nerdd-module 0.2.1__tar.gz → 0.2.3__tar.gz

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Files changed (71) hide show
  1. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/PKG-INFO +1 -1
  2. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/file_reader.py +6 -3
  3. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module.egg-info/PKG-INFO +1 -1
  4. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/setup.py +1 -1
  5. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/LICENSE +0 -0
  6. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/README.md +0 -0
  7. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/__init__.py +0 -0
  8. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/abstract_model.py +0 -0
  9. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/cli.py +0 -0
  10. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/__init__.py +0 -0
  11. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/auto_configuration.py +0 -0
  12. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/configuration.py +0 -0
  13. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/default_configuration.py +0 -0
  14. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/dict_configuration.py +0 -0
  15. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/merged_configuration.py +0 -0
  16. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/package_configuration.py +0 -0
  17. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/config/yaml_configuration.py +0 -0
  18. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/__init__.py +0 -0
  19. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/csv_writer.py +0 -0
  20. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/depth_first_explorer.py +0 -0
  21. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/explorer.py +0 -0
  22. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/gzip_reader.py +0 -0
  23. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/inchi_reader.py +0 -0
  24. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/list_reader.py +0 -0
  25. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/mol_reader.py +0 -0
  26. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/reader.py +0 -0
  27. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/reader_registry.py +0 -0
  28. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/sdf_reader.py +0 -0
  29. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/sdf_writer.py +0 -0
  30. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/smiles_reader.py +0 -0
  31. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/string_reader.py +0 -0
  32. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/tar_reader.py +0 -0
  33. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/writer.py +0 -0
  34. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/writer_registry.py +0 -0
  35. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/zip_reader.py +0 -0
  36. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/polyfills/__init__.py +0 -0
  37. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/polyfills/files.py +0 -0
  38. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/polyfills/get_entry_points.py +0 -0
  39. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/__init__.py +0 -0
  40. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/check_valid_smiles.py +0 -0
  41. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/chembl_structure_pipeline.py +0 -0
  42. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/empty_pipeline.py +0 -0
  43. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/filter_by_element.py +0 -0
  44. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/filter_by_weight.py +0 -0
  45. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/pipeline.py +0 -0
  46. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/registry.py +0 -0
  47. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/remove_stereochemistry.py +0 -0
  48. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/preprocessing/step.py +0 -0
  49. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/problem.py +0 -0
  50. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/version.py +0 -0
  51. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module.egg-info/SOURCES.txt +0 -0
  52. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module.egg-info/dependency_links.txt +0 -0
  53. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module.egg-info/requires.txt +0 -0
  54. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module.egg-info/top_level.txt +0 -0
  55. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/setup.cfg +0 -0
  56. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/__init__.py +0 -0
  57. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/conftest.py +0 -0
  58. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/models/AtomicMassModel.py +0 -0
  59. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/models/MolWeightModel.py +0 -0
  60. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/models/MolWeightModelWithExplicitMolIds.py +0 -0
  61. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/models/MolWeightModelWithExplicitMols.py +0 -0
  62. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/models/__init__.py +0 -0
  63. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/steps/__init__.py +0 -0
  64. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/steps/checks.py +0 -0
  65. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/steps/molecules.py +0 -0
  66. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/steps/predictors.py +0 -0
  67. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/steps/preprocessing.py +0 -0
  68. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/test_atom_property_prediction.py +0 -0
  69. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/test_molecule_property_prediction.py +0 -0
  70. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/test_preprocessing.py +0 -0
  71. {nerdd-module-0.2.1 → nerdd-module-0.2.3}/tests/test_reading_formats.py +0 -0
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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1
  Metadata-Version: 2.1
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  Name: nerdd-module
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- Version: 0.2.1
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+ Version: 0.2.3
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  Summary: Base package to create NERDD modules
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  Home-page: https://github.com/molinfo-vienna/nerdd-module.git
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  Maintainer: Steffen Hirte
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module/io/file_reader.py RENAMED
@@ -18,14 +18,17 @@ class FileReader(Reader):
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  assert isinstance(filename, str), "input must be a string"
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  try:
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- path = Path(filename).absolute()
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+ path = Path(filename)
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+
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+ if not path.is_absolute():
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+ path = self.data_dir / path
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  except:
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  raise ValueError("input must be a valid path")
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- assert path.is_relative_to(self.data_dir), "input must be a relative path"
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+ assert self.data_dir in path.parents, "input must be a relative path"
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  assert path.exists(), "input must be a valid file"
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- with open(filename, "rb") as f:
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+ with open(path, "rb") as f:
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  for entry in explore(f):
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  if len(entry.source) == 1 and entry.source[0] == "raw_input":
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  source = tuple()
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/nerdd_module.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: nerdd-module
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- Version: 0.2.1
3
+ Version: 0.2.3
4
4
  Summary: Base package to create NERDD modules
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5
  Home-page: https://github.com/molinfo-vienna/nerdd-module.git
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  Maintainer: Steffen Hirte
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/setup.py RENAMED
@@ -16,7 +16,7 @@ rdkit_requirement = ["rdkit>=2022.3.3"] if not rdkit_installed else []
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  setup(
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  name="nerdd-module",
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- version="0.2.1",
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+ version="0.2.3",
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  maintainer="Steffen Hirte",
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  maintainer_email="steffen.hirte@univie.ac.at",
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  packages=find_packages(),
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/LICENSE RENAMED
File without changes
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/README.md RENAMED
File without changes
{nerdd-module-0.2.1 → nerdd-module-0.2.3}/setup.cfg RENAMED
File without changes