.index_pats(\n",
+    "    s.data.reshape(-1, *sig_shape), PC=detector.pc, verbose=2\n",
+    ")"
    ]
   },
   {
@@ -508,7 +517,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ckey = plot.IPFColorKeyTSL(xmap.phases[0].point_group, direction=Vector3d.xvector())\n",
+    "ckey = plot.IPFColorKeyTSL(\n",
+    "    xmap.phases[0].point_group, direction=Vector3d.xvector()\n",
+    ")\n",
     "ckey.plot()"
    ]
   },

diff --git a/doc/tutorials/kinematical_ebsd_simulations.ipynb b/doc/tutorials/kinematical_ebsd_simulations.ipynb
@@ -517,7 +517,11 @@
     "grain2 = (115, 27, -95)\n",
     "rot = Rotation.from_euler(\n",
     "    np.deg2rad(\n",
-    "        [[grain1, grain2, grain2], [grain1, grain2, grain2], [grain1, grain2, grain2]]\n",
+    "        [\n",
+    "            [grain1, grain2, grain2],\n",
+    "            [grain1, grain2, grain2],\n",
+    "            [grain1, grain2, grain2],\n",
+    "        ]\n",
     "    )\n",
     ")\n",
     "\n",
@@ -802,7 +806,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mp_sic = simulator_sic.calculate_master_pattern(hemisphere=\"both\", half_size=200)"
+    "mp_sic = simulator_sic.calculate_master_pattern(\n",
+    "    hemisphere=\"both\", half_size=200\n",
+    ")"
    ]
   },
   {

diff --git a/doc/tutorials/load_save_data.ipynb b/doc/tutorials/load_save_data.ipynb
@@ -76,7 +76,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "emsoft_master_pattern = \"emsoft_ebsd_master_pattern/ni_mc_mp_20kv_uint8_gzip_opts9.h5\"\n",
+    "emsoft_master_pattern = (\n",
+    "    \"emsoft_ebsd_master_pattern/ni_mc_mp_20kv_uint8_gzip_opts9.h5\"\n",
+    ")\n",
     "s_mp = kp.load(filename=datadir + emsoft_master_pattern)\n",
     "s_mp"
    ]
@@ -327,7 +329,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s_da = kp.signals.LazyEBSD(da.random.random((20, 10, 60, 60), chunks=(2, 10, 60, 60)))\n",
+    "s_da = kp.signals.LazyEBSD(\n",
+    "    da.random.random((20, 10, 60, 60), chunks=(2, 10, 60, 60))\n",
+    ")\n",
     "print(s_da)\n",
     "s_da.data"
    ]
@@ -358,7 +362,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "for signal_type in [\"EBSD\", \"VirtualBSEImage\", \"ECPMasterPattern\", \"EBSDMasterPattern\"]:\n",
+    "for signal_type in [\n",
+    "    \"EBSD\",\n",
+    "    \"VirtualBSEImage\",\n",
+    "    \"ECPMasterPattern\",\n",
+    "    \"EBSDMasterPattern\",\n",
+    "]:\n",
     "    s_hs.set_signal_type(signal_type)\n",
     "    print(s_hs)"
    ]
@@ -446,7 +455,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s_mp2 = hs.load(temp_dir + \"master_pattern.hspy\", signal_type=\"EBSDMasterPattern\")\n",
+    "s_mp2 = hs.load(\n",
+    "    temp_dir + \"master_pattern.hspy\", signal_type=\"EBSDMasterPattern\"\n",
+    ")\n",
     "s_mp2"
    ]
   },
@@ -587,7 +598,10 @@
    "outputs": [],
    "source": [
     "s_mp = kp.load(\n",
-    "    datadir + emsoft_master_pattern, projection=\"lambert\", hemisphere=\"both\", energy=20\n",
+    "    datadir + emsoft_master_pattern,\n",
+    "    projection=\"lambert\",\n",
+    "    hemisphere=\"both\",\n",
+    "    energy=20,\n",
     ")\n",
     "\n",
     "print(s_mp)\n",
@@ -620,7 +634,9 @@
    "outputs": [],
    "source": [
     "# Load a dummy pattern\n",
-    "s_mp = kp.load(filename=datadir + \"emsoft_ecp_master_pattern/ecp_master_pattern.h5\")\n",
+    "s_mp = kp.load(\n",
+    "    filename=datadir + \"emsoft_ecp_master_pattern/ecp_master_pattern.h5\"\n",
+    ")\n",
     "\n",
     "print(s_mp)\n",
     "print(s_mp.projection)\n",
@@ -651,7 +667,9 @@
    "outputs": [],
    "source": [
     "# Load a dummy pattern\n",
-    "s_mp = kp.load(filename=datadir + \"emsoft_tkd_master_pattern/tkd_master_pattern.h5\")\n",
+    "s_mp = kp.load(\n",
+    "    filename=datadir + \"emsoft_tkd_master_pattern/tkd_master_pattern.h5\"\n",
+    ")\n",
     "\n",
     "print(s_mp)\n",
     "print(s_mp.projection)\n",
@@ -1156,7 +1174,10 @@
    "outputs": [],
    "source": [
     "nav_size = vbse.axes_manager.navigation_size\n",
-    "_ = [plt.imsave(temp_dir + f\"vbse{i}.png\", vbse.inav[i].data) for i in range(nav_size)]"
+    "_ = [\n",
+    "    plt.imsave(temp_dir + f\"vbse{i}.png\", vbse.inav[i].data)\n",
+    "    for i in range(nav_size)\n",
+    "]"
    ]
   },
   {

diff --git a/doc/tutorials/mandm2021_sunday_short_course.ipynb b/doc/tutorials/mandm2021_sunday_short_course.ipynb
@@ -64,7 +64,9 @@
     "from orix import io, quaternion, sampling, vector\n",
     "\n",
     "\n",
-    "plt.rcParams.update({\"figure.facecolor\": \"w\", \"font.size\": 15, \"figure.dpi\": 75})"
+    "plt.rcParams.update(\n",
+    "    {\"figure.facecolor\": \"w\", \"font.size\": 15, \"figure.dpi\": 75}\n",
+    ")"
    ]
   },
   {
@@ -1175,7 +1177,9 @@
    ],
    "source": [
     "detector.plot(\n",
-    "    coordinates=\"gnomonic\", pattern=s.inav[0, 0].data, draw_gnomonic_circles=True\n",
+    "    coordinates=\"gnomonic\",\n",
+    "    pattern=s.inav[0, 0].data,\n",
+    "    draw_gnomonic_circles=True,\n",
     ")"
    ]
   },
@@ -1219,7 +1223,11 @@
    ],
    "source": [
     "dynsim = mp.get_patterns(\n",
-    "    rotations=rot, detector=detector, energy=20, dtype_out=s.data.dtype, compute=True\n",
+    "    rotations=rot,\n",
+    "    detector=detector,\n",
+    "    energy=20,\n",
+    "    dtype_out=s.data.dtype,\n",
+    "    compute=True,\n",
     ")\n",
     "dynsim"
    ]

diff --git a/doc/tutorials/pattern_matching.ipynb b/doc/tutorials/pattern_matching.ipynb
@@ -170,7 +170,9 @@
    ],
    "source": [
     "energy = 20\n",
-    "mp = kp.data.nickel_ebsd_master_pattern_small(projection=\"lambert\", energy=energy)\n",
+    "mp = kp.data.nickel_ebsd_master_pattern_small(\n",
+    "    projection=\"lambert\", energy=energy\n",
+    ")\n",
     "mp"
    ]
   },
@@ -472,7 +474,9 @@
     "for i in range(3):\n",
     "    ax[i].imshow(sim.inav[i].data, cmap=\"gray\")\n",
     "    euler = np.rad2deg(sim.xmap[i].rotations.to_euler())[0]\n",
-    "    ax[i].set_title(f\"($\\phi_1, \\Phi, \\phi_2)$ = {np.array_str(euler, precision=1)}\")\n",
+    "    ax[i].set_title(\n",
+    "        f\"($\\phi_1, \\Phi, \\phi_2)$ = {np.array_str(euler, precision=1)}\"\n",
+    "    )\n",
     "    ax[i].axis(\"off\")\n",
     "fig.tight_layout()"
    ]
@@ -975,7 +979,9 @@
     "    energy=energy,\n",
     "    signal_mask=signal_mask,\n",
     "    method=\"minimize\",  # Default\n",
-    "    method_kwargs=dict(method=\"Nelder-Mead\", options=dict(fatol=1e-4)),  # Default\n",
+    "    method_kwargs=dict(\n",
+    "        method=\"Nelder-Mead\", options=dict(fatol=1e-4)\n",
+    "    ),  # Default\n",
     "    compute=True,  # Default\n",
     ")"
    ]
@@ -1607,7 +1613,11 @@
     "    f\"PC after PC refinement:\\t{detector_refined2.pc_average}\"\n",
     ")\n",
     "\n",
-    "pc_to_plot = (detector_refined2.pcx, detector_refined2.pcy, detector_refined2.pcz)\n",
+    "pc_to_plot = (\n",
+    "    detector_refined2.pcx,\n",
+    "    detector_refined2.pcy,\n",
+    "    detector_refined2.pcz,\n",
+    ")\n",
     "fig, ax = plt.subplots(ncols=3, figsize=(15, 3))\n",
     "for a, to_plot, label in zip(ax, pc_to_plot, (\"x\", \"y\", \"z\")):\n",
     "    im = a.imshow(to_plot)\n",

diff --git a/doc/tutorials/pattern_processing.ipynb b/doc/tutorials/pattern_processing.ipynb
@@ -402,7 +402,9 @@
    "outputs": [],
    "source": [
     "s7 = s3.deepcopy()\n",
-    "s7.fft_filter(transfer_function=w_low * w_high, function_domain=\"frequency\", shift=True)\n",
+    "s7.fft_filter(\n",
+    "    transfer_function=w_low * w_high, function_domain=\"frequency\", shift=True\n",
+    ")\n",
     "\n",
     "_, ax = plt.subplots(figsize=(13, 6), ncols=2)\n",
     "ax[0].imshow(s3.inav[0, 0].data, cmap=\"gray\")\n",

diff --git a/doc/tutorials/pc_calibration_moving_screen_technique.ipynb b/doc/tutorials/pc_calibration_moving_screen_technique.ipynb
@@ -121,7 +121,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, (ax0, ax1) = plt.subplots(ncols=2, sharex=True, sharey=True, figsize=(20, 10))\n",
+    "fig, (ax0, ax1) = plt.subplots(\n",
+    "    ncols=2, sharex=True, sharey=True, figsize=(20, 10)\n",
+    ")\n",
     "ax0.imshow(s_in.data, cmap=\"gray\")\n",
     "_ = ax1.imshow(s_out5mm.data, cmap=\"gray\")"
    ]
@@ -340,7 +342,10 @@
    "outputs": [],
    "source": [
     "sim.plot(\n",
-    "    coordinates=\"gnomonic\", pattern=s_in.data, zone_axes_labels=False, zone_axes=False\n",
+    "    coordinates=\"gnomonic\",\n",
+    "    pattern=s_in.data,\n",
+    "    zone_axes_labels=False,\n",
+    "    zone_axes=False,\n",
     ")"
    ]
   }

diff --git a/doc/tutorials/reference_frames.ipynb b/doc/tutorials/reference_frames.ipynb
@@ -527,7 +527,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mp = kp.data.nickel_ebsd_master_pattern_small(projection=\"lambert\", hemisphere=\"upper\")"
+    "mp = kp.data.nickel_ebsd_master_pattern_small(\n",
+    "    projection=\"lambert\", hemisphere=\"upper\"\n",
+    ")"
    ]
   },
   {
@@ -543,7 +545,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "detector2 = kp.detectors.EBSDDetector((100, 120), pc=(0.4, 0.2, 0.5), sample_tilt=70)\n",
+    "detector2 = kp.detectors.EBSDDetector(\n",
+    "    (100, 120), pc=(0.4, 0.2, 0.5), sample_tilt=70\n",
+    ")\n",
     "detector2"
    ]
   },
@@ -651,7 +655,9 @@
     "\n",
     "# Some wrangling to display a nice table\n",
     "for software, pc_i in pcs.items():\n",
-    "    print(f\"{software:<9} {pc_i[0, 0]:>6.3f} {pc_i[0, 1]:>6.3f} {pc_i[0, 2]:>6.3f}\")"
+    "    print(\n",
+    "        f\"{software:<9} {pc_i[0, 0]:>6.3f} {pc_i[0, 1]:>6.3f} {pc_i[0, 2]:>6.3f}\"\n",
+    "    )"
    ]
   },
   {