refactor: change get_objective_function into a static method and getter#174
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sbillinge merged 6 commits intodiffpy:john-developmentfrom Nov 26, 2025
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do we know why tests are not running in CI? |
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Out of credits, maybe? Otherwise I have no idea. |
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It is saying: |
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Ok, can we fix that on this pr? |
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Yes, it's fixed now. It broke because the scripts were moved to |
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These issues cropping up are making me realize the package is a bit "dirty", probably because it originated from an old fork. I can keep patching things but a better solution might be to re-cut the package with |
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## john-development #174 +/- ##
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Coverage ? 77.50%
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Files ? 3
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Hits ? 31
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It passed now. The |
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I will merge this. But I agree, let's do a quick recut so we are sure everything is up to date. Let's also migrate to 3.12 - 3.14 while we are at it |
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Feb 19, 2026
* Initial commit of John refactor of SNMF (#140) * added my files * [pre-commit.ci] auto fixes from pre-commit hooks * Updated X and Y optimizers, now produces formatted but partially incorrect output * removed duplicate class * Working build (no normalization) --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * fix stop condition and add Y/A normalization (#141) Co-authored-by: John Halloran <jhalloran@oxy.edu> * Added x normalization (#143) Co-authored-by: John Halloran <jhalloran@oxy.edu> Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com> * Loop cleanup and scikit-learn style parameters (#146) * Cleaned up looping behavior and aligned some params with scikit-learn. * Combined quadratic solvers --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * feat: Add random state feature. (#150) * feat: Add random state feature. * Add class docstring * components->n_components * Updated docstring * Shorten and reformat docstring * docstring typo * Flag self.rng as private * Make logic for n_components and Y0 more rigid * added class attributes to docstring * fix: cleaner import of SNMFOptimizer * fix: correct class instantiation after change in import --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com> * refactor: Remove old tests and source files (#160) Co-authored-by: John Halloran <jhalloran@oxy.edu> * style: convert variables to lowercase (#159) * style: Convert variables to lowercase * chore: Add news item * style: lowercase remaining variables * style: fix indentation on docstrings * style: rename and make public certain attributes * style: update docstring defaults --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * Fixes to class attributes and style (#163) * fix: use symmetric initial phase fractions * style: don't store objective function in a class attribute, just use history --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * Restored functionality to working state (#165) * docs: update docstring and imports * style: remove non-class function from class * fix: using working quadratic solver for weights * fix: restore working MATLAB-like loop functionality --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * feat: add live plotting of updates (#166) * feat: add live plotting of updates * style: make plotting vars lowercase --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * test: add initial test of optimizer (#167) * test: add initial test of optimizer * style: switch to local imports and plural folders * style: add README to sNMF test --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * Replace 1D apply_interpolation with np.interp (#168) * refactor: get residual matrix without a helper * perf: remove unused derivatives from apply_interpolation * chore: remove old residual matrix and reference to derivatives * refactor: replace remaining apply_interpolation with np.interp * style: remove references to old variable names --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * refactor: reconstruct separate from residuals (#169) * refactor: reconstruct separate from residuals * fix: inputs to reconstruct_matrix should not be optional * docs: updated default documentation for init_weights --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * refactor: move optimization out of init and into fit (#170) * style: per sklearn, attributes learned from data end with underscore * refactor: move optimization out of init and into fit * fix: use new fit() for test * style: end fit() with return self * docs: update docstring to reflect new functionality * refactor: use rho and eta in fit * feat: use reset for sequential refinements * fix: use copies for safety --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * refactor: apply_interpolation_matrix() is now compute_stretched_components() (#171) * fix: guard against zero/NaN stretches in apply_interpolation_matrix * refactor: use broadcasting instead of np.tile in apply_interpolation_matrix * refactor: flatten from a single buffer in apply_interpolation_matrix() * refactor: drastically simplify indexing in apply_interpolation_matrix() and remove legacy MATLAB terminology * style: rename apply_interpolation_matrix() to compute_stretched_components() --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * refactor: change get_objective_function into a static method and getter (#174) * refactor: compute objective function in a static method and retrieve via getter * refactor: change get_objective_function into a static method and getter * fix: update location for _tests-on-pr.yml * fix: use expected name for requirements/tests.txt * fix: add cvxpy to requirements/conda.txt * fix: add matplotlib to requirements/conda.txt --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * skpkg: apply black to all files in the project directory (#176) Co-authored-by: John Halloran <jhalloran@oxy.edu> * chore: update package to latest scikit-package version (#178) * chore: update to latest version of scikit-package * chore: restore citation information * fix: restore missing requirements * [pre-commit.ci] auto fixes from pre-commit hooks * fix: restore historical changelog --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * feat: skip updating stretch if stretching factor is zero (#181) * style: make line length <80 throughout * feat: skip updating stretch() if stretching factor is zero * chore: fix codespell complaint * fix: use correct version of rho * style: clean up several lines and remove noqa --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * docs: revamp documentation (#182) * refactor: move doc to docs and update requirements * docs: remove old tables and recreate getting started page * docs: load documentation from snmf_class.py --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> * refactor: change references of snmf to stretched-nmf (#185) * chore: use new name in scikit-package space * refactor: rename references throughout program snmf -> stretched-nmf * refactor: rename project references * chore: add news item for package-name-update * chore: CI toml issue --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> --------- Co-authored-by: John Halloran <jhalloran@oxy.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Simon Billinge <sbillinge@users.noreply.github.com>
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get_objective_function()now passes tocompute_objective_function()compute_objective_function()