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SimonHeybrockSimonHeybrock
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Merge pull request #99 from scipp/update-ess-reduce-nexus
Update for restructured NeXus base workflow from `ess.reduce.nexus`
2 parents 45b8fd4 + 42534de commit 90e3a57

16 files changed

+90
-83
lines changed

‎pyproject.toml

+1-1
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@@ -31,7 +31,7 @@ requires-python = ">=3.10"
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# Make sure to list one dependency per line.
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dependencies = [
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"dask",
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"essreduce>=24.10.0",
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"essreduce>=24.10.2",
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"graphviz",
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"numpy",
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"plopp",

‎requirements/base.in

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@@ -3,7 +3,7 @@
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# --- END OF CUSTOM SECTION ---
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# The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
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dask
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essreduce>=24.10.0
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essreduce>=24.10.2
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graphviz
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numpy
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plopp

‎requirements/base.txt

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@@ -1,4 +1,4 @@
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# SHA1:3edca7ef7f02d8df072e91ce62fa7acd26cc0825
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# SHA1:86f9288f7221f3a8506d1cc40db8a4584011b0e0
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#
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# This file is autogenerated by pip-compile-multi
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# To update, run:
@@ -15,15 +15,15 @@ comm==0.2.2
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# via ipywidgets
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contourpy==1.3.0
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# via matplotlib
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cyclebane==24.6.0
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cyclebane==24.10.0
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# via sciline
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cycler==0.12.1
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# via matplotlib
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dask==2024.9.1
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# via -r base.in
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decorator==5.1.1
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# via ipython
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essreduce==24.10.0
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essreduce==24.10.2
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# via -r base.in
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exceptiongroup==1.2.2
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# via ipython
@@ -43,7 +43,7 @@ importlib-metadata==8.5.0
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# via dask
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ipydatawidgets==4.3.5
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# via pythreejs
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ipython==8.27.0
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ipython==8.28.0
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# via ipywidgets
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ipywidgets==8.1.5
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# via
@@ -65,9 +65,9 @@ matplotlib-inline==0.1.7
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# via ipython
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mpltoolbox==24.5.1
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# via scippneutron
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networkx==3.3
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networkx==3.4
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# via cyclebane
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numpy==2.1.1
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numpy==2.1.2
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# via
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# -r base.in
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# contourpy
@@ -125,7 +125,7 @@ scipp==24.9.1
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# scippnexus
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scippneutron==24.9.0
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# via -r base.in
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scippnexus==24.9.1
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scippnexus==24.10.0
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# via
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# -r base.in
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# essreduce
@@ -140,7 +140,7 @@ six==1.16.0
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# python-dateutil
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stack-data==0.6.3
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# via ipython
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toolz==0.12.1
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toolz==1.0.0
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# via
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# dask
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# partd

‎requirements/basetest.txt

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@@ -7,15 +7,15 @@
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#
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certifi==2024.8.30
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# via requests
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charset-normalizer==3.3.2
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charset-normalizer==3.4.0
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# via requests
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exceptiongroup==1.2.2
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# via pytest
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idna==3.10
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# via requests
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iniconfig==2.0.0
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# via pytest
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numpy==2.1.1
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numpy==2.1.2
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# via pandas
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packaging==24.1
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# via
@@ -39,7 +39,7 @@ requests==2.32.3
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# via pooch
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six==1.16.0
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# via python-dateutil
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tomli==2.0.1
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tomli==2.0.2
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# via pytest
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tzdata==2024.2
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# via pandas

‎requirements/ci.txt

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@@ -11,11 +11,11 @@ certifi==2024.8.30
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# via requests
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chardet==5.2.0
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# via tox
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charset-normalizer==3.3.2
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charset-normalizer==3.4.0
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# via requests
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colorama==0.4.6
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# via tox
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distlib==0.3.8
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distlib==0.3.9
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# via virtualenv
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filelock==3.16.1
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# via
@@ -44,11 +44,11 @@ requests==2.32.3
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# via -r ci.in
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smmap==5.0.1
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# via gitdb
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tomli==2.0.1
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tomli==2.0.2
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# via
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# pyproject-api
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# tox
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tox==4.21.0
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tox==4.21.2
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# via -r ci.in
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typing-extensions==4.12.2
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# via tox

‎requirements/dev.txt

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@@ -81,7 +81,7 @@ pip-compile-multi==2.6.4
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# via -r dev.in
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pip-tools==7.4.1
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# via pip-compile-multi
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plumbum==1.8.3
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plumbum==1.9.0
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# via copier
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prometheus-client==0.21.0
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# via jupyter-server
@@ -115,7 +115,7 @@ terminado==0.18.1
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# jupyter-server-terminals
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toposort==1.10
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# via pip-compile-multi
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types-python-dateutil==2.9.0.20240906
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types-python-dateutil==2.9.0.20241003
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# via arrow
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uri-template==1.3.0
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# via jsonschema

‎requirements/docs.txt

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@@ -26,9 +26,9 @@ bleach==6.1.0
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# via nbconvert
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certifi==2024.8.30
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# via requests
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charset-normalizer==3.3.2
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charset-normalizer==3.4.0
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# via requests
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debugpy==1.8.6
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debugpy==1.8.7
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# via ipykernel
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defusedxml==0.7.1
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# via nbconvert
@@ -60,7 +60,7 @@ jinja2==3.1.4
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# sphinx
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jsonschema==4.23.0
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# via nbformat
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jsonschema-specifications==2023.12.1
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jsonschema-specifications==2024.10.1
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# via jsonschema
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jupyter-client==8.6.3
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# via
@@ -81,7 +81,7 @@ markdown-it-py==3.0.0
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# via
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# mdit-py-plugins
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# myst-parser
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markupsafe==2.1.5
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markupsafe==3.0.1
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# via
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# jinja2
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# nbconvert
@@ -150,7 +150,7 @@ snowballstemmer==2.2.0
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# via sphinx
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soupsieve==2.6
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# via beautifulsoup4
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sphinx==8.0.2
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sphinx==8.1.0
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# via
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# -r docs.in
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# myst-parser
@@ -160,7 +160,7 @@ sphinx==8.0.2
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# sphinx-copybutton
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# sphinx-design
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# sphinxcontrib-bibtex
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sphinx-autodoc-typehints==2.4.4
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sphinx-autodoc-typehints==2.5.0
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# via -r docs.in
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sphinx-copybutton==0.5.2
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# via -r docs.in
@@ -182,7 +182,7 @@ sphinxcontrib-serializinghtml==2.0.0
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# via sphinx
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tinycss2==1.3.0
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# via nbconvert
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tomli==2.0.1
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tomli==2.0.2
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# via sphinx
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tornado==6.4.1
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# via

‎requirements/nightly.txt

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@@ -16,7 +16,7 @@ comm==0.2.2
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# via ipywidgets
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contourpy==1.3.0
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# via matplotlib
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cyclebane==24.6.0
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cyclebane==24.10.0
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# via sciline
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cycler==0.12.1
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# via matplotlib
@@ -42,7 +42,7 @@ importlib-metadata==8.5.0
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# via dask
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ipydatawidgets==4.3.5
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# via pythreejs
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ipython==8.27.0
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ipython==8.28.0
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# via ipywidgets
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ipywidgets==8.1.5
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# via
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# via ipython
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mpltoolbox==24.5.1
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# via scippneutron
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networkx==3.3
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networkx==3.4
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# via cyclebane
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parso==0.8.4
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# via jedi
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# scippnexus
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stack-data==0.6.3
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# via ipython
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toolz==0.12.1
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toolz==1.0.0
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# via
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# dask
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# partd

‎requirements/static.txt

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@@ -7,7 +7,7 @@
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#
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cfgv==3.4.0
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# via pre-commit
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distlib==0.3.8
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distlib==0.3.9
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# via virtualenv
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filelock==3.16.1
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# via virtualenv
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# via pre-commit
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platformdirs==4.3.6
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# via virtualenv
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pre-commit==3.8.0
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pre-commit==4.0.1
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# via -r static.in
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pyyaml==6.0.2
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# via pre-commit

‎requirements/wheels.txt

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#
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# pip-compile-multi
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#
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build==1.2.2
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build==1.2.2.post1
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# via -r wheels.in
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packaging==24.1
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# via build
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pyproject-hooks==1.2.0
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# via build
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tomli==2.0.1
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tomli==2.0.2
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# via build

‎src/ess/dream/io/geant4.py

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Original file line numberDiff line numberDiff line change
@@ -4,19 +4,20 @@
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import numpy as np
55
import sciline
66
import scipp as sc
7+
import scippnexus as snx
78

89
from ess.powder.types import (
910
CalibratedDetector,
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CalibrationData,
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CalibrationFilename,
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DetectorData,
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Filename,
14-
NeXusDetector,
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NeXusComponent,
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NeXusDetectorName,
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NeXusSample,
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NeXusSource,
17+
Position,
1818
RunType,
1919
)
20+
from ess.reduce.nexus.types import CalibratedBeamline
2021
from ess.reduce.nexus.workflow import GenericNeXusWorkflow
2122

2223
MANTLE_DETECTOR_ID = sc.index(7)
@@ -60,9 +61,23 @@ def load_geant4_csv(file_path: Filename[RunType]) -> AllRawDetectors[RunType]:
6061

6162
def extract_geant4_detector(
6263
detectors: AllRawDetectors[RunType], detector_name: NeXusDetectorName
63-
) -> NeXusDetector[RunType]:
64+
) -> NeXusComponent[snx.NXdetector, RunType]:
6465
"""Extract a single detector from a loaded GEANT4 simulation."""
65-
return NeXusDetector[RunType](detectors["instrument"][detector_name])
66+
return NeXusComponent[snx.NXdetector, RunType](
67+
detectors["instrument"][detector_name]
68+
)
69+
70+
71+
def get_calibrated_geant4_detector(
72+
detector: NeXusComponent[snx.NXdetector, RunType],
73+
) -> CalibratedDetector[RunType]:
74+
"""
75+
Replacement for :py:func:`ess.reduce.nexus.workflow.get_calibrated_detector`.
76+
77+
Since the Geant4 detectors already have computed positions as well as logical shape,
78+
this just extracts the relevant event data.
79+
"""
80+
return detector['events'].copy(deep=False)
6681

6782

6883
def _load_raw_events(file_path: str) -> sc.DataArray:
@@ -171,21 +186,21 @@ def geant4_load_calibration(filename: CalibrationFilename) -> CalibrationData:
171186

172187

173188
def dummy_assemble_detector_data(
174-
detector: CalibratedDetector[RunType],
189+
detector: CalibratedBeamline[RunType],
175190
) -> DetectorData[RunType]:
176191
"""Dummy assembly of detector data, detector already contains neutron data."""
177192
return DetectorData[RunType](detector)
178193

179194

180-
def dummy_source() -> NeXusSource[RunType]:
181-
return NeXusSource[RunType](
182-
sc.DataGroup(position=sc.vector([np.nan, np.nan, np.nan], unit="mm"))
195+
def dummy_source_position() -> Position[snx.NXsource, RunType]:
196+
return Position[snx.NXsource, RunType](
197+
sc.vector([np.nan, np.nan, np.nan], unit="mm")
183198
)
184199

185200

186-
def dummy_sample() -> NeXusSample[RunType]:
187-
return NeXusSample[RunType](
188-
sc.DataGroup(position=sc.vector([np.nan, np.nan, np.nan], unit="mm"))
201+
def dummy_sample_position() -> Position[snx.NXsample, RunType]:
202+
return Position[snx.NXsample, RunType](
203+
sc.vector([np.nan, np.nan, np.nan], unit="mm")
189204
)
190205

191206

@@ -197,7 +212,8 @@ def LoadGeant4Workflow() -> sciline.Pipeline:
197212
wf.insert(extract_geant4_detector)
198213
wf.insert(load_geant4_csv)
199214
wf.insert(geant4_load_calibration)
215+
wf.insert(get_calibrated_geant4_detector)
200216
wf.insert(dummy_assemble_detector_data)
201-
wf.insert(dummy_source)
202-
wf.insert(dummy_sample)
217+
wf.insert(dummy_source_position)
218+
wf.insert(dummy_sample_position)
203219
return wf

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