nerdd-module 0.3.18__tar.gz → 0.3.20__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/PKG-INFO +1 -1
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/package_configuration.py +10 -4
- nerdd_module-0.3.20/nerdd_module/converters/problem_list_converter.py +39 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/simple_model.py +6 -1
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module.egg-info/PKG-INFO +1 -1
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/pyproject.toml +1 -1
- nerdd_module-0.3.18/nerdd_module/converters/problem_list_converter.py +0 -21
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/LICENSE +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/README.md +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/cli.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/configuration.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/default_configuration.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/dict_configuration.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/merged_configuration.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/models.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/search_yaml_configuration.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/config/yaml_configuration.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/basic_type_converter.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/converter.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/converter_config.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/mol_converter.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/representation_converter.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/converters/void_converter.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/depth_first_explorer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/explorer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/file_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/gzip_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/inchi_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/list_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/mol_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/reader_config.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/sdf_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/smiles_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/string_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/tar_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/input/zip_reader.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/assign_mol_id_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/assign_name_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/convert_representations_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/enforce_schema_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/model.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/read_input_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/model/write_output_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/csv_writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/file_writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/iterator_writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/pandas_writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/record_list_writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/sdf_writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/output/writer.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/block_logs.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/files.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/get_entry_points.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/literal.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/typed_dict.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/types.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/polyfills/version.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/check_valid_smiles.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/chembl_structure_pipeline.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/filter_by_element.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/filter_by_weight.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/preprocessing_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/remove_stereochemistry.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/preprocessing/sanitize.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/problem.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/py.typed +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/steps/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/steps/map_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/steps/output_step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/steps/step.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/checks.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/files.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/models/AtomicMassModel.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/models/MolWeightModel.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/models/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/predictions.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/preprocessing/DummyPreprocessingStep.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/preprocessing/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/tests/representations.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/util/__init__.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/util/call_with_mappings.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/util/package.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module/version.py +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module.egg-info/SOURCES.txt +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module.egg-info/dependency_links.txt +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module.egg-info/requires.txt +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/nerdd_module.egg-info/top_level.txt +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/setup.cfg +0 -0
- {nerdd_module-0.3.18 → nerdd_module-0.3.20}/tests/test_features.py +0 -0
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class PackageConfiguration(Configuration):
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def __init__(self, package: str) -> None:
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def __init__(self, package: str, filename: str = "nerdd.yml") -> None:
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super().__init__()
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package_path = package.split(".")
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package_root = package_path[0]
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remaining_path = package_path[1:]
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# get the resource directory
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try:
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root_dir = files(
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root_dir = files(package_root)
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except ModuleNotFoundError:
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root_dir = None
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self.config: Configuration = DictConfiguration({})
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logger.info(f"Found configuration file in package: {config_file}")
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self.config = YamlConfiguration(
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self.config = YamlConfiguration(
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)
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self.config = DictConfiguration({})
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import logging
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from typing import Any, List, Union, cast
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from ..problem import Problem
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from .converter import Converter
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from .converter_config import ConverterConfig
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__all__ = ["ProblemListIdentityConverter", "ProblemListConverter"]
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logger = logging.getLogger(__name__)
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class ProblemListIdentityConverter(Converter):
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return input
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config = ConverterConfig(
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data_types="problem_list",
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output_formats=["pandas", "iterator", "record_list"],
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)
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class ProblemListConverter(Converter):
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problem_list: List[Union[Problem, str]] = cast(List[Union[Problem, str]], input)
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def _represent(problem: Union[Problem, str]) -> str:
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return f"{problem.type}: {problem.message}"
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logger.warning("Item is not an instance of Problem: %s", problem)
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return problem
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return "; ".join([_represent(problem) for problem in problem_list])
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config = ConverterConfig(
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data_types="problem_list",
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output_formats=["csv", "sdf"],
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)
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default_properties_end = [
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{
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{
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"name": "problems",
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"visible_name": "Problems",
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"type": "problem_list",
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"visible": False,
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},
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configs = [
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