Merge pull request #136 from scipp/update_to_scipp0.15

Update to scippneutron=0.8
scipp · Aug 4, 2022 · 4a16288 · 4a16288
2 parents 8475ee9 + 0903261
commit 4a16288
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Showing 19 changed files with 92 additions and 103 deletions.
diff --git a/.buildconfig/ci.yml b/.buildconfig/ci.yml
@@ -2,7 +2,7 @@
 # Copyright (c) 2022 Scipp contributors (https://github.com/scipp)
 
 # This file was autogenerated using:
-#   - conda create -f environment.yml
+#   - conda env create -f environment.yml
 #   - conda activate ess-developer
 #   - conda env export --no-builds --file ci.yml
 
@@ -11,6 +11,7 @@ channels:
   - scipp
   - mantid
   - conda-forge
+  - nodefaults
 dependencies:
   - _libgcc_mutex=0.1
   - _openmp_mutex=4.5
@@ -20,7 +21,7 @@ dependencies:
   - argon2-cffi-bindings=21.2.0
   - asttokens=2.0.5
   - atk-1.0=2.36.0
-  - attrs=21.4.0
+  - attrs=22.1.0
   - babel=2.10.3
   - backcall=0.2.0
   - backports=1.0
@@ -39,10 +40,10 @@ dependencies:
   - cached_property=1.5.2
   - cairo=1.16.0
   - certifi=2022.6.15
-  - cffi=1.15.0
-  - charset-normalizer=2.0.12
+  - cffi=1.15.1
+  - charset-normalizer=2.1.0
   - colorama=0.4.5
-  - confuse=1.7.0
+  - confuse=2.0.0
   - cryptography=36.0.2
   - curl=7.82.0
   - cycler=0.11.0
@@ -54,7 +55,7 @@ dependencies:
   - double-conversion=3.1.7
   - eigen=3.4.0
   - entrypoints=0.4
-  - executing=0.8.3
+  - executing=0.9.1
   - expat=2.4.8
   - ffmpeg=4.3.2
   - flake8=4.0.1
@@ -66,7 +67,7 @@ dependencies:
   - fontconfig=2.14.0
   - fonts-conda-ecosystem=1
   - fonts-conda-forge=1
-  - fonttools=4.33.3
+  - fonttools=4.34.4
   - freeimage=3.18.0
   - freetype=2.10.4
   - fribidi=1.0.10
@@ -79,23 +80,23 @@ dependencies:
   - gnutls=3.6.13
   - graphite2=1.3.13
   - graphlib-backport=1.0.3
-  - graphviz=4.0.0
+  - graphviz=5.0.0
   - gsl=2.6
   - gtk2=2.24.33
   - gts=0.7.6
   - h5py=3.1.0
-  - harfbuzz=4.3.0
+  - harfbuzz=5.1.0
   - hdf4=4.2.15
   - hdf5=1.10.6
   - icu=70.1
   - idna=3.3
-  - imagesize=1.3.0
+  - imagesize=1.4.1
   - imath=3.1.5
   - importlib-metadata=4.11.4
-  - importlib_resources=5.8.0
+  - importlib_resources=5.9.0
   - iniconfig=1.1.1
   - ipydatawidgets=4.3.1.post1
-  - ipykernel=6.15.0
+  - ipykernel=6.15.1
   - ipympl=0.9.1
   - ipython=8.4.0
   - ipython_genutils=0.2.0
@@ -104,19 +105,19 @@ dependencies:
   - jinja2=3.1.2
   - jpeg=9e
   - jsoncpp=1.9.4
-  - jsonschema=4.6.0
+  - jsonschema=4.9.0
   - jupyter_client=7.3.4
-  - jupyter_core=4.10.0
+  - jupyter_core=4.11.1
   - jupyterlab_pygments=0.2.2
   - jupyterlab_widgets=1.1.1
   - jxrlib=1.1
   - keyutils=1.6.1
-  - kiwisolver=1.4.3
+  - kiwisolver=1.4.4
   - krb5=1.19.3
   - lame=3.100
   - lcms2=2.12
   - ld_impl_linux-64=2.36.1
-  - lerc=3.0
+  - lerc=4.0.0
   - libblas=3.9.0
   - libbrotlicommon=1.0.9
   - libbrotlidec=1.0.9
@@ -132,7 +133,7 @@ dependencies:
   - libgd=2.3.3
   - libgfortran-ng=12.1.0
   - libgfortran5=12.1.0
-  - libglib=2.70.2
+  - libglib=2.72.1
   - libglu=9.0.0
   - libgomp=12.1.0
   - libgpg-error=1.45
@@ -149,7 +150,7 @@ dependencies:
   - libpng=1.6.37
   - libraw=0.20.2
   - librdkafka=1.8.2.post2
-  - librsvg=2.54.3
+  - librsvg=2.54.4
   - libsodium=1.0.18
   - libssh2=1.10.0
   - libstdcxx-ng=12.1.0
@@ -158,8 +159,8 @@ dependencies:
   - libtool=2.4.6
   - libuuid=2.32.1
   - libvorbis=1.3.7
-  - libwebp=1.2.2
-  - libwebp-base=1.2.2
+  - libwebp=1.2.3
+  - libwebp-base=1.2.3
   - libxcb=1.13
   - libxml2=2.9.14
   - libzip=1.8.0
@@ -174,7 +175,7 @@ dependencies:
   - mistune=0.8.4
   - munkres=1.1.4
   - muparser=2.3.2
-  - nbclient=0.6.4
+  - nbclient=0.6.6
   - nbconvert=6.5.0
   - nbconvert-core=6.5.0
   - nbconvert-pandoc=6.5.0
@@ -194,14 +195,15 @@ dependencies:
   - packaging=21.3
   - pandoc=2.18
   - pandocfilters=1.5.0
-  - pango=1.50.7
+  - pango=1.50.8
   - parso=0.8.3
   - pcre=8.45
   - pexpect=4.8.0
   - pickleshare=0.7.5
-  - pillow=9.1.1
-  - pip=22.1.2
+  - pillow=9.2.0
+  - pip=22.2.1
   - pixman=0.40.0
+  - pkgutil-resolve-name=1.3.10
   - pluggy=1.0.0
   - poco=1.11.1
   - pooch=1.6.0
@@ -226,25 +228,25 @@ dependencies:
   - pytest=7.1.2
   - python=3.8.12
   - python-dateutil=2.8.2
-  - python-fastjsonschema=2.15.3
-  - python-graphviz=0.20
+  - python-fastjsonschema=2.16.1
+  - python-graphviz=0.20.1
   - python_abi=3.8
   - pythreejs=2.3.0
   - pytz=2022.1
   - pyyaml=6.0
   - pyzmq=23.2.0
   - rapidjson=1.1.0
   - readline=8.1.2
-  - requests=2.28.0
-  - scipp=0.14.0
-  - scippneutron=0.7.0
-  - scippnexus=0.1.4
-  - scipy=1.8.1
+  - requests=2.28.1
+  - scipp=0.15.1
+  - scippneutron=0.8.0
+  - scippnexus=0.1.7
+  - scipy=1.9.0
   - send2trash=1.8.0
-  - setuptools=62.6.0
+  - setuptools=63.3.0
   - six=1.16.0
   - snowballstemmer=2.2.0
-  - soupsieve=2.3.1
+  - soupsieve=2.3.2.post1
   - sphinx=4.5.0
   - sphinx-book-theme=0.2.0
   - sphinx-copybutton=0.5.0
@@ -254,20 +256,20 @@ dependencies:
   - sphinxcontrib-jsmath=1.0.1
   - sphinxcontrib-qthelp=1.0.3
   - sphinxcontrib-serializinghtml=1.1.5
-  - sqlite=3.39.0
+  - sqlite=3.39.2
   - stack_data=0.3.0
   - tbb=2020.2
   - tbb-devel=2020.2
   - terminado=0.15.0
   - tinycss2=1.1.1
   - tk=8.6.12
   - tomli=2.0.1
-  - tornado=6.1
+  - tornado=6.2
   - traitlets=5.3.0
   - traittypes=0.2.1
   - unicodedata2=14.0.0
   - unixodbc=2.3.10
-  - urllib3=1.26.9
+  - urllib3=1.26.11
   - utfcpp=3.2.1
   - vtk=9.0.1
   - wcwidth=0.2.5
@@ -291,10 +293,10 @@ dependencies:
   - yaml=0.2.5
   - yapf=0.32.0
   - zeromq=4.3.4
-  - zipp=3.8.0
+  - zipp=3.8.1
   - zlib=1.2.12
   - zstd=1.5.2
   - pip:
     - nb-clean==2.1.0
-    - orsopy==1.0.0
-    - sphinx-autodoc-typehints==1.18.3
+    - orsopy==1.0.1
+    - sphinx-autodoc-typehints==1.19.1
diff --git a/docs/conf.py b/docs/conf.py
@@ -92,6 +92,9 @@
 # The master toctree document.
 master_doc = 'index'
 
+# Turn warnings into errors
+warning_is_error = True
+
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.

diff --git a/docs/instruments/amor/amor_reduction.ipynb b/docs/instruments/amor/amor_reduction.ipynb
@@ -765,8 +765,7 @@
     "theta_edges = sc.linspace(dim='theta', start=0.0, stop=1.2, num=nbins, unit='deg')\n",
     "wavelength_edges = sc.linspace(dim='wavelength', start=0, stop=15.0,\n",
     "                               num=nbins, unit='angstrom')\n",
-    "binned = sc.bin(sample_theta,\n",
-    "                edges=[sc.to_unit(theta_edges, 'rad'), wavelength_edges])\n",
+    "binned = sample_theta.bin(theta=theta_edges.to(unit='rad'), wavelength=wavelength_edges)\n",
     "binned"
    ]
   },

diff --git a/docs/instruments/external/powgen/powgen_reduction.ipynb b/docs/instruments/external/powgen/powgen_reduction.ipynb
@@ -184,9 +184,8 @@
    },
    "outputs": [],
    "source": [
-    "sample = sc.bin(sample, edges=[\n",
-    "    sc.array(dims=['tof'], values=[0.0, 16666.67], unit='us')\n",
-    "])"
+    "sample = sample.bin(\n",
+    "    tof=sc.array(dims=['tof'], values=[0.0, 16666.67], unit='us'))"
    ]
   },
   {

diff --git a/docs/instruments/loki/sans2d_reduction.ipynb b/docs/instruments/loki/sans2d_reduction.ipynb
@@ -266,7 +266,7 @@
     "\n",
     "binned = sc.Dataset()\n",
     "for key in ds:\n",
-    "    binned[key] = sc.bin(ds[key], edges=[tof_masked_region])\n",
+    "    binned[key] = ds[key].bin(tof=tof_masked_region)\n",
     "    binned[key].masks['bragg_peaks'] = sc.array(dims=['tof'], values=[False, True, False])\n",
     "binned"
    ]

diff --git a/docs/instruments/loki/sans2d_to_I_of_Q.ipynb b/docs/instruments/loki/sans2d_to_I_of_Q.ipynb
@@ -289,7 +289,7 @@
     "                               mask_tof_min, mask_tof_max,\n",
     "                               sample.coords['tof']['tof', -1]], dim='tof')\n",
     "\n",
-    "sample = sc.bin(sample, edges=[tof_masked_region])\n",
+    "sample = sample.bin(tof=tof_masked_region)\n",
     "sample.masks['bragg_peaks'] = sc.array(dims=['tof'], values=[False, True, False])\n",
     "sample"
    ]

diff --git a/docs/techniques/wfm/reducing-wfm-data.ipynb b/docs/techniques/wfm/reducing-wfm-data.ipynb
@@ -361,7 +361,7 @@
     "                     unit=sc.units.counts, with_variances=True),\n",
     "        coords={\n",
     "            'time': sc.array(dims=['time'], values=item[\"valid_times\"], unit=sc.units.us)})\n",
-    "    ds[key] = sc.histogram(da, bins=time_coord)\n",
+    "    ds[key] = da.hist(time=time_coord)\n",
     "\n",
     "ds"
    ]
@@ -635,7 +635,7 @@
     "                     unit=sc.units.counts, with_variances=True),\n",
     "        coords={\n",
     "            'tof': sc.array(dims=['tof'], values=item[\"arrival_times\"].values, unit=sc.units.us)})\n",
-    "    ds_no_wfm[key] = sc.histogram(da, bins=time_coord_no_wfm)\n",
+    "    ds_no_wfm[key] = da.hist(tof=time_coord_no_wfm)\n",
     "\n",
     "ds_no_wfm"
    ]
@@ -777,7 +777,7 @@
     "                     with_variances=True),\n",
     "        coords={\n",
     "            'time': sc.array(dims=['event'], values=item[\"valid_times\"], unit=sc.units.us)})\n",
-    "    ds_event[key] = sc.bin(da, edges=[time_coord])\n",
+    "    ds_event[key] = da.bin(time=time_coord)\n",
     "\n",
     "ds_event"
    ]
@@ -815,7 +815,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(ds_event.bins.sum())"
+    "sc.plot(ds_event.hist())"
    ]
   },
   {
@@ -853,17 +853,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bab0141b",
+   "id": "a9b9f757-05f9-4566-bc5a-f67a7549332f",
    "metadata": {},
    "outputs": [],
    "source": [
-    "sc.plot(sc.histogram(stitched_event,\n",
-    "                     bins=sc.linspace(\n",
-    "                         dim='tof',\n",
-    "                         start=stitched_event.coords['tof']['tof', 0].value,\n",
-    "                         stop=stitched_event.coords['tof']['tof', -1].value,\n",
-    "                         num=257,\n",
-    "                         unit=stitched_event.coords['tof'].unit)))"
+    "sc.plot({key: item.hist(tof=256) for key, item in stitched_event.items()})"
    ]
   },
   {
@@ -881,8 +875,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "rebinned = sc.bin(stitched_event[\"sample\"], edges=[stitched[\"sample\"].coords['tof']])\n",
-    "sc.plot({\"events\": rebinned.bins.sum(), \"histogram\": stitched[\"sample\"]}, errorbars=False)"
+    "rebinned = stitched_event[\"sample\"].bin(tof=stitched[\"sample\"].coords['tof'])\n",
+    "sc.plot({\"events\": rebinned.hist(), \"histogram\": stitched[\"sample\"]}, errorbars=False)"
    ]
   },
   {
@@ -913,8 +907,7 @@
    "outputs": [],
    "source": [
     "# Normalizing binned data is done using the sc.lookup helper\n",
-    "hist = sc.histogram(\n",
-    "    converted_event[\"vanadium\"], bins=converted[\"sample\"].coords['wavelength'])\n",
+    "hist = converted_event[\"vanadium\"].hist(wavelength=converted[\"sample\"].coords['wavelength'])\n",
     "normalized_event = converted_event[\"sample\"].bins / sc.lookup(func=hist, dim='wavelength')"
    ]
   },
@@ -933,8 +926,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "to_plot = sc.bin(normalized_event,\n",
-    "                            edges=[converted[\"sample\"].coords['wavelength']]).bins.sum()\n",
+    "to_plot = normalized_event.bin(wavelength=converted[\"sample\"].coords['wavelength']).hist()\n",
     "sc.plot({\"stitched_event\": to_plot, \"original\": original})"
    ]
   },

diff --git a/environment.yml b/environment.yml
@@ -20,7 +20,7 @@ dependencies:
   - pytest
   - pythreejs
   - python-graphviz
-  - scippneutron>=0.7
+  - scippneutron>=0.8
   - sphinx
   - sphinx-book-theme=0.2  # custom buttons in top bar do not work with version 0.3
   - sphinx-copybutton