refactor: merge john-development to main (#187)

* 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>

Author: 4 people

.codespell/ignore_words.txt

@@ -6,3 +6,6 @@ mater
 
 ;; Frobenius norm used in np.linalg.norm
 fro
+
+;; alternative spelling of socioeconomic used in code of conduct
+socio-economic

.flake8

@@ -6,8 +6,8 @@ exclude =
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
-max-line-length = 115
+    docs/source/conf.py
+max-line-length = 79
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
 extend-ignore = E203

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -34,7 +34,7 @@ Please let the maintainer know that all checks are done and the package is ready
 <!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
-- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
 - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
 - [ ] Tag the maintainer for conda-forge release.
 

.github/workflows/build-wheel-release-upload.yml

@@ -7,10 +7,10 @@ on:
       - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
-  release:
+  build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       maintainer_GITHUB_username: sbillinge
     secrets:

.github/workflows/check-news-item.yml

@@ -9,4 +9,4 @@ jobs:
   check-news-item:
     uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -14,7 +14,7 @@ jobs:
   matrix-coverage:
     uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       headless: false
     secrets:

.github/workflows/publish-docs-on-release.yml

@@ -7,6 +7,6 @@ jobs:
   docs:
     uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       headless: false

.github/workflows/tests-on-pr.yml

@@ -8,7 +8,7 @@ jobs:
   tests-on-pr:
     uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
-      project: diffpy.snmf
+      project: diffpy.stretched-nmf
       c_extension: false
       headless: false
     secrets:

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py

AUTHORS.rst

@@ -1,7 +1,7 @@
 Authors
 =======
 
-Billinge Group and community contributors.
+Simon Billinge, John Halloran, Billinge Group members
 
 Contributors
 ------------