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New user interface; major refactor of API and backend; docs and tests #11

Merged
merged 59 commits into from
Aug 27, 2024
Merged

New user interface; major refactor of API and backend; docs and tests #11

merged 59 commits into from
Aug 27, 2024

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harmsm
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@harmsm harmsm commented Aug 27, 2024

User experience

  • User calls one function (dataprob.setup) to set up a calculation and a second (f.fit()) to run a calculation.
  • Dataframe-centric interface
  • Library now has plotting capabilities

Under the hood

  • ModelWrapper now holds fit parameters as pandas.DataFrame, with handles for setting and reading
  • Fitter now takes ModelWrapper as an argument
  • Removed FitParameters class

Docs and testing

  • Full documentation, ready for readthedocs
  • 100% unit test coverage
  • Multiple integrated unit tests

harmsm added 30 commits August 5, 2024 23:01
@harmsm
model_wrapper now handles kwargs
73fd3f5
@harmsm
added VectorModelWrapper class to wrap models that take vector inputs
4f71731
@harmsm
added ability to read parameter spreadsheet
0a66a18
@harmsm
added ability to set modelwrapper parameters effeciently
6d93ac9
@harmsm
added openpyxl dependency
e2d2b79
@harmsm
full unit test coverage on model_wrapper, minor bug fixes
f7b00c2
@harmsm
built user-facing wrap_model function
09a4a65
@harmsm
added ModelWrapper.dataframe property
8a1b0a4
@harmsm
added __repr__ to key classes
50d59ad
@harmsm
renamed BayesianFitter --> BayesianSampler
d8829e6
@harmsm
removed 'name' attribute from FitParameter
8b30152
@harmsm
better default y_stdev setting, with warning
d24852f
@harmsm
cleaned up Fitter.model setter, removed mw.values
dfab76a
@harmsm
minor code cleanup
8e53e81
@harmsm
git fixed table rst in docstrings
e088d26
@harmsm
intermediate commit; ModelWrapper now uses pandas
6269c7d
@harmsm
intermediate commit; VectorModelWrapper now working
921c9fa
@harmsm
intermediate commit, model_wrapper/ submodule tests passing
e52bd0f
@harmsm
intermediate commit; fitter almost working
e7a1b9c
@harmsm
base fitter now passing all tests
8e47702
@harmsm
full test coverage of fitters/base
416bcb3
@harmsm
MLFitter now has full test coverage
7732414
@harmsm
dataframe now processor now explicitly casts col to float
b9a408f
@harmsm
refactor on bayesian side; almost complete testing
8bbc3f9
@harmsm
new bayesian implementation almost fully tested
1e55a68
@harmsm
ml and bayesian now working and passing all tests
f7b227b
@harmsm
nearly complete test coverage, all working
341f3be
@harmsm
100% test coverage
f988415
@harmsm
updating docs and examples
062af69
@harmsm
Merge pull request #1 from harmsm/remove_FitParameter
fdef15e 
Remove fit parameter
harmsm added 29 commits August 14, 2024 22:12
@harmsm
Merge branch 'main' of github.com:harmsm/dataprob into remove_FitPara…
b6454aa 
…meter
@harmsm
updating docs
fc77912
@harmsm
Merge branch 'remove_FitParameter'
fbe8392
@harmsm
model_wrapper now sets non_fit_kwargs on initialization
b197b76
@harmsm
updated non_fit_parameters --> non_fit_kwargs
cf01eb0
@harmsm
model now passed into fitter directly
b4c87d7
@harmsm
added plotting functionality
83ace3d
@harmsm
plotting suite complete
6179970
@harmsm
small graphical styling change
795bc92
@harmsm
added publicly accessible non_fit_kwargs
c01190d
@harmsm
removed too-clever mw.variable setter/getter
307d4b5
@harmsm
Fitter args to fit() rather than __init__
569b0d0
@harmsm
intermediate commit; refactor to util
2edadc2
@harmsm
removed y_obs and y_std setters
61d7e45
@harmsm
fixing bad github workflow test
3e2ff85
@harmsm
cleaning up tests
fa98c49
@harmsm
removed an unnecessary abstraction layer in ModelWrapper
ea5dd49
@harmsm
added dataprob.setup interface
b8964b1
@harmsm
docstring and import cleanup throughtout
dc9e641
@harmsm
adding integrated tests, fixing bugs they reveal
c29a1af
@harmsm
more integrated tests, small api clean up revealed by tests
4230e56
@harmsm
adding more integrated tests and matched notebook examples
2839946
@harmsm
np.array(df["x"]) -> np.array(df["x"]).copy()
55978d5
@harmsm
updating readme and docstrings
cfd7c7f
@harmsm
added docs and synced with code
5e5595c
@harmsm
tweaked numerical tests; doc cleanup
b58621e
@harmsm
tweaking uncertainty for better numerical stability on linear extrap
8494211
@harmsm
disabling flawed test
fed33e3
@harmsm
added double numerical test
d355dda
@harmsm harmsm merged commit d47d3d6 into harmslab:main Aug 27, 2024
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@harmsm