Merge branch 'main' into fix-orso-aggregates

jokasimr · web-flow · commit 71a645ed60f1 · 2025-05-07T14:01:38.000+02:00
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -1,9 +1,9 @@
 # SHA1:e1f1193e2c78c1dda6ffc784197fb6babbad9245
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 annotated-types==0.7.0
     # via pydantic
@@ -17,7 +17,7 @@ cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2025.4.0
+dask==2025.4.1
     # via -r base.in
 dnspython==2.7.0
     # via email-validator
@@ -37,7 +37,7 @@ h5py==3.13.0
     #   scippnexus
 idna==3.10
     # via email-validator
-importlib-metadata==8.6.1
+importlib-metadata==8.7.0
     # via dask
 kiwisolver==1.4.8
     # via matplotlib
@@ -51,7 +51,7 @@ matplotlib==3.10.1
     # via
     #   mpltoolbox
     #   plopp
-mpltoolbox==24.5.1
+mpltoolbox==25.4.0
     # via scippneutron
 networkx==3.4.2
     # via cyclebane
@@ -60,7 +60,6 @@ numpy==2.2.5
     #   contourpy
     #   h5py
     #   matplotlib
-    #   mpltoolbox
     #   pandas
     #   scipp
     #   scippneutron
@@ -82,9 +81,9 @@ plopp==25.4.1
     # via
     #   -r base.in
     #   scippneutron
-pydantic==2.11.3
+pydantic==2.11.4
     # via scippneutron
-pydantic-core==2.33.1
+pydantic-core==2.33.2
     # via pydantic
 pyparsing==3.2.3
     # via matplotlib
@@ -105,7 +104,7 @@ sciline==25.4.1
     # via
     #   -r base.in
     #   essreduce
-scipp==25.4.0
+scipp==25.5.0
     # via
     #   -r base.in
     #   essreduce
diff --git a/requirements/basetest.txt b/requirements/basetest.txt
@@ -1,13 +1,13 @@
 # SHA1:54ed0e3deb2d458e91bae14067e84eaad659f5fd
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
-certifi==2025.1.31
+certifi==2025.4.26
     # via requests
-charset-normalizer==3.4.1
+charset-normalizer==3.4.2
     # via requests
 exceptiongroup==1.2.2
     # via pytest
diff --git a/requirements/ci.txt b/requirements/ci.txt
@@ -1,17 +1,17 @@
 # SHA1:6344d52635ea11dca331a3bc6eb1833c4c64d585
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 cachetools==5.5.2
     # via tox
-certifi==2025.1.31
+certifi==2025.4.26
     # via requests
 chardet==5.2.0
     # via tox
-charset-normalizer==3.4.1
+charset-normalizer==3.4.2
     # via requests
 colorama==0.4.6
     # via tox
diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -1,9 +1,9 @@
 # SHA1:efd19a3a98c69fc3d6d6233ed855de7e4a208f74
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 -r base.txt
 -r ci.txt
diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -1,9 +1,9 @@
 # SHA1:4f1b07bf44faee3c2f897a673e9229b4276d29f9
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 -r base.txt
 accessible-pygments==0.0.5
@@ -28,9 +28,9 @@ bleach[css]==6.2.0
     # via nbconvert
 bqplot==0.12.44
     # via ipydatagrid
-certifi==2025.1.31
+certifi==2025.4.26
     # via requests
-charset-normalizer==3.4.1
+charset-normalizer==3.4.2
     # via requests
 comm==0.2.2
     # via
@@ -64,7 +64,7 @@ ipykernel==6.29.5
     # via -r docs.in
 ipympl==0.9.7
     # via -r docs.in
-ipython==8.35.0
+ipython==8.36.0
     # via
     #   -r docs.in
     #   ipykernel
diff --git a/requirements/mypy.txt b/requirements/mypy.txt
@@ -1,9 +1,9 @@
 # SHA1:859ef9c15e5e57c6c91510133c01f5751feee941
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 -r test.txt
 mypy==1.15.0
diff --git a/requirements/nightly.txt b/requirements/nightly.txt
@@ -1,18 +1,18 @@
 # SHA1:1d5357c0111d56b227d417d6b9ca1c0de673c437
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 --index-url https://pypi.anaconda.org/scipp-nightly-wheels/simple/
 --extra-index-url https://pypi.org/simple
 
 annotated-types==0.7.0
     # via pydantic
-certifi==2025.1.31
+certifi==2025.4.26
     # via requests
-charset-normalizer==3.4.1
+charset-normalizer==3.4.2
     # via requests
 click==8.1.8
     # via dask
@@ -24,7 +24,7 @@ cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2025.4.0
+dask==2025.4.1
     # via -r nightly.in
 dnspython==2.7.0
     # via email-validator
@@ -48,7 +48,7 @@ idna==3.10
     # via
     #   email-validator
     #   requests
-importlib-metadata==8.6.1
+importlib-metadata==8.7.0
     # via dask
 iniconfig==2.1.0
     # via pytest
@@ -64,7 +64,7 @@ matplotlib==3.10.1
     # via
     #   mpltoolbox
     #   plopp
-mpltoolbox==24.5.1
+mpltoolbox==25.4.0
     # via scippneutron
 networkx==3.4.2
     # via cyclebane
@@ -73,7 +73,6 @@ numpy==2.2.5
     #   contourpy
     #   h5py
     #   matplotlib
-    #   mpltoolbox
     #   pandas
     #   scipp
     #   scippneutron
@@ -103,9 +102,9 @@ pluggy==1.5.0
     # via pytest
 pooch==1.8.2
     # via -r nightly.in
-pydantic==2.11.3
+pydantic==2.11.4
     # via scippneutron
-pydantic-core==2.33.1
+pydantic-core==2.33.2
     # via pydantic
 pyparsing==3.2.3
     # via matplotlib
diff --git a/requirements/static.txt b/requirements/static.txt
@@ -1,9 +1,9 @@
 # SHA1:5a0b1bb22ae805d8aebba0f3bf05ab91aceae0d8
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 cfgv==3.4.0
     # via pre-commit
diff --git a/requirements/test.txt b/requirements/test.txt
@@ -1,9 +1,9 @@
 # SHA1:ef2ee9576d8a9e65b44e2865a26887eed3fc49d1
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 -r base.txt
 -r basetest.txt
diff --git a/requirements/wheels.txt b/requirements/wheels.txt
@@ -1,9 +1,9 @@
 # SHA1:80754af91bfb6d1073585b046fe0a474ce868509
 #
-# This file is autogenerated by pip-compile-multi
+# This file was generated by pip-compile-multi.
 # To update, run:
 #
-#    pip-compile-multi
+#    requirements upgrade
 #
 build==1.2.2.post1
     # via -r wheels.in
diff --git a/src/ess/amor/data.py b/src/ess/amor/data.py
@@ -2,8 +2,6 @@
 # Copyright (c) 2025 Scipp contributors (https://github.com/scipp)
 import re
 
-from ..reflectometry.types import Filename, ReferenceRun, SampleRun
-
 _version = "2"
 
 
@@ -76,27 +74,27 @@ def _make_pooch():
 _pooch = _make_pooch()
 
 
-def amor_old_sample_run() -> Filename[SampleRun]:
-    return Filename[SampleRun](_pooch.fetch("sample.nxs"))
+def amor_old_sample_run() -> str:
+    return _pooch.fetch("sample.nxs")
 
 
-def amor_old_reference_run() -> Filename[ReferenceRun]:
-    return Filename[ReferenceRun](_pooch.fetch("reference.nxs"))
+def amor_old_reference_run() -> str:
+    return _pooch.fetch("reference.nxs")
 
 
-def amor_run(number: int | str) -> Filename[SampleRun]:
+def amor_run(number: int | str) -> str:
     fnames = [
         name
         for name in _pooch.registry.keys()
         if re.match(f'amor\\d{{4}}n{int(number):06d}.hdf', name)
     ]
     if len(fnames) != 1:
         raise ValueError(f'Expected exactly one matching file, found {len(fnames)}')
-    return Filename[SampleRun](_pooch.fetch(fnames[0]))
+    return _pooch.fetch(fnames[0])
 
 
-def amor_psi_software_result(number: int | str) -> Filename[SampleRun]:
-    return Filename[SampleRun](_pooch.fetch(f"{int(number):03d}.Rqz.ort"))
+def amor_psi_software_result(number: int | str) -> str:
+    return _pooch.fetch(f"{int(number):03d}.Rqz.ort")
 
 
 __all__ = [
diff --git a/src/ess/reflectometry/gui.py b/src/ess/reflectometry/gui.py
@@ -2,6 +2,7 @@
 # Copyright (c) 2025 Scipp contributors (https://github.com/scipp)
 import glob
 import os
+import re
 import uuid
 from collections.abc import Callable
 
@@ -902,7 +903,12 @@ def toggle_line(name, value, figure):
         self.plot_log.children = (box, *self.plot_log.children)
 
     def get_filepath_from_run(self, run):
-        return os.path.join(self.path, f'amor2024n{run:0>6}.hdf')
+        fname = next(
+            name
+            for name in os.listdir(self.path)
+            if re.match(f'amor\\d{{4}}n{int(run):06d}.hdf', name)
+        )
+        return os.path.join(self.path, fname)
 
     def get_row_key(self, row):
         reference_metadata = (
diff --git a/tests/amor/pipeline_test.py b/tests/amor/pipeline_test.py
@@ -10,8 +10,9 @@
 from scipp.testing import assert_allclose
 
 from ess import amor
-from ess.amor import data  # noqa: F401
+from ess.amor import data
 from ess.reflectometry import orso
+from ess.reflectometry.tools import scale_reflectivity_curves_to_overlap
 from ess.reflectometry.types import (
     Filename,
     ProtonCurrent,
@@ -105,13 +106,40 @@ def test_orso_pipeline(amor_pipeline: sciline.Pipeline):
 
 @pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")
 @pytest.mark.filterwarnings("ignore:Invalid transformation, missing attribute")
-def test_save_reduced_orso_file(amor_pipeline: sciline.Pipeline, output_folder: Path):
+def test_save_reduced_orso_file(output_folder: Path):
     from orsopy import fileio
 
-    amor_pipeline[SampleRotation[SampleRun]] = sc.scalar(0.85, unit="deg")
-    amor_pipeline[Filename[SampleRun]] = amor.data.amor_run(608)
-    res = amor_pipeline.compute(orso.OrsoIofQDataset)
-    fileio.orso.save_orso(datasets=[res], fname=output_folder / 'amor_reduced_iofq.ort')
+    wf = sciline.Pipeline(providers=amor.providers, params=amor.default_parameters())
+    wf[SampleSize[SampleRun]] = sc.scalar(10.0, unit="mm")
+    wf[SampleSize[ReferenceRun]] = sc.scalar(10.0, unit="mm")
+    wf[YIndexLimits] = sc.scalar(11), sc.scalar(41)
+    wf[WavelengthBins] = sc.geomspace("wavelength", 3, 12.5, 2000, unit="angstrom")
+    wf[ZIndexLimits] = sc.scalar(170), sc.scalar(266)
+    wf = with_filenames(
+        wf, SampleRun, [data.amor_run(4079), data.amor_run(4080), data.amor_run(4081)]
+    )
+    wf[Filename[ReferenceRun]] = data.amor_run(4152)
+    wf[QBins] = sc.geomspace(dim="Q", start=0.01, stop=0.06, num=201, unit="1/angstrom")
+    r = wf.compute(ReflectivityOverQ)
+    _, (s,) = scale_reflectivity_curves_to_overlap(
+        [r.hist()],
+        critical_edge_interval=(
+            sc.scalar(0.01, unit='1/angstrom'),
+            sc.scalar(0.014, unit='1/angstrom'),
+        ),
+    )
+    wf[ReflectivityOverQ] = s * r
+    wf[orso.OrsoCreator] = orso.OrsoCreator(
+        fileio.base.Person(
+            name="Max Mustermann",
+            affiliation="European Spallation Source ERIC",
+            contact="max.mustermann@ess.eu",
+        )
+    )
+    fileio.orso.save_orso(
+        datasets=[wf.compute(orso.OrsoIofQDataset)],
+        fname=output_folder / 'amor_reduced_iofq.ort',
+    )
 
 
 @pytest.mark.filterwarnings("ignore:Failed to convert .* into a transformation")

Original file line number	Diff line number	Diff line change
`@@ -1,13 +1,13 @@`
`1`	`1`	`# SHA1:54ed0e3deb2d458e91bae14067e84eaad659f5fd`
`2`	`2`	`#`
`3`		`-# This file is autogenerated by pip-compile-multi`
	`3`	`+# This file was generated by pip-compile-multi.`
`4`	`4`	`# To update, run:`
`5`	`5`	`#`
`6`		`-# pip-compile-multi`
	`6`	`+# requirements upgrade`
`7`	`7`	`#`
`8`		`-certifi==2025.1.31`
	`8`	`+certifi==2025.4.26`
`9`	`9`	`# via requests`
`10`		`-charset-normalizer==3.4.1`
	`10`	`+charset-normalizer==3.4.2`
`11`	`11`	`# via requests`
`12`	`12`	`exceptiongroup==1.2.2`
`13`	`13`	`# via pytest`
Original file line number	Diff line number	Diff line change
`@@ -1,9 +1,9 @@`
`1`	`1`	`# SHA1:efd19a3a98c69fc3d6d6233ed855de7e4a208f74`
`2`	`2`	`#`
`3`		`-# This file is autogenerated by pip-compile-multi`
	`3`	`+# This file was generated by pip-compile-multi.`
`4`	`4`	`# To update, run:`
`5`	`5`	`#`
`6`		`-# pip-compile-multi`
	`6`	`+# requirements upgrade`
`7`	`7`	`#`
`8`	`8`	`-r base.txt`
`9`	`9`	`-r ci.txt`
Original file line number	Diff line number	Diff line change
`@@ -1,9 +1,9 @@`
`1`	`1`	`# SHA1:859ef9c15e5e57c6c91510133c01f5751feee941`
`2`	`2`	`#`
`3`		`-# This file is autogenerated by pip-compile-multi`
	`3`	`+# This file was generated by pip-compile-multi.`
`4`	`4`	`# To update, run:`
`5`	`5`	`#`
`6`		`-# pip-compile-multi`
	`6`	`+# requirements upgrade`
`7`	`7`	`#`
`8`	`8`	`-r test.txt`
`9`	`9`	`mypy==1.15.0`
Original file line number	Diff line number	Diff line change
`@@ -1,9 +1,9 @@`
`1`	`1`	`# SHA1:5a0b1bb22ae805d8aebba0f3bf05ab91aceae0d8`
`2`	`2`	`#`
`3`		`-# This file is autogenerated by pip-compile-multi`
	`3`	`+# This file was generated by pip-compile-multi.`
`4`	`4`	`# To update, run:`
`5`	`5`	`#`
`6`		`-# pip-compile-multi`
	`6`	`+# requirements upgrade`
`7`	`7`	`#`
`8`	`8`	`cfgv==3.4.0`
`9`	`9`	`# via pre-commit`
Original file line number	Diff line number	Diff line change
`@@ -1,9 +1,9 @@`
`1`	`1`	`# SHA1:ef2ee9576d8a9e65b44e2865a26887eed3fc49d1`
`2`	`2`	`#`
`3`		`-# This file is autogenerated by pip-compile-multi`
	`3`	`+# This file was generated by pip-compile-multi.`
`4`	`4`	`# To update, run:`
`5`	`5`	`#`
`6`		`-# pip-compile-multi`
	`6`	`+# requirements upgrade`
`7`	`7`	`#`
`8`	`8`	`-r base.txt`
`9`	`9`	`-r basetest.txt`
Original file line number	Diff line number	Diff line change
`@@ -1,9 +1,9 @@`
`1`	`1`	`# SHA1:80754af91bfb6d1073585b046fe0a474ce868509`
`2`	`2`	`#`
`3`		`-# This file is autogenerated by pip-compile-multi`
	`3`	`+# This file was generated by pip-compile-multi.`
`4`	`4`	`# To update, run:`
`5`	`5`	`#`
`6`		`-# pip-compile-multi`
	`6`	`+# requirements upgrade`
`7`	`7`	`#`
`8`	`8`	`build==1.2.2.post1`
`9`	`9`	`# via -r wheels.in`