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2897, 2922: Use latest version of external (numpy, scipy, PySide) packages #3141

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merged 6 commits into from
Dec 3, 2024
Merged

2897, 2922: Use latest version of external (numpy, scipy, PySide) packages #3141

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6c6448f
Update requirements.txt to allow latest versions of numpy, scipy, and…
krzywon Oct 28, 2024
56a0225
numpy.NaN -> numpy.nan
krzywon Oct 28, 2024
fd26edb
Apply compatibility patch to BumpsFitting.py to allow for bumps v0 an…
krzywon Oct 28, 2024
0ca1b82
Include periodictable in parallel repos until next version is released
krzywon Oct 28, 2024
e17d2d6
Go back to using pip installed version of periodictable
krzywon Oct 28, 2024
2b3969b
Update documentation related to bumps returns to ensure consistent be…
krzywon Dec 3, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ jobs:
run: |
git clone --depth=50 --branch=master https://github.com/SasView/sasdata.git ../sasdata
git clone --depth=50 --branch=master https://github.com/SasView/sasmodels.git ../sasmodels
git clone --depth=50 --branch=master https://github.com/bumps/bumps.git ../bumps
git clone --depth=50 --branch=v0.9.3 https://github.com/bumps/bumps.git ../bumps

- name: Build and install sasdata
run: |
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8 changes: 4 additions & 4 deletions build_tools/requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
# Alphabetized list of OS and version agnostic dependencies
appdirs
bumps
cffi
docutils
dominate
Expand All @@ -14,16 +13,19 @@ lxml
mako
matplotlib
numba
numpy
periodictable
pybind11
pylint
pyopengl
pyparsing
PySide6
pytest
pytest_qt
pytest-mock
pytools
qtconsole
scipy
six
sphinx
superqt
Expand All @@ -38,6 +40,4 @@ zope
pywin32; platform_system == "Windows"

# Alphabetized list of version-pinned packages
numpy==1.26.4 # 2.0.0 deprecates many functions used in the codebase (and potentially in dependencies)
PySide6==6.4.3 # Later versions do not mesh well with pyinstaller < 6.0
scipy==1.13.1 # 1.14 deprecates some functions used in the codebase (and potentially in dependencies)
bumps==0.* # v1.+ is very experimental
15 changes: 11 additions & 4 deletions src/sas/sascalc/fit/BumpsFitting.py
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Expand Up @@ -316,7 +316,14 @@ def fit(self, msg_q=None,
# Check if uncertainty is missing for any parameter
uncertainty_warning = False

for fitness in problem.models:
for fitting_module in problem.models:
# CRUFT: This makes BumpsFitting compatible with bumps v0.9 and v1.0
if isinstance(fitting_module, SasFitness):
# Bumps v1.x+ - A Fitness object is returned
fitness = fitting_module
else:
# Bumps v0.x - A module is returned that holds the Fitness object
fitness = fitting_module.fitness
pars = fitness.fitted_pars + fitness.computed_pars
par_names = fitness.fitted_par_names + fitness.computed_par_names

Expand Down Expand Up @@ -346,8 +353,8 @@ def fit(self, msg_q=None,

# TODO: Let the GUI decided how to handle success/failure.
if not fitting_result.success:
fitting_result.stderr[:] = np.NaN
fitting_result.fitness = np.NaN
fitting_result.stderr[:] = np.nan
fitting_result.fitness = np.nan

all_results.append(fitting_result)

Expand Down Expand Up @@ -398,7 +405,7 @@ def abort_test():
try:
best, fbest = fitdriver.fit()
except Exception as exc:
best, fbest = None, np.NaN
best, fbest = None, np.nan
errors.extend([str(exc), traceback.format_exc()])
finally:
mapper.stop_mapper(fitdriver.mapper)
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