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Cleanup API / models / simulators / estimators / unittests #130

Merged
merged 37 commits into from
Mar 7, 2022
Merged

Cleanup API / models / simulators / estimators / unittests #130

merged 37 commits into from
Mar 7, 2022

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picciama
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@picciama picciama commented Mar 3, 2022 •
edited

Changes

  • simulators removed
  • estimators standalone without models/estimators.
  • api restructured
  • added type hints everywhere in models, estimators, utils
  • cleanup of unitests

Fixes

#115

@picciama
linting using black / isort, fixed imports
365bcab
@picciama
separate properties from input_data
425f0a6
@picciama
major refactoring removing train/models:
1535856 
- model classes deleted
- use model_vars directly in estimator
- model_vars contains model from models/ submodule and can access its attributes
- duplicate param_bounds together with ProcessModel class deleted as it is obsolote now
- imports cleaned and fixed
@picciama
refactoring numpy estimator:
eb1e551 
- remove dependency of input_data and model
- move everything to model_vars
- debugging state
@picciama
cleanup: working fitting procedure:
fd06d26 
- fixed recursion error due to __setattr__ __getattr__ logic in pickle
- refactored model_vars -> modelContainer
- detached train/estimators from models/estimators
@picciama
code reformatting with black / isort and linting
b25b315
@picciama
remove unnecessary compute()
da23c4f
@picciama
add missing decorators
23ee162
@picciama
override theta_loc/scale in training
01a4574
@picciama
unittests cleanup
fd50d5c
@picciama
support InputDataGLM when simulating
d5b0721
@picciama
removed @dask_compute
66fe624
@picciama
reintroduced compute()
784c28e
@picciama
cleanup, fix imports and syntax errors
f1ae683
@picciama
fixed imports, api and type annotations using mypy
a3cb3c4
@picciama
reformatting using black
8385c87
@picciama
cleanup using flake8, mypy, black, isort
c186b3d
@picciama
added type hints everywhere / fixed mypy issues
2e2c755
@picciama
reformatting using black / isort
cfaf056
@picciama picciama self-assigned this Mar 3, 2022
@picciama picciama mentioned this pull request Mar 4, 2022
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@picciama picciama linked an issue Mar 4, 2022 that may be closed by this pull request
print(test.model) throws RecursionError #115
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ilan-gold
ilan-gold requested changes Mar 4, 2022
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A first pass, looking really strong though! The API is super clean - estimator gets a model and does its thing. Model can simulate data. Great!

batchglm/models/base_glm/estimator.py Outdated Show resolved Hide resolved
batchglm/models/base_glm/model.py Show resolved Hide resolved
batchglm/models/base_glm/model.py Outdated Show resolved Hide resolved
batchglm/models/base_glm/model.py Show resolved Hide resolved
batchglm/models/base_glm/model.py Show resolved Hide resolved
batchglm/train/numpy/base_glm/estimator.py Show resolved Hide resolved
batchglm/train/numpy/base_glm/estimator.py Show resolved Hide resolved
batchglm/train/numpy/base_glm/estimator.py Outdated Show resolved Hide resolved
batchglm/train/numpy/glm_nb/estimator.py Show resolved Hide resolved
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@picciama picciama merged commit f589348 into development Mar 7, 2022
@picciama picciama deleted the mp/integrate_simulator branch March 7, 2022 16:57
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@ilan-gold ilan-gold ilan-gold requested changes

@davidsebfischer davidsebfischer Awaiting requested review from davidsebfischer

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print(test.model) throws RecursionError
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