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Background models mathematical fixes #351

Merged
merged 4 commits into from
Jul 13, 2022
Merged

Background models mathematical fixes #351

merged 4 commits into from
Jul 13, 2022

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luisfabib
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@luisfabib luisfabib commented Jul 11, 2022 •
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  • Fixed two small mathematical errors in bg_homfractal and bg_homfractal_phase.
  • Adopted the sign convention for the time-dependent phase shift equations of physical background models. Now the equations agrees with the convention used in https://mr.copernicus.org/articles/3/101/2022/
  • Added more robust tests for the physical background models based on numerical integration.

@luisfabib luisfabib added the bugfix Patches something that isn't working label Jul 11, 2022
@luisfabib luisfabib added this to the v0.15.0 milestone Jul 11, 2022
@luisfabib luisfabib requested a review from stestoll July 11, 2022 06:41
stestoll
stestoll previously approved these changes Jul 11, 2022
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@luisfabib luisfabib changed the title Fix sign of background phase shift's time-dependence Background models mathematical fixes Jul 11, 2022
@luisfabib luisfabib requested a review from stestoll July 11, 2022 19:17
@stestoll stestoll merged commit a4b74fc into main Jul 13, 2022
@stestoll stestoll deleted the fix/bg_phaseshift_sign branch July 13, 2022 12:57
luisfabib added a commit that referenced this pull request Jul 30, 2022
@luisfabib
Background models mathematical fixes (#351)
8d7ee72 
* bg_models: fix sign of background phase-shift's time-dependence

* add strong tests against numerical integration

* fix small mathematical errors in bg_homfractal models
luisfabib added a commit that referenced this pull request Jul 30, 2022
@luisfabib
Release v0.14.3 (#357)
11f4b1d 
* docs: force light theme even in dark themed browsers (#350)

* fit: avoid unfreezing of all parameters when applying normalization (#352)

* Background models mathematical fixes (#351)

* bg_models: fix sign of background phase-shift's time-dependence

* add strong tests against numerical integration

* fix small mathematical errors in bg_homfractal models

* Fix scheduled CI test suite (#353)

* fix scheduled CI

- deprecate testing of Python 3.6 and 3.7
- add MKL linking to Windows
- fix pip installation errors

* fix typo in package name

* Modelling system quality of life improvements (#354)

* model: add method setas to import parameter metadata

* add hyperparameter info to results summary

* improve attribute request error messages in FitResult object

* improve error messaging during model evaluation

* bump VERSION to v0.14.3

* update CHANGELOG

* minor documentation update

* Fix errors in GHA publishing workflow (#355)

* fix build and publish to PyPI and Anaconda

- deprecate conda support for python 3.6 and 3.7

* minor edit

* Minor edits to files edited in previous PRs (#356)

* fix minor logic error

* minor documentation update

* fix minor bug
luisfabib added a commit that referenced this pull request Aug 10, 2022
@luisfabib @edmundxcvi
Release v0.14.4 (#370)
56856d9 
* bumb version to v0.15.0-dev (#307)

* examples: fix identifiablity analysis grid values (#314)

* remove line that should be substituted by the subsequent GHA (#313)

* Use Scipy's `eigh` instead of Numpy's to avoid convergence error (#311)

* Use Scipy's eigh instead of Numpy's to avoid convergence error

* fix error

* Enable the pickling of DeerLab's objects  (#312)

* fix pickling of fit result objects

* add save and load utility functions for pickling, add test

* improve test

* fix pickling of model objects

* fix pickling of merged and linearly combined models

* fix pickling of model objects with linked parameters

* fix some tests

* fix pickling of model objects with functionalized parameters

- introduces the dill package as a dependency

* fix error

* improve docstrings and add to API reference

* rename save to store_pickle and load to load_pickle

add safety warning about reading pickles

* rename imports

* remove unused import

* fix another import error

* `docs`: add important note to user guide on experimental deadtime correction  (#320)

* Fix dependency of DeerLab's documentation logo on system fonts (#328)

* add specific web font of DeerLab's title font

* docs: make web logo independent of system fonts

* docs: minor CSS fixes

* fix minor bug when printing fit results with most parameters frozen (#329)

* Fix bug when propagating bootstrapped uncertainty in presence of round-off errors (#325)

* UQresult: expand join() method to work with bootstrapped results

* fix bug when propagating bootstrapped results with round-off errors

* docs: add docstring for evaluate and propagate methods (#321)

* docs: minor edits, CSS fixes, and one 404 fix (#331)

* docs: minor edits, CSS fixes, and one 404 fix

* add missing functions to reference

* minor edit and fix

* Remove hard dependency of the DeerLab's installation routine and scripts on MKL (#330)

* installation: remove hard dependency of installer on MKL 

- simplify setup.py
- update workflows 
- add new script for linking against MKL in Windows

* fixr random numerical error and warning during tests

* check failing tests

* CI workflow, do not use caching

* change Ci job names

* Avoid use of pre-release Numpy versions during installation (#336)

* setup.py: avoid installation of numpy pre-releases

* Fix randomly failing GHA WinOS workflow (#337)

* refactor CI workflow

* reintroduce MKL for GHA WinOS runners

* fix MKL upgrade script

* answer yes to uninstall

* Prevent potential future bugs when normalizing distributions throughout (#335)

* `bootstrap_analysis`: better noise estimation and add option to specify noise levels (#334)

* bootstrap_analysis: allow specifying noise levels

- otherwise estimate noise level from experimental dataset not from the fit residuals

* refactor bootstrap_analysis for more general and faster tests

* Fix automated upload to PyPI via token (#338)

* Correct behavior of L-curve selection methods (#340)

* selregparam: fix behavior of L-curve (LC method)  selection criterion

* selregparam: prevent `np.log(0)=np.inf ` cases in L-curve methods

* selregparam: remove useless line from a debugging stage

* Remove unused lines in `dipolarmodel` (#341)

* Fix apparent typo

* Remove unused lines

Co-authored-by: Luis Fabregas <luis.fabregas@phys.chem.ethz.ch>

* `dipolarmodel`: Fix error when specifying a limited excitation bandwidth (#342)

* dipolarmodel: fix bug when specifying the excitation bandwidth

* small fix

* fix logic error

* fit: properly pass the user-supplied noise level to the bootstrapping (#343)

* remove unused lines in example (#345)

* Fix documentation navigation menu on mobile phones and collapsed windows and other edits (#346)

* fix navigation menu on mobile phone and collapsed windows

* remove unnecessary navbar items

* remove non-existent references

* minor CSS fix

* docs: force light theme even in dark themed browsers (#350)

* fit: avoid unfreezing of all parameters when applying normalization (#352)

* Background models mathematical fixes (#351)

* bg_models: fix sign of background phase-shift's time-dependence

* add strong tests against numerical integration

* fix small mathematical errors in bg_homfractal models

* Fix scheduled CI test suite (#353)

* fix scheduled CI

- deprecate testing of Python 3.6 and 3.7
- add MKL linking to Windows
- fix pip installation errors

* fix typo in package name

* Modelling system quality of life improvements (#354)

* model: add method setas to import parameter metadata

* add hyperparameter info to results summary

* improve attribute request error messages in FitResult object

* improve error messaging during model evaluation

* Fix errors in GHA publishing workflow (#355)

* fix build and publish to PyPI and Anaconda

- deprecate conda support for python 3.6 and 3.7

* minor edit

* Minor edits to files edited in previous PRs (#356)

* fix minor logic error

* minor documentation update

* fix minor bug

* docs: fix theme package version to solve dark theme issues (#359)

* docs: fix theme package version to solve dark theme issues

* upgrade Python version in workflows

* use older Sphinx version to build for compatibility

* UQResults: add docstrings for undocumented attributes (#360)

* dd_randcoil: fix description of model parameters (#361)

* add chemistry travel award funding to support page (#364)

* Fix PyPI and Anaconda build and upload workflows (#363)

* fix PyPI build and upload workflow according to official Python docs

* fix GHA for conda build and upload

* docs: fix multiple CSS issues and flex container bugs (#365)

* bump VERSION to v0.14.4

* update the changelog

* `fit`: add missing arguments to docstring (#367)

* `dipolarmodel`: add `pulselength` optional argument to experiment models (#368)

* model: add start values and frozen values to the printed parameter table (#369)

* update changelog

Co-authored-by: edmundxcvi <59712516+edmundxcvi@users.noreply.github.com>
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