Merge pull request #40 from scipp/guideline-adherence

Guideline adherence

Author: jokasimr

conda/meta.yaml

@@ -20,6 +20,7 @@ requirements:
     - sciline>=23.9.1
     - scipp>=23.8.0
     - scippneutron>=23.9.0
+    - essreduce
     - python>=3.10
 
 test:

docs/examples/amor.ipynb

@@ -20,7 +20,8 @@
     "import scipp as sc\n",
     "import sciline\n",
     "from essreflectometry.amor import providers, default_parameters\n",
-    "from essreflectometry.types import *"
+    "from essreflectometry.types import *\n",
+    "from essreflectometry.amor.data import providers as amor_data"
    ]
   },
   {
@@ -29,27 +30,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "params = {\n",
-    "    **default_parameters,\n",
-    "    QBins: sc.geomspace(dim='Q', start=0.008, stop=0.075, num=200, unit='1/angstrom'),\n",
-    "    SampleRotation[Sample]: sc.scalar(0.7989, unit='deg'),\n",
-    "    Filename[Sample]: \"sample.nxs\",\n",
-    "    SampleRotation[Reference]: sc.scalar(0.8389, unit='deg'),\n",
-    "    Filename[Reference]: \"reference.nxs\",\n",
-    "    WavelengthEdges: sc.array(dims=['wavelength'], values=[2.4, 16.0], unit='angstrom'),\n",
-    "}"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pipeline = sciline.Pipeline(\n",
-    "    providers,\n",
-    "    params=params\n",
-    ")"
+    "pl = sciline.Pipeline(\n",
+    "    (*providers, *amor_data),\n",
+    "    params=default_parameters\n",
+    ")\n",
+    "\n",
+    "pl[QBins] = sc.geomspace(dim='Q', start=0.008, stop=0.075, num=200, unit='1/angstrom')\n",
+    "pl[SampleRotation[Sample]] = sc.scalar(0.7989, unit='deg')\n",
+    "pl[PoochFilename[Sample]] = \"sample.nxs\"\n",
+    "pl[SampleRotation[Reference]] = sc.scalar(0.8389, unit='deg')\n",
+    "pl[PoochFilename[Reference]] = \"reference.nxs\"\n",
+    "pl[WavelengthEdges] = sc.array(dims=['wavelength'], values=[2.4, 16.0], unit='angstrom')"
    ]
   },
   {
@@ -58,7 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pipeline.visualize((NormalizedIofQ, QResolution), graph_attr={'rankdir': 'LR'})"
+    "pl.visualize((NormalizedIofQ, QResolution), graph_attr={'rankdir': 'LR'})"
    ]
   },
   {
@@ -68,7 +59,7 @@
    "outputs": [],
    "source": [
     "# Compute I over Q and the standard deviation of Q\n",
-    "ioq, qstd = pipeline.compute((NormalizedIofQ, QResolution)).values()"
+    "ioq, qstd = pl.compute((NormalizedIofQ, QResolution)).values()"
    ]
   },
   {
@@ -103,7 +94,7 @@
    "outputs": [],
    "source": [
     "from essreflectometry.types import ThetaData\n",
-    "pipeline.compute(ThetaData[Sample])\\\n",
+    "pl.compute(ThetaData[Sample])\\\n",
     "    .bins.concat('detector_number')\\\n",
     "    .hist(\n",
     "        theta=sc.linspace(dim='theta', start=0.0, stop=1.2, num=165, unit='deg').to(unit='rad'),\n",
@@ -149,22 +140,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "providers_with_metadata = (\n",
-    "    *providers,\n",
-    "    *orso.providers,\n",
-    "    *amor_orso.providers,\n",
-    ")\n",
+    "for p in (*orso.providers, *amor_orso.providers):\n",
+    "    pl.insert(p)\n",
     "\n",
-    "params[orso.OrsoCreator] = orso.OrsoCreator(fileio.base.Person(\n",
+    "pl[orso.OrsoCreator] = orso.OrsoCreator(fileio.base.Person(\n",
     "    name='Max Mustermann',\n",
     "    affiliation='European Spallation Source ERIC',\n",
     "    contact='[email protected]',\n",
-    "))\n",
-    "\n",
-    "metadata_pipeline = sciline.Pipeline(\n",
-    "    providers_with_metadata,\n",
-    "    params=params\n",
-    ")"
+    "))"
    ]
   },
   {
@@ -180,7 +163,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iofq_dataset = metadata_pipeline.compute(orso.OrsoIofQDataset)"
+    "iofq_dataset = pl.compute(orso.OrsoIofQDataset)"
    ]
   },
   {
@@ -243,7 +226,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iofq_dataset.info.reduction.corrections = orso.find_corrections(metadata_pipeline.get(orso.OrsoIofQDataset))"
+    "iofq_dataset.info.reduction.corrections = orso.find_corrections(pl.get(orso.OrsoIofQDataset))"
    ]
   },
   {

pyproject.toml

@@ -39,6 +39,7 @@ dependencies = [
   "sciline>=23.9.1",
   "scipp>=23.8.0",
   "scippneutron>=23.9.0",
+  "essreduce",
 ]
 
 dynamic = ["version"]

requirements/base.in

@@ -11,3 +11,4 @@ orsopy
 sciline>=23.9.1
 scipp>=23.8.0
 scippneutron>=23.9.0
+essreduce

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:697621007a6df52e05884bd9bf630052e4aa6fbe
+# SHA1:1b431955cc8f1e9144b3b02f13d86b0693935140
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -15,16 +15,18 @@ click==8.1.7
     # via dask
 cloudpickle==3.0.0
     # via dask
-comm==0.2.1
+comm==0.2.2
     # via ipywidgets
 contourpy==1.2.0
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-dask==2024.2.0
+dask==2024.3.0
     # via -r base.in
 decorator==5.1.1
     # via ipython
+essreduce==24.3.11
+    # via -r base.in
 exceptiongroup==1.2.0
     # via ipython
 executing==2.0.1
@@ -41,11 +43,11 @@ h5py==3.10.0
     #   scippnexus
 idna==3.6
     # via requests
-importlib-metadata==7.0.1
+importlib-metadata==7.0.2
     # via dask
 ipydatawidgets==4.3.5
     # via pythreejs
-ipython==8.22.1
+ipython==8.22.2
     # via ipywidgets
 ipywidgets==8.1.2
     # via
@@ -73,9 +75,9 @@ numpy==1.26.4
     #   scipp
     #   scippneutron
     #   scipy
-orsopy==1.1.0
+orsopy==1.2.0
     # via -r base.in
-packaging==23.2
+packaging==24.0
     # via
     #   dask
     #   matplotlib
@@ -102,9 +104,9 @@ pure-eval==0.2.2
     # via stack-data
 pygments==2.17.2
     # via ipython
-pyparsing==3.1.1
+pyparsing==3.1.2
     # via matplotlib
-python-dateutil==2.8.2
+python-dateutil==2.9.0.post0
     # via
     #   -r base.in
     #   matplotlib
@@ -122,12 +124,15 @@ sciline==24.2.1
 scipp==24.2.0
     # via
     #   -r base.in
+    #   essreduce
     #   scippneutron
     #   scippnexus
 scippneutron==24.1.0
     # via -r base.in
-scippnexus==23.12.1
-    # via scippneutron
+scippnexus==24.3.1
+    # via
+    #   essreduce
+    #   scippneutron
 scipy==1.12.0
     # via
     #   scippneutron
@@ -142,7 +147,7 @@ toolz==0.12.1
     # via
     #   dask
     #   partd
-traitlets==5.14.1
+traitlets==5.14.2
     # via
     #   comm
     #   ipython
@@ -158,5 +163,5 @@ wcwidth==0.2.13
     # via prompt-toolkit
 widgetsnbextension==4.0.10
     # via ipywidgets
-zipp==3.17.0
+zipp==3.18.0
     # via importlib-metadata

requirements/basetest.txt

@@ -9,11 +9,11 @@ exceptiongroup==1.2.0
     # via pytest
 iniconfig==2.0.0
     # via pytest
-packaging==23.2
+packaging==24.0
     # via pytest
 pluggy==1.4.0
     # via pytest
-pytest==8.0.1
+pytest==8.1.1
     # via -r basetest.in
 tomli==2.0.1
     # via pytest

requirements/ci.txt

@@ -5,7 +5,7 @@
 #
 #    pip-compile-multi
 #
-cachetools==5.3.2
+cachetools==5.3.3
     # via tox
 certifi==2024.2.2
     # via requests
@@ -27,7 +27,7 @@ gitpython==3.1.42
     # via -r ci.in
 idna==3.6
     # via requests
-packaging==23.2
+packaging==24.0
     # via
     #   -r ci.in
     #   pyproject-api
@@ -48,7 +48,7 @@ tomli==2.0.1
     # via
     #   pyproject-api
     #   tox
-tox==4.13.0
+tox==4.14.1
     # via -r ci.in
 urllib3==2.2.1
     # via requests

requirements/dev.txt

@@ -46,7 +46,7 @@ isoduration==20.11.0
     # via jsonschema
 jinja2-ansible-filters==1.3.2
     # via copier
-json5==0.9.17
+json5==0.9.22
     # via jupyterlab-server
 jsonpointer==2.4
     # via jsonschema
@@ -55,21 +55,21 @@ jsonschema[format-nongpl]==4.21.1
     #   jupyter-events
     #   jupyterlab-server
     #   nbformat
-jupyter-events==0.9.0
+jupyter-events==0.9.1
     # via jupyter-server
-jupyter-lsp==2.2.2
+jupyter-lsp==2.2.4
     # via jupyterlab
-jupyter-server==2.12.5
+jupyter-server==2.13.0
     # via
     #   jupyter-lsp
     #   jupyterlab
     #   jupyterlab-server
     #   notebook-shim
-jupyter-server-terminals==0.5.2
+jupyter-server-terminals==0.5.3
     # via jupyter-server
-jupyterlab==4.1.2
+jupyterlab==4.1.4
     # via -r dev.in
-jupyterlab-server==2.25.3
+jupyterlab-server==2.25.4
     # via jupyterlab
 notebook-shim==0.2.4
     # via jupyterlab
@@ -79,17 +79,17 @@ pathspec==0.12.1
     # via copier
 pip-compile-multi==2.6.3
     # via -r dev.in
-pip-tools==7.4.0
+pip-tools==7.4.1
     # via pip-compile-multi
 plumbum==1.8.2
     # via copier
 prometheus-client==0.20.0
     # via jupyter-server
 pycparser==2.21
     # via cffi
-pydantic==2.6.1
+pydantic==2.6.4
     # via copier
-pydantic-core==2.16.2
+pydantic-core==2.16.3
     # via pydantic
 python-json-logger==2.0.7
     # via jupyter-events
@@ -107,25 +107,25 @@ rfc3986-validator==0.1.1
     #   jupyter-events
 send2trash==1.8.2
     # via jupyter-server
-sniffio==1.3.0
+sniffio==1.3.1
     # via
     #   anyio
     #   httpx
-terminado==0.18.0
+terminado==0.18.1
     # via
     #   jupyter-server
     #   jupyter-server-terminals
 toposort==1.10
     # via pip-compile-multi
-types-python-dateutil==2.8.19.20240106
+types-python-dateutil==2.8.19.20240311
     # via arrow
 uri-template==1.3.0
     # via jsonschema
 webcolors==1.13
     # via jsonschema
 websocket-client==1.7.0
     # via jupyter-server
-wheel==0.42.0
+wheel==0.43.0
     # via pip-tools
 
 # The following packages are considered to be unsafe in a requirements file: