Merge pull request #161 from scipp/deprecation_warnings

Remove deprecation warnings from docs notebooks

Author: nvaytet

docs/buildconfig/config.yaml

@@ -0,0 +1,2 @@
+plot:
+  use_plopp: true

docs/conf.py

@@ -3,6 +3,7 @@
 
 import doctest
 import os
+import pathlib
 import sys
 from datetime import date
 from typing import Any, Dict, Optional
@@ -264,3 +265,7 @@ def add_buttons(
     # Specific lines in Github blobs cannot be found by linkcheck.
     r'https?://github\.com/.*?/blob/[a-f0-9]+/.+?#',
 ]
+
+# Set env variable to enable plopp
+docs_dir = pathlib.Path(__file__).parent.absolute()
+os.environ["SCIPPDIR"] = os.path.join(docs_dir, 'buildconfig')

docs/instruments/external/powgen/powgen_reduction.ipynb

@@ -32,6 +32,7 @@
     "%matplotlib widget\n",
     "import scipp as sc\n",
     "import scippneutron as scn\n",
+    "import plopp as pp\n",
     "\n",
     "import ess\n",
     "from ess.diffraction.external import load_calibration\n",
@@ -131,7 +132,7 @@
    },
    "outputs": [],
    "source": [
-    "sample.plot()"
+    "sample.hist(spectrum=500, tof=400).plot()"
    ]
   },
   {
@@ -151,7 +152,7 @@
    },
    "outputs": [],
    "source": [
-    "powgen.instrument_view(sample)"
+    "scn.instrument_view(sample.hist())"
    ]
   },
   {
@@ -486,7 +487,7 @@
    },
    "outputs": [],
    "source": [
-    "sc.histogram(all_spectra, bins=dspacing_edges).plot()"
+    "all_spectra.hist(dspacing=dspacing_edges).plot()"
    ]
   },
   {
@@ -557,7 +558,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized = sc.histogram(normalized, bins=dspacing_edges)"
+    "normalized = normalized.hist(dspacing=dspacing_edges)"
    ]
   },
   {
@@ -623,7 +624,7 @@
    },
    "outputs": [],
    "source": [
-    "normalized.plot(projection='1d')"
+    "pp.superplot(normalized)"
    ]
   }
  ],

docs/instruments/loki/sans2d_reduction.ipynb

@@ -35,7 +35,8 @@
     "import scipp as sc\n",
     "from ess import loki, sans\n",
     "from ess.logging import configure_workflow\n",
-    "import scippneutron as scn"
+    "import scippneutron as scn\n",
+    "import plopp as pp"
    ]
   },
   {
@@ -233,7 +234,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "scn.instrument_view(ds['sample'], pixel_size=0.0075)"
+    "scn.instrument_view(ds['sample'].hist(), pixel_size=0.0075)"
    ]
   },
   {
@@ -327,7 +328,7 @@
     "    q_bins=q_bins,\n",
     "    gravity=gravity,\n",
     "    monitor_non_background_range=monitor_non_background_range)\n",
-    "sample_q.plot()"
+    "sample_q.hist().plot()"
    ]
   },
   {
@@ -345,7 +346,7 @@
     "    q_bins=q_bins,\n",
     "    gravity=gravity,\n",
     "    monitor_non_background_range=monitor_non_background_range)\n",
-    "background_q.plot()"
+    "background_q.hist().plot()"
    ]
   },
   {
@@ -376,8 +377,7 @@
    "source": [
     "fig1, ax1 = plt.subplots(1, 2, figsize=(10, 4))\n",
     "sc.plot(result, ax=ax1[0])\n",
-    "sc.plot(result, norm='log', ax=ax1[1])\n",
-    "fig1"
+    "sc.plot(result, norm='log', ax=ax1[1])"
    ]
   },
   {
@@ -456,8 +456,7 @@
     "\n",
     "fig2, ax2 = plt.subplots(1, 2, figsize=(10, 4))\n",
     "sc.plot(collapsed, ax=ax2[0])\n",
-    "sc.plot(collapsed, norm='log', legend=False, ax=ax2[1])\n",
-    "fig2"
+    "sc.plot(collapsed, norm='log', ax=ax2[1])"
    ]
   },
   {

docs/instruments/loki/sans2d_to_I_of_Q.ipynb

@@ -258,7 +258,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "scn.instrument_view(sample, pixel_size=0.0075)"
+    "scn.instrument_view(sample.hist(), pixel_size=0.0075)"
    ]
   },
   {
@@ -301,7 +301,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sample)"
+    "sc.plot(sample.hist(tof=200).sum('spectrum'))"
    ]
   },
   {
@@ -428,9 +428,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "p = sc.plot(monitors['sample'], norm='log')\n",
-    "sc.plot(monitors['direct'], norm='log', ax=p.ax, color=['C2', 'C3'])\n",
-    "p"
+    "sc.plot({**{f'sample-{key}': val for key, val in monitors['sample'].items()},\n",
+    "         **{f'direct-{key}': val for key, val in monitors['direct'].items()}}\n",
+    "        , norm='log')"
    ]
   },
   {
@@ -646,7 +646,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sample_q, norm='log')"
+    "sc.plot(sample_q.hist(), norm='log')"
    ]
   },
   {
@@ -706,7 +706,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sample_normalized)"
+    "sc.plot(sample_normalized.hist())"
    ]
   },
   {

docs/techniques/wfm/introduction-to-wfm.ipynb

@@ -1056,7 +1056,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "del ax6.texts[3:]\n",
+    "for t in ax6.texts[3:]:\n",
+    "    t.remove()\n",
     "ax6.set_xlim(-1.0e3, 2.0e4)\n",
     "ax6.set_ylim(-1.5, 10.0)\n",
     "fig6.canvas.draw_idle()\n",
@@ -1100,9 +1101,10 @@
     "    ax7.plot([(coords['source_pulse_t_0'] + (0.5 * coords['source_pulse_length'])).value,\n",
     "              arrival_times['wavelength', i].value],\n",
     "             [0.0, sc.norm(coords['position']).value], color='r')\n",
-    "del ax7.texts[3:]\n",
     "ax7.set_xlim(-1.0e3, 2.0e4)\n",
-    "ax7.set_ylim(-1.5, 10.0)"
+    "ax7.set_ylim(-1.5, 10.0)\n",
+    "for t in ax7.texts[3:]:\n",
+    "    t.remove()"
    ]
   },
   {

environment.yml

@@ -24,6 +24,7 @@ dependencies:
   - pytest=7.2.1
   - python-graphviz=0.20.1
   - pythreejs=2.4.1
+  - scipp==22.11.0
   - scippneutron==22.12.4
   - sphinx=4.5.0
   - sphinx-book-theme=0.3.3

src/ess/diffraction/corrections.py

@@ -78,7 +78,7 @@ def normalize_by_vanadium(data: sc.DataArray, *, vanadium: sc.DataArray,
     :
         `data` normalized by `vanadium`.
     """
-    norm = sc.lookup(sc.histogram(vanadium, bins=edges), dim=edges.dim)
+    norm = sc.lookup(vanadium.hist({edges.dim: edges}), dim=edges.dim)
     # Converting to unit 'one' because the division might produce a unit
     # with a large scale if the proton charges in data and vanadium were
     # measured with different units.

src/ess/diffraction/grouping.py

@@ -4,10 +4,7 @@
 from scippneutron.conversion.graph import beamline
 
 
-def group_by_two_theta(data: sc.DataArray,
-                       *,
-                       edges: sc.Variable,
-                       replace_dim: str = 'spectrum') -> sc.DataArray:
+def group_by_two_theta(data: sc.DataArray, *, edges: sc.Variable) -> sc.DataArray:
     """
     Group data into two_theta bins.
 
@@ -18,17 +15,11 @@ def group_by_two_theta(data: sc.DataArray,
         or coords or attrs that can be used to compute it.
     edges:
         Bin edges in two_theta. `data` is grouped into those bins.
-    replace_dim:
-        Dimension that is replaced by two_theta.
-        All events are concatenated along this dimension.
 
     Returns
     -------
     :
         `data` grouped into two_theta bins.
     """
-    data = data.transform_coords('two_theta', graph=beamline.beamline(scatter=True))
-    return sc.groupby(data,
-                      'two_theta',
-                      bins=edges.to(unit=data.coords['two_theta'].unit,
-                                    copy=False)).bins.concat(replace_dim)
+    out = data.transform_coords('two_theta', graph=beamline.beamline(scatter=True))
+    return out.bin(two_theta=edges.to(unit=out.coords['two_theta'].unit, copy=False))

src/ess/external/powgen/instrument_view.py

@@ -28,12 +28,14 @@ def instrument_view(da: sc.DataArray,
     kwargs:
         See :func:`scippneutron.instrument_view`
     """
-    if 'camera' not in kwargs:
-        kwargs = {
-            **kwargs, 'camera': {
-                'position': sc.vector(value=[-3, 3, 3], unit=da.coords[positions].unit)
-            }
-        }
+    # TODO: the camera argument does not work with the Plopp instrument view
+    # if 'camera' not in kwargs:
+    #     kwargs = {
+    #         **kwargs, 'camera': {
+    #             'position': sc.vector(value=[-3, 3, 3],
+    #                                   unit=da.coords[positions].unit)
+    #         }
+    #     }
     return scn.instrument_view(da,
                                positions=positions,
                                components=components,

src/ess/sans/i_of_q.py

@@ -169,7 +169,7 @@ def _convert_dense_to_q_and_merge_spectra(
     data_q.coords['wavelength'] = data_q.attrs.pop('wavelength')
     for i in range(wavelength_bands.sizes['wavelength'] - 1):
         band = data_q['wavelength', wavelength_bands[i]:wavelength_bands[i + 1]]
-        bands.append(sc.histogram(band, bins=q_bins).sum('spectrum'))
+        bands.append(band.hist({q_bins.dim: q_bins}).sum('spectrum'))
     q_summed = sc.concat(bands, 'wavelength')
     return q_summed