Realize dev features#162
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c-w-feldmann
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Apr 17, 2025
c-w-feldmann
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- Removes unnecessary functions
- Refactors code
- Allows to use models as input via Feature union
- Support for elements which do not work well with single instance processing
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* remove copy method * remove additional_attributes and to_json method * remove mol counter * remove finish method * Allow None in as `identifier`
* remove standard scaler
* require python 3.11 and higher * remove tests for 3.10 * import Self from typing * make zip strict * Optional -> None * remove typing.Union * import Callable from collections
* Remove ABCMorganFingerprintPipelineElement * fix types and imports * add explainablity to PathFP * fix additional output * remove unnecessary comment * deduplicate code * use properties * use properties * move properties to MolToRDKitGenFPElement * rework test without modifying the functionallity * add test to assure that mappings and original fp match * move bitmapping to individual classes * test bitmapping for mol2path * broaden expected types * black * negate return statement to restore intended behaviour * extend tests to PathFP
# Conflicts: # molpipeline/estimators/nearest_neighbor.py # molpipeline/experimental/explainability/explainer.py # molpipeline/mol2any/mol2path_fingerprint.py
# Conflicts: # molpipeline/any2mol/sdf2mol.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2mol/filter.py # molpipeline/utils/value_conversions.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py # molpipeline/abstract_pipeline_elements/mol2any/mol2floatvector.py # molpipeline/abstract_pipeline_elements/mol2mol/filter.py # molpipeline/error_handling.py # molpipeline/estimators/connected_component_clustering.py # molpipeline/estimators/nearest_neighbor.py # molpipeline/estimators/similarity_transformation.py # molpipeline/experimental/explainability/explainer.py # molpipeline/mol2any/mol2morgan_fingerprint.py # molpipeline/mol2any/mol2path_fingerprint.py # molpipeline/mol2mol/standardization.py # molpipeline/utils/kernel.py # tests/test_elements/test_any2mol/test_auto2mol.py # tests/test_elements/test_mol2any/test_mol2concatenated.py # tests/test_elements/test_mol2any/test_mol2morgan_fingerprint.py # tests/test_elements/test_mol2any/test_mol2path_fingerprint.py # tests/test_elements/test_mol2any/test_mol2rdkit_phys_chem.py # tests/test_estimators/test_leader_picker_clustering.py # tests/test_pipeline.py
# Conflicts: # molpipeline/abstract_pipeline_elements/core.py # molpipeline/abstract_pipeline_elements/mol2any/mol2floatvector.py # molpipeline/any2mol/sdf2mol.py # molpipeline/error_handling.py # molpipeline/estimators/chemprop/abstract.py # molpipeline/estimators/chemprop/models.py # molpipeline/experimental/custom_filter.py # molpipeline/mol2any/mol2morgan_fingerprint.py # molpipeline/mol2any/mol2net_charge.py # molpipeline/mol2any/mol2path_fingerprint.py # molpipeline/mol2any/mol2rdkit_phys_chem.py # molpipeline/pipeline/_skl_pipeline.py # molpipeline/utils/molpipeline_types.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py # molpipeline/estimators/nearest_neighbor.py # molpipeline/mol2any/mol2net_charge.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py # molpipeline/any2mol/sdf2mol.py # molpipeline/experimental/custom_filter.py # molpipeline/experimental/explainability/explainer.py # molpipeline/mol2any/mol2morgan_fingerprint.py # molpipeline/utils/subpipeline.py
# Conflicts: # molpipeline/abstract_pipeline_elements/core.py # molpipeline/abstract_pipeline_elements/mol2any/mol2floatvector.py # molpipeline/experimental/explainability/fingerprint_utils.py # molpipeline/mol2any/mol2net_charge.py # molpipeline/mol2any/mol2rdkit_phys_chem.py # molpipeline/utils/molpipeline_types.py # notebooks/02_scaffold_split_with_custom_estimators.ipynb # tests/test_experimental/test_explainability/test_shap_explainers.py # tests/test_utils/test_comparison.py
# Conflicts: # molpipeline/abstract_pipeline_elements/core.py # molpipeline/abstract_pipeline_elements/mol2any/mol2floatvector.py # molpipeline/mol2any/mol2rdkit_phys_chem.py # tests/test_elements/test_mol2any/test_mol2net_charge.py # tests/test_experimental/test_explainability/test_shap_explainers.py
# Conflicts: # molpipeline/experimental/explainability/fingerprint_utils.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py # tests/test_elements/test_mol2any/test_mol2maccs_key_fingerprint.py # tests/test_elements/test_mol2any/test_mol2morgan_fingerprint.py # tests/test_elements/test_mol2any/test_mol2path_fingerprint.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2any/mol2floatvector.py # molpipeline/mol2any/mol2net_charge.py # molpipeline/mol2any/mol2rdkit_phys_chem.py # molpipeline/utils/molpipeline_types.py
# Conflicts: # molpipeline/pipeline/_skl_pipeline.py # molpipeline/utils/molpipeline_types.py
# Conflicts: # molpipeline/abstract_pipeline_elements/mol2mol/filter.py # molpipeline/experimental/uncertainty/utils.py
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