Galaxy-ml

Changes

- Updates scikit-learn to 1.1.x, tensorflow to v2.10.x, xgboost to 1.7.x.
- Add github workflow to test tools using docker container as dependencies.
- Restructure search algos in searchCV tool.
- Serialize html repr for models.
- Test utils and tools in python 3.9.

Bug Fixes

- Fix some tool lint errors
- Fix lots of flake8 errors but ignoring F401,F821, I100 and W503.

Changes

- Updates tensorflow to v2.5.x, scikit-optimize to v0.9.0.
- Further clean up or reorganize the model persistence module.

Bug Fixes

- That bayesSearchCV doesn't work with sklearn v0.24+ now is solved by the upgrade of the library.
- Tensorflow error with numpy in model configuration tool is now solved.

Changes

- Updates scikit-learn to v0.24.x, tensorflow to v2.4.x, xgboost to v1.3.x, mlxtend to v0.17.x, skrebate to v.62, imbalanced-learn to v0.8.x and so on.
- Makes load_model and save_model util methods in keras_galaxy_model module.
- Refactors `_SafePickler` and moves it from `utils` to `model_persist`.
- Refactors `dump_model_to_h5` and `load_model_from_h5` to dynamically save and load xgboost and tensorflow models.
- Replaces pickled models with `h5mlm` models in all tools.

Bug Fixes

-

Changes

- Makes image deep learning tool.
- Adds `BayesSearchCV` in searchcv tool.
- Makes new metric `spearman_correlation_score` and its corresponding scorer.
- Adds a new parameter `n_stratification_bins` to `OrderedKFold` and `RepeatedOrderedKFold`.
- Adds multi-output classification support for `KerasGClassification` and
`KerasGBactchClassifier`.

Bug Fixes

- Fixes dependencies issue, numpy < 1.19, h5py < 3, tensorflow-estimator==1.15.1.
- Fixes various test issues.

Changes

- Makes `validation_fraction` in keras galaxy models to replace `validation_data`. `validation_data` still can be set via fit_params. In such a case, the `validation_fraction` is ignored.
- Makes `galaxy_ml.model_validations._fit_and_score` depreciated in tools. Update: `_fit_and_score` is still needed for `KerasGBatchClassifier`.
- Makes `verbose` in `model.fit` for keras galaxy models.
- Adds `drop_last_proba` for stacking classifiers in stacking ensembles tools.
- Expands secondary scoring of binarize target scorers to all scores.
- Adds `gen_compute_scores` in `utils` and cleans params ending with `_dir` in `clean_params`.
- Adds utils `dump_model_to_h5` and `load_model_from_h5` which support sklearn/keras arbitrary mix and hyperparameter stored.

Bug Fixes

- Fixes `BinaraizeTargetClassifier` pickle error when persisting a fitted object.

Changes

- Changes all `predict_score` to `decision_functions`.

Bug Fixes

- Fixes `_SafePickler` desn't recognize `binarize_target` module.
- Fixes `GridSearchCV` has no `predict_score` issue.