pymetadata 0.5.0__tar.gz → 0.5.1__tar.gz

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  1. {pymetadata-0.5.0 → pymetadata-0.5.1}/.bumpversion.toml +1 -1
  2. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/workflows/main.yml +14 -1
  3. {pymetadata-0.5.0 → pymetadata-0.5.1}/PKG-INFO +1 -1
  4. {pymetadata-0.5.0 → pymetadata-0.5.1}/RELEASE.md +18 -17
  5. pymetadata-0.5.1/release-notes/0.5.1.md +10 -0
  6. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/__init__.py +1 -1
  7. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/omex.py +2 -0
  8. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/CONTRIBUTING.rst +0 -0
  9. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/ISSUE_TEMPLATE/01-bug-report.md +0 -0
  10. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/ISSUE_TEMPLATE/02-question.md +0 -0
  11. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/ISSUE_TEMPLATE/03-feature-request.md +0 -0
  12. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  13. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  14. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/SUPPORT.rst +0 -0
  15. {pymetadata-0.5.0 → pymetadata-0.5.1}/.github/workflows/ruff.yml +0 -0
  16. {pymetadata-0.5.0 → pymetadata-0.5.1}/.gitignore +0 -0
  17. {pymetadata-0.5.0 → pymetadata-0.5.1}/.pre-commit-config.yaml +0 -0
  18. {pymetadata-0.5.0 → pymetadata-0.5.1}/.python-version +0 -0
  19. {pymetadata-0.5.0 → pymetadata-0.5.1}/.ruff.toml +0 -0
  20. {pymetadata-0.5.0 → pymetadata-0.5.1}/.zenodo.json +0 -0
  21. {pymetadata-0.5.0 → pymetadata-0.5.1}/LICENSE +0 -0
  22. {pymetadata-0.5.0 → pymetadata-0.5.1}/README.rst +0 -0
  23. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/composite_annotations.md +0 -0
  24. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/about.txt +0 -0
  25. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/android-chrome-192x192.png +0 -0
  26. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/android-chrome-512x512.png +0 -0
  27. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/apple-touch-icon.png +0 -0
  28. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/favicon-16x16.png +0 -0
  29. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/favicon-32x32.png +0 -0
  30. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/favicon.ico +0 -0
  31. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/favicon_io.zip +0 -0
  32. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/pymetadata-100x100-300dpi.png +0 -0
  33. {pymetadata-0.5.0 → pymetadata-0.5.1}/docs/images/favicon/site.webmanifest +0 -0
  34. {pymetadata-0.5.0 → pymetadata-0.5.1}/pyproject.toml +0 -0
  35. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.10.md +0 -0
  36. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.11.md +0 -0
  37. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.12.md +0 -0
  38. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.13.md +0 -0
  39. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.14.md +0 -0
  40. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.15.md +0 -0
  41. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.16.md +0 -0
  42. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.17.md +0 -0
  43. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.18.md +0 -0
  44. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.19.md +0 -0
  45. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.2.md +0 -0
  46. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.20.md +0 -0
  47. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.21.md +0 -0
  48. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.22.md +0 -0
  49. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.3.md +0 -0
  50. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.4.md +0 -0
  51. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.5.md +0 -0
  52. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.6.md +0 -0
  53. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.7.md +0 -0
  54. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.8.md +0 -0
  55. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.0.9.md +0 -0
  56. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.1.0.md +0 -0
  57. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.1.md +0 -0
  58. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.10.md +0 -0
  59. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.2.md +0 -0
  60. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.3.md +0 -0
  61. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.4.md +0 -0
  62. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.5.md +0 -0
  63. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.6.md +0 -0
  64. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.7.md +0 -0
  65. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.8.md +0 -0
  66. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.2.9.md +0 -0
  67. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.0.md +0 -0
  68. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.1.md +0 -0
  69. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.10.md +0 -0
  70. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.11.md +0 -0
  71. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.2.md +0 -0
  72. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.3.md +0 -0
  73. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.4.md +0 -0
  74. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.5.md +0 -0
  75. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.6.md +0 -0
  76. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.7.md +0 -0
  77. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.8.md +0 -0
  78. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.3.9.md +0 -0
  79. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.4.0.md +0 -0
  80. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.4.1.md +0 -0
  81. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.4.2.md +0 -0
  82. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.4.3.md +0 -0
  83. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.4.4.md +0 -0
  84. {pymetadata-0.5.0 → pymetadata-0.5.1}/release-notes/0.5.0.md +0 -0
  85. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/cache.py +0 -0
  86. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/chebi.py +0 -0
  87. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/console.py +0 -0
  88. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/core/__init__.py +0 -0
  89. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/core/annotation.py +0 -0
  90. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/core/creator.py +0 -0
  91. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/core/synonym.py +0 -0
  92. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/core/xref.py +0 -0
  93. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/__init__.py +0 -0
  94. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/cache_path_example.py +0 -0
  95. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/omex_example.py +0 -0
  96. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/test_from_files.omex +0 -0
  97. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/test_from_omex.omex +0 -0
  98. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/testomex/README.md +0 -0
  99. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/testomex/manifest.xml +0 -0
  100. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/testomex/models/omex_comp.xml +0 -0
  101. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/testomex/models/omex_comp_flat.xml +0 -0
  102. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/results/testomex/models/omex_minimal.xml +0 -0
  103. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/examples/test.omex +0 -0
  104. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/identifiers/__init__.py +0 -0
  105. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/identifiers/miriam.py +0 -0
  106. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/identifiers/registry.py +0 -0
  107. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/log.py +0 -0
  108. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/metadata/__init__.py +0 -0
  109. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/metadata/eco.py +0 -0
  110. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/metadata/kisao.py +0 -0
  111. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/metadata/sbo.py +0 -0
  112. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/omex_v2.py +0 -0
  113. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/ontologies/__init__.py +0 -0
  114. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/ontologies/ols.py +0 -0
  115. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/ontologies/ontology.py +0 -0
  116. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/py.typed +0 -0
  117. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/resources/chebi_webservice_wsdl.xml +0 -0
  118. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/resources/ontologies/README.md +0 -0
  119. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/resources/templates/ontology_enum.pytemplate +0 -0
  120. {pymetadata-0.5.0 → pymetadata-0.5.1}/src/pymetadata/unichem.py +0 -0
  121. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/core/test_annotation.py +0 -0
  122. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/core/test_creator.py +0 -0
  123. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/data/omex/BIOMD0000000001.omex +0 -0
  124. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/data/omex/CombineArchiveShowCase.omex +0 -0
  125. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/data/omex/CombineArchiveShowCase_manifest.xml +0 -0
  126. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/data/omex/CompModels.omex +0 -0
  127. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/data/omex/CompModels_manifest.xml +0 -0
  128. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/data/omex/iCGB21FR.omex +0 -0
  129. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_chebi.py +0 -0
  130. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_ols.py +0 -0
  131. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_omex.py +0 -0
  132. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_ontology.py +0 -0
  133. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_registry.py +0 -0
  134. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_sbo_kisao.py +0 -0
  135. {pymetadata-0.5.0 → pymetadata-0.5.1}/tests/test_unichem.py +0 -0
  136. {pymetadata-0.5.0 → pymetadata-0.5.1}/tox.ini +0 -0
  137. {pymetadata-0.5.0 → pymetadata-0.5.1}/uv.lock +0 -0
@@ -1,5 +1,5 @@
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  [tool.bumpversion]
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- current_version = "0.5.0"
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+ current_version = "0.5.1"
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  commit = true
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  parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
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  serialize = ["{major}.{minor}.{patch}"]
@@ -7,8 +7,21 @@ jobs:
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  strategy:
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  fail-fast: false
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  matrix:
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- os: [ubuntu-latest]
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+ os: [ubuntu-latest, windows-latest, macos-latest]
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  python-version: ["3.10", "3.11", "3.12", "3.13"]
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+ exclude:
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+ - os: windows-latest
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+ python-version: "3.10"
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+ - os: windows-latest
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+ python-version: "3.11"
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+ - os: windows-latest
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+ python-version: "3.13"
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+ - os: macos-latest
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+ python-version: "3.10"
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+ - os: macos-latest
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+ python-version: "3.11"
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+ - os: macos-latest
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+ python-version: "3.13"
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  steps:
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  - uses: actions/checkout@v4
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pymetadata
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- Version: 0.5.0
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+ Version: 0.5.1
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  Summary: pymetadata are python utilities for working with metadata.
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  Author-email: Matthias König <konigmatt@googlemail.com>
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  Maintainer-email: Matthias König <konigmatt@googlemail.com>
@@ -12,32 +12,33 @@
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  * test installation in virtualenv from pypi
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  ```
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- mkvirtualenv test --python=python3.13
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- (test) pip install pymetadata
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+ uv venv --python 3.13
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+ uv pip install pymetadata
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  ```
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18
 
19
- ## setup environment
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-
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- https://github.com/tox-dev/tox-uv
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- uv tool install tox --with tox-uv
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- tox r -e py312
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- tox run-parallel
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-
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-
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- # install dev dependencies:
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+ # Install dev dependencies:
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  ```bash
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- # install dependencies
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+ # install core dependencies
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  uv sync
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  # install dev dependencies
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  uv pip install -r pyproject.toml --extra dev
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- # install tox-uv support
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+ ```
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+
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+ ## Setup tox testing
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+ See information on https://github.com/tox-dev/tox-uv
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+ ```bash
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  uv tool install tox --with tox-uv
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  ```
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+ Run single tox target
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+ ```bash
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+ tox r -e py312
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+ ```
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+ Run all tests in parallel
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+ ```bash
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+ tox run-parallel
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+ ```
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- # pre-commit
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+ # Setup pre-commit
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  pip install pre-commit
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  pre-commit install
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-
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  pre-commit run
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-
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-
@@ -0,0 +1,10 @@
1
+ # Release notes for pymetadata 0.5.1
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+ ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
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+
4
+ We are pleased to release the next version of pymetadata including the
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+ following changes:
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+
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+ ## Features & fixes
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+ - Fix #52 windows paths
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+
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+ Your pymetadata team
@@ -3,7 +3,7 @@
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3
  from pathlib import Path
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4
 
5
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  __author__ = "Matthias Koenig"
6
- __version__ = "0.5.0"
6
+ __version__ = "0.5.1"
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7
 
8
8
 
9
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  program_name: str = "pymetadata"
@@ -574,6 +574,8 @@ class Omex:
574
574
  for file in files:
575
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  file_path = os.path.join(root, file)
576
576
  location = f"./{os.path.relpath(file_path, directory)}"
577
+ # bugfix for windows paths
578
+ location = location.replace("\\", "/")
577
579
  if location == "./manifest.xml":
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580
  # manifest is created from the internal manifest entries
579
581
  continue
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