mutcleaner 0.1.0.post1.dev40__tar.gz → 0.2.0__tar.gz

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Files changed (74) hide show
  1. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/PKG-INFO +1 -1
  2. mutcleaner-0.2.0/doc/changelog/CHANGELOG_0.2.0.md +26 -0
  3. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/conf.py +1 -1
  4. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/__init__.py +1 -1
  5. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/PKG-INFO +1 -1
  6. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/SOURCES.txt +1 -0
  7. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/.github/workflows/docs.yml +0 -0
  8. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/.gitignore +0 -0
  9. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/CONTRIBUTING.md +0 -0
  10. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/LICENSE +0 -0
  11. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/README.md +0 -0
  12. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/Makefile +0 -0
  13. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/changelog/CHANGELOG_0.1.0.md +0 -0
  14. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/make.bat +0 -0
  15. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/requirements.in +0 -0
  16. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/requirements.txt +0 -0
  17. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/_static/custom.css +0 -0
  18. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/api/index.rst +0 -0
  19. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/index.rst +0 -0
  20. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/user_guide/common_workflow.md +0 -0
  21. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/user_guide/index.rst +0 -0
  22. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/user_guide/overview.md +0 -0
  23. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/user_guide/supported_datasets.md +0 -0
  24. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/__init__.py +0 -0
  25. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/antitoxin_pard3_cleaner.py +0 -0
  26. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/antitoxin_pard3_custom_cleaners.py +0 -0
  27. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/archstabms_1e10_cleaner.py +0 -0
  28. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/archstabms_1e10_custom_cleaners.py +0 -0
  29. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/base_config.py +0 -0
  30. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/basic_cleaners.py +0 -0
  31. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/cdna_proteolysis_cleaner.py +0 -0
  32. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/cdna_proteolysis_custom_cleaners.py +0 -0
  33. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/ctxm_cleaner.py +0 -0
  34. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/ddg_dtm_cleaners.py +0 -0
  35. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/human_domainome_custom_cleaners.py +0 -0
  36. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/human_domainome_sup2_cleaner.py +0 -0
  37. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/human_myoglobin_cleaner.py +0 -0
  38. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/human_myoglobin_custom_cleaners.py +0 -0
  39. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/proteingym_dms_substitutions_cleaner.py +0 -0
  40. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/proteingym_dms_substitutions_custom_cleaners.py +0 -0
  41. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/rbd_ace2_cleaner.py +0 -0
  42. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/rbd_antibody_cleaner.py +0 -0
  43. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/rbd_custom_cleaner.py +0 -0
  44. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/cleaners/trpb_cleaner.py +0 -0
  45. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/__init__.py +0 -0
  46. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/alphabet.py +0 -0
  47. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/codon.py +0 -0
  48. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/constants.py +0 -0
  49. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/dataset.py +0 -0
  50. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/mutation.py +0 -0
  51. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/pipeline.py +0 -0
  52. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/sequence.py +0 -0
  53. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/core/types.py +0 -0
  54. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/__init__.py +0 -0
  55. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/cleaner_workers.py +0 -0
  56. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/data_source.py +0 -0
  57. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/dataset_builders.py +0 -0
  58. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/label_resolvers.py +0 -0
  59. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/mutation_converter.py +0 -0
  60. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/raw_data_downloader.py +0 -0
  61. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/sequence_io.py +0 -0
  62. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/utils/type_converter.py +0 -0
  63. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/dependency_links.txt +0 -0
  64. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/requires.txt +0 -0
  65. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/top_level.txt +0 -0
  66. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/pyproject.toml +0 -0
  67. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/setup.cfg +0 -0
  68. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tests/test_dataset.py +0 -0
  69. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tests/test_mutation.py +0 -0
  70. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tests/test_pipeline.py +0 -0
  71. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tests/test_sequence.py +0 -0
  72. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tools/changelog.py +0 -0
  73. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tools/generate_changelog.sh +0 -0
  74. {mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/tools/release.sh +0 -0
{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mutcleaner
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- Version: 0.1.0.post1.dev40
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+ Version: 0.2.0
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  Summary: An efficient framework for cleaning, standardizing, and processing biological mutation data.
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  Author: Yuxiang Tang, Ziyu Shi
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  License-Expression: BSD-3-Clause
mutcleaner-0.2.0/doc/changelog/CHANGELOG_0.2.0.md ADDED
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+ # Changelog
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+
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+ All notable changes to this project will be documented in this file.
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+
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+ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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+ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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+
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+ ## [0.2.0] - 2026-06-02
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+
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+ ### Added
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+
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+ - Added ACE2-RBD & Antibody-RBD cleaner-related files for the data preprocessing workflow. ([#5](https://github.com/xulab-research/MutCleaner/pull/5)) by @Lodaisthirsty
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+
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+ ### Other Changes
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+
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+ - Make the records in the dataset more detailed. ([#2](https://github.com/xulab-research/MutCleaner/pull/2)) by @Lodaisthirsty
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+
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+ ### Contributors
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+
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+ A total of 2 people contributed to this release. People with a "+" by their names contributed a patch for the first time.
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+
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+ - Yancheng Shi +
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+ - Ziyu Shi
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+
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+
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+ **Full Changelog**: [v0.1.0..v0.2.0](https://github.com/xulab-research/MutCleaner/compare/v0.1.0..v0.2.0)
{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/doc/source/conf.py RENAMED
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  project = "mutcleaner"
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  copyright = "2026, Ziyu Shi, Yuxiang Tang"
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  author = "Yuxiang Tang and Ziyu Shi"
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- release = "0.1.0"
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+ release = "0.2.0"
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  extensions = [
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  "sphinx.ext.autodoc",
{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner/__init__.py RENAMED
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  __author__ = "Yuxiang Tang and Ziyu Shi"
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- __version__ = "0.1.0"
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+ __version__ = "0.2.0"
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  from .core import (
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  # Alphabet
{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: mutcleaner
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- Version: 0.1.0.post1.dev40
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+ Version: 0.2.0
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  Summary: An efficient framework for cleaning, standardizing, and processing biological mutation data.
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  Author: Yuxiang Tang, Ziyu Shi
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  License-Expression: BSD-3-Clause
{mutcleaner-0.1.0.post1.dev40 → mutcleaner-0.2.0}/mutcleaner.egg-info/SOURCES.txt RENAMED
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  doc/requirements.in
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  doc/requirements.txt
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  doc/changelog/CHANGELOG_0.1.0.md
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+ doc/changelog/CHANGELOG_0.2.0.md
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  doc/source/conf.py
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  doc/source/index.rst
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  doc/source/_static/custom.css