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refactor: update sasview api for test_sas.py #126

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Merged
sbillinge merged 8 commits into from
Aug 5, 2025
Merged

refactor: update sasview api for test_sas.py #126

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96e1ff3
refactor: update sasview api for test_sas.py
zmx27 Jul 30, 2025
6112cdd
chore: add news file
zmx27 Jul 30, 2025
c68f981
chore: remove comments and use public function to load models
zmx27 Aug 1, 2025
5854969
chore: skip characteristic function tests, add fixme to tolerances an…
zmx27 Aug 3, 2025
a2d280a
chore: redo error messages for source code and pytest skips
zmx27 Aug 4, 2025
1bdd326
chore: modified messages and news file according to feedback
zmx27 Aug 4, 2025
ac23c4c
chore: add sasmodels to requirements folder and move load_standard_mo…
zmx27 Aug 4, 2025
29ef13e
chore: add sasmodels imports inside test functions
zmx27 Aug 5, 2025
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23 changes: 23 additions & 0 deletions news/fix-sasmodels.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
**Added:**

* <news item>

**Changed:**

* Refactored code utilizing sasmodels to use the new sasview api.
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@sbillinge sbillinge Aug 1, 2025

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please move to fixed. This is a bug fix not a change. Reserve changes for changes in behavior that a user might need to know about.


**Deprecated:**

* <news item>

**Removed:**

* <news item>

**Fixed:**

* <news item>

**Security:**

* <news item>
19 changes: 16 additions & 3 deletions src/diffpy/srfit/sas/sasparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,6 @@

from diffpy.srfit.exceptions import ParseError
from diffpy.srfit.fitbase.profileparser import ProfileParser
from diffpy.srfit.sas.sasimport import sasimport
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@zmx27 zmx27 Jul 30, 2025

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I deleted the import from this file as not used but I haven't deleted sasimport yet because the sas package in sasview still exists, and we still need to import from it.



class SASParser(ProfileParser):
Expand Down Expand Up @@ -102,10 +101,15 @@ def parseFile(self, filename):
Raises IOError if the file cannot be read
Raises ParseError if the file cannot be parsed
"""
import sasdata.dataloader.loader as ld

Loader = sasimport("sas.dataloader.loader").Loader
Loader = ld.Loader
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please could you make ld more readable. maybe sas_dataloader?

loader = Loader()

# Convert Path object to string if needed
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@zmx27 zmx27 Jul 30, 2025

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load seems to expect a string now because it's calling .lower() on filename. In the source code, the traceback leads to the lookup() function in sasdata.data_util.registry, which calls:

path_lower = path.lower()

if not isinstance(filename, str):
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why not just data = loader.load(str(filename)). I don't think we have to wrap this in a conditional.

filename = str(filename)

try:
data = loader.load(filename)
except RuntimeError as e:
Expand All @@ -118,7 +122,16 @@ def parseFile(self, filename):
self._meta["filename"] = filename
self._meta["datainfo"] = data

self._banks.append([data.x, data.y, data.dx, data.dy])
# Handle case where loader returns a list of data objects
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remove comment. Just make you code as readable as possible.

if isinstance(data, list):
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@zmx27 zmx27 Jul 30, 2025

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The loader returns a list now. From source code:

def load(self, file_path_list: Union[List[Union[str, Path]], str, Path],
             format: Optional[Union[List[str], str]] = None
             ) -> List[Union[Data1D, Data2D]]:

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we presumably don't need the conditional then. If it returns a list then just treat a list. We don't have to backwards compatible because we are only supporting recent versions of all dependencies.

# If it's a list, iterate through each data object
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remove gratuitous comments

for data_obj in data:
self._banks.append(
[data_obj.x, data_obj.y, data_obj.dx, data_obj.dy]
)
else:
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remove this else

# If it's a single data object, use it directly
self._banks.append([data.x, data.y, data.dx, data.dy])
self.selectBank(0)
return

Expand Down
10 changes: 9 additions & 1 deletion src/diffpy/srfit/sas/sasprofile.py
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Expand Up @@ -82,7 +82,15 @@ def __init__(self, datainfo):
datainfo
The DataInfo object this wraps.
"""
self._datainfo = datainfo
# Handle case where datainfo is a list (new sasdata behavior)
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@sbillinge sbillinge Aug 1, 2025

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see above. We can now assume the datatype is a list.

if isinstance(datainfo, list):
if len(datainfo) == 0:
raise ValueError("Empty datainfo list provided")
# Use the first data object if it's a list
self._datainfo = datainfo[0]
else:
# Single datainfo object (legacy behavior)
self._datainfo = datainfo
Profile.__init__(self)

self._xobs = self._datainfo.x
Expand Down
8 changes: 5 additions & 3 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,18 @@
import six

import diffpy.srfit.equation.literals as literals
from diffpy.srfit.sas.sasimport import sasimport

logger = logging.getLogger(__name__)


@lru_cache()
def has_sas():
try:
sasimport("sas.pr.invertor")
sasimport("sas.models")
import sas
import sasmodels

del sas
del sasmodels
return True
except ImportError:
return False
Expand Down
16 changes: 9 additions & 7 deletions tests/test_characteristicfunctions.py
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Expand Up @@ -19,8 +19,10 @@
import numpy
import pytest

# Use the updated SasView model API to load models
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@sbillinge sbillinge Aug 1, 2025

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please remove comments

from sasmodels.sasview_model import _make_standard_model

import diffpy.srfit.pdf.characteristicfunctions as cf
from diffpy.srfit.sas.sasimport import sasimport

# # Global variables to be assigned in setUp
# cf = None
Expand All @@ -34,7 +36,7 @@ def testSphere(sas_available):
pytest.skip("sas package not available")
radius = 25
# Calculate sphere cf from SphereModel
SphereModel = sasimport("sas.models.SphereModel").SphereModel
SphereModel = _make_standard_model("sphere")
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@sbillinge sbillinge Aug 1, 2025

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it seems a bit odd that we are importing a private function. Are we sure this is the way we are supposed to be using the API?

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@zmx27 zmx27 Aug 1, 2025

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I'll keep looking into this

model = SphereModel()
model.setParam("radius", radius)
ff = cf.SASCF("sphere", model)
Expand All @@ -56,10 +58,10 @@ def testSpheroid(sas_available):
prad = 20.9
erad = 33.114
# Calculate cf from EllipsoidModel
EllipsoidModel = sasimport("sas.models.EllipsoidModel").EllipsoidModel
EllipsoidModel = _make_standard_model("ellipsoid")
model = EllipsoidModel()
model.setParam("radius_a", prad)
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I could not find any mention of the use of radius_a and radius_b in the documentation for sasview, even ones that dated back to version 4.x (the latest release is version 6.1.0). I can only assume that suitable replacements are radius_polar and radius_equatorial, which are the parameters that the ellipsoid model now uses.

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@sbillinge sbillinge Aug 1, 2025

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EllipsoidModel must have a major and a minor axis, so these presumably refer to this? What are these axes called in EllipsoidModel?

model.setParam("radius_b", erad)
model.setParam("radius_polar", prad)
model.setParam("radius_equatorial", erad)
ff = cf.SASCF("spheroid", model)
r = numpy.arange(0, 100, 1 / numpy.pi, dtype=float)
fr1 = ff(r)
Expand All @@ -79,7 +81,7 @@ def testShell(sas_available):
radius = 19.2
thickness = 7.8
# Calculate cf from VesicleModel
VesicleModel = sasimport("sas.models.VesicleModel").VesicleModel
VesicleModel = _make_standard_model("vesicle")
model = VesicleModel()
model.setParam("radius", radius)
model.setParam("thickness", thickness)
Expand All @@ -103,7 +105,7 @@ def testCylinder(sas_available):
radius = 100
length = 30

CylinderModel = sasimport("sas.models.CylinderModel").CylinderModel
CylinderModel = _make_standard_model("cylinder")
model = CylinderModel()
model.setParam("radius", radius)
model.setParam("length", length)
Expand Down
20 changes: 12 additions & 8 deletions tests/test_sas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,10 @@
import numpy
import pytest

# Use the updated SasView model API to load models
from sasmodels.sasview_model import _make_standard_model

from diffpy.srfit.sas import SASGenerator, SASParser, SASProfile
from diffpy.srfit.sas.sasimport import sasimport

# ----------------------------------------------------------------------------
# FIXME: adjust sensitivity of the pytest.approx statements when ready to test
Expand Down Expand Up @@ -113,7 +115,7 @@ def testParser(sas_available, datafile):
def test_generator(sas_available):
if not sas_available:
pytest.skip("sas package not available")
SphereModel = sasimport("sas.models.SphereModel").SphereModel
SphereModel = _make_standard_model("sphere")
model = SphereModel()
gen = SASGenerator("sphere", model)
for pname in model.params:
Expand All @@ -140,25 +142,27 @@ def test_generator(sas_available):
def testGenerator2(sas_available, datafile):
if not sas_available:
pytest.skip("sas package not available")
EllipsoidModel = sasimport("sas.models.EllipsoidModel").EllipsoidModel
EllipsoidModel = _make_standard_model("ellipsoid")
model = EllipsoidModel()
gen = SASGenerator("ellipsoid", model)

# Load the data using SAS tools
Loader = sasimport("sas.dataloader.loader").Loader
import sasdata.dataloader.loader as ld

Loader = ld.Loader
loader = Loader()
data = datafile("sas_ellipsoid_testdata.txt")
datainfo = loader.load(data)
datainfo = loader.load(str(data))
profile = SASProfile(datainfo)

gen.setProfile(profile)
gen.scale.value = 1.0
gen.radius_a.value = 20
gen.radius_b.value = 400
gen.radius_polar.value = 20
gen.radius_equatorial.value = 400
gen.background.value = 0.01

y = gen(profile.xobs)
diff = profile.yobs - y
res = numpy.dot(diff, diff)
assert 0 == pytest.approx(res)
assert 0 == pytest.approx(res, abs=1e-3)
return
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