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refactor!: enrichment classes #42

Merged
merged 73 commits into from
Mar 7, 2024
Merged

refactor!: enrichment classes #42

merged 73 commits into from
Mar 7, 2024

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leo-desbureaux-tellae
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@leo-desbureaux-tellae leo-desbureaux-tellae commented Mar 5, 2024 •
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  • New enrichment classes (Close Improve code #17)
    • Refactor code into SyntheticPopulationEnrichment classes, dedicated to the population enrichment process
    • Refactor code into EnrichmentSource classes, dedicated to the source data used for enrichment
    • These classes are used in composition: SyntheticPopulationEnrichment instances contain an instance of an EnrichmentSource class
    • Cleaner methods and fewer calls
  • Analysis instance creation is exposed in the new classes (Close Modality specification in analysis functions #36)
  • Use and store a random number generator in enrichment classes (Close Use random state in enrichment classes #30)
  • Improved documentation
  • Added a new test suite for new modules, removed some tests

These changes introduce questions about a potential need for even more refactoring, see #41

@leo-desbureaux-tellae
refactored common bhepop2 code in parent class
f7c0e80
@leo-desbureaux-tellae
removed 'parameters' parameter and parameters_schema attr
c123c75
@leo-desbureaux-tellae
removed add_defaults_and_validate_against_schema function
9c600ba
@leo-desbureaux-tellae
moved enrichment classes in enrichment package
eab8269
@leo-desbureaux-tellae
make _validate_and_process_inputs abstract
9bef8b9
@leo-desbureaux-tellae
use feature_name attribute in Bhepop2Enrichment
2472300
@leo-desbureaux-tellae
create QuantitativeAttributes class
b149e64
@leo-desbureaux-tellae
move uniform enrich to a class in enrichment.uniform
992f754
@leo-desbureaux-tellae
remove @AbstractMethod decorator from analyze_features
9ffcbdd 
raise NotImplementedError instead
@leo-desbureaux-tellae
generalised plot title management
7c22978 
make analysis_table private and added property
@leo-desbureaux-tellae
use feature_name as X label in qualitative plots
9037278
@leo-desbureaux-tellae
implement get_analysis_instance in Bhepop2 classes
7b6bbb5
@leo-desbureaux-tellae
fix example notebook
a724f13
@leo-desbureaux-tellae
add classes representing enrichment distributions
d88a767 
wip
@leo-desbureaux-tellae
fix quantitative draw
5143f0f
@leo-desbureaux-tellae
remove debug pandas options
40862ef
@leo-desbureaux-tellae
renamed many classes and modules
ec098c5 
changed modalities.py to marginal.py
changed distributions namespace for source(s) or enrichment source(s)
@leo-desbureaux-tellae
add a descriptive diagram for enrichment classes
47bc5eb
@leo-desbureaux-tellae
move ALL_LABEL constant to marginal.py
40facd1
@leo-desbureaux-tellae
add docstrings
1dfe831
@leo-desbureaux-tellae
add a name attribute to EnrichmentSource
dd04e26 
more docstrings
@leo-desbureaux-tellae
added a Bhepop2Logger class
6c57dcf
@leo-desbureaux-tellae
more docs
841c589
@leo-desbureaux-tellae
add missing name arg in MarginalDistributions
4d4f0cc
@leo-desbureaux-tellae
rename marginal module into marginal_distributions
5276ea5 
move QuantitativeAttributes to bhepop2.sources.base
@leo-desbureaux-tellae
fix test_bhepop2_enrich
888ffd8
@leo-desbureaux-tellae
fix demos
7c0df99
@leo-desbureaux-tellae
add back uniform enrich with new classes
200ad52
@leo-desbureaux-tellae
black style
488219d
@leo-desbureaux-tellae
update sphinx docs
6afa107
@leo-desbureaux-tellae
remove useless test
78da10d
@leo-desbureaux-tellae
added tests from new package structure
1b09f8e
@leo-desbureaux-tellae
black style
8dc7855
@leo-desbureaux-tellae
remove unused tests
f12905d
@leo-desbureaux-tellae
improve test code
0ec9903
@leo-desbureaux-tellae
style
7ba6791
@leo-desbureaux-tellae
add missing call to _validate_quantitative_parameters
a76e622
@leo-desbureaux-tellae
add tests for sources.base
88f7b90
@leo-desbureaux-tellae
add test for global_distribution
7b1e6d1
@leo-desbureaux-tellae
rename EnrichmentSource._evaluate_feature_values into _evaluate_featu…
dfe307f 
…re_on_population
@leo-desbureaux-tellae
remove rng from EnrichmentSource and pass rng to get_value_for_featur…
80f5a43 
…e() method
@leo-desbureaux-tellae
add test for get_value_for_feature
88cc242
@leo-desbureaux-tellae
added check feature values
38dd3a3
@leo-desbureaux-tellae
move build cross_table to functions module
56adf9d
@leo-desbureaux-tellae
add tests for marginal_distributions.py
85696ac
@leo-desbureaux-tellae
remove test_qualitative.py
53fc567
@leo-desbureaux-tellae
black style
7f8ae51
@leo-desbureaux-tellae
install dev_requirements in test action
6aa070d
@leo-desbureaux-tellae
add kaleido to dev_requirements
f8072ea
@leo-desbureaux-tellae
cleanup
cb3e225
@leo-desbureaux-tellae
remove set of source rng
153a815
@leo-desbureaux-tellae
change rng assert
812f258
@leo-desbureaux-tellae
update mocker with new _evaluate_feature_on_population
e97e402
@leo-desbureaux-tellae
remove rng assert
b0bacb4
@leo-desbureaux-tellae
fix typo in previous commit
bfd4ea8
@leo-desbureaux-tellae
black style
2bd2ca5
@leo-desbureaux-tellae
add missing pytest-mock in dev_requirements.txt
60117e4
@leo-desbureaux-tellae leo-desbureaux-tellae mentioned this pull request Mar 7, 2024
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@leo-desbureaux-tellae leo-desbureaux-tellae merged commit cb76b19 into main Mar 7, 2024
1 check passed
@leo-desbureaux-tellae leo-desbureaux-tellae deleted the refactor/parent_class branch March 7, 2024 17:11
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Modality specification in analysis functions Use random state in enrichment classes Improve code
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@leo-desbureaux-tellae