pymetadata 0.5.2__tar.gz → 0.5.4__tar.gz

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  1. {pymetadata-0.5.2 → pymetadata-0.5.4}/.bumpversion.toml +1 -1
  2. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/CONTRIBUTING.rst +1 -1
  3. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/01-bug-report.md +1 -1
  4. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/workflows/main.yml +1 -1
  5. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/workflows/mypy.yml +2 -2
  6. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/workflows/ruff.yml +2 -2
  7. pymetadata-0.5.4/.pre-commit-config.yaml +35 -0
  8. pymetadata-0.5.4/.python-version +1 -0
  9. {pymetadata-0.5.2 → pymetadata-0.5.4}/.ruff.toml +1 -1
  10. {pymetadata-0.5.2 → pymetadata-0.5.4}/LICENSE +1 -1
  11. {pymetadata-0.5.2 → pymetadata-0.5.4}/PKG-INFO +6 -7
  12. {pymetadata-0.5.2 → pymetadata-0.5.4}/README.md +5 -5
  13. {pymetadata-0.5.2 → pymetadata-0.5.4}/RELEASE.md +7 -6
  14. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/composite_annotations.md +2 -2
  15. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/site.webmanifest +1 -1
  16. {pymetadata-0.5.2 → pymetadata-0.5.4}/pyproject.toml +0 -1
  17. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.17.md +0 -1
  18. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.18.md +1 -1
  19. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.19.md +1 -1
  20. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.20.md +1 -1
  21. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.21.md +1 -1
  22. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.22.md +1 -1
  23. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.1.0.md +1 -1
  24. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.1.md +1 -1
  25. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.10.md +1 -1
  26. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.2.md +1 -1
  27. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.3.md +1 -1
  28. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.4.md +1 -1
  29. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.5.md +1 -1
  30. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.6.md +2 -2
  31. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.7.md +1 -1
  32. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.8.md +1 -1
  33. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.2.9.md +1 -1
  34. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.0.md +1 -1
  35. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.1.md +1 -1
  36. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.10.md +1 -1
  37. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.11.md +1 -1
  38. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.2.md +1 -1
  39. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.3.md +1 -1
  40. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.4.md +1 -1
  41. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.5.md +1 -1
  42. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.6.md +1 -1
  43. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.7.md +1 -1
  44. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.8.md +1 -1
  45. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.3.9.md +1 -1
  46. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.0.md +1 -1
  47. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.1.md +1 -1
  48. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.2.md +1 -1
  49. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.3.md +1 -1
  50. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.4.4.md +1 -1
  51. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.5.0.md +1 -1
  52. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.5.1.md +1 -1
  53. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.5.2.md +2 -2
  54. pymetadata-0.5.4/release-notes/0.5.3.md +11 -0
  55. pymetadata-0.5.4/release-notes/0.5.4.md +11 -0
  56. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/__init__.py +1 -1
  57. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/chebi.py +21 -29
  58. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/annotation.py +4 -1
  59. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/cache_path_example.py +0 -1
  60. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/identifiers/registry.py +11 -33
  61. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/eco.py +1246 -1340
  62. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/kisao.py +83 -26
  63. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/sbo.py +131 -378
  64. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/ontologies/ontology.py +6 -5
  65. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/resources/templates/ontology_enum.pytemplate +0 -2
  66. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/unichem.py +2 -2
  67. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/core/test_annotation.py +5 -0
  68. pymetadata-0.5.4/uv.lock +1410 -0
  69. pymetadata-0.5.2/.pre-commit-config.yaml +0 -12
  70. pymetadata-0.5.2/.python-version +0 -1
  71. pymetadata-0.5.2/src/pymetadata/resources/chebi_webservice_wsdl.xml +0 -509
  72. pymetadata-0.5.2/uv.lock +0 -1180
  73. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/02-question.md +0 -0
  74. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/03-feature-request.md +0 -0
  75. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/ISSUE_TEMPLATE/config.yml +0 -0
  76. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  77. {pymetadata-0.5.2 → pymetadata-0.5.4}/.github/SUPPORT.rst +0 -0
  78. {pymetadata-0.5.2 → pymetadata-0.5.4}/.gitignore +0 -0
  79. {pymetadata-0.5.2 → pymetadata-0.5.4}/.zenodo.json +0 -0
  80. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/about.txt +0 -0
  81. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/android-chrome-192x192.png +0 -0
  82. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/android-chrome-512x512.png +0 -0
  83. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/apple-touch-icon.png +0 -0
  84. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon-16x16.png +0 -0
  85. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon-32x32.png +0 -0
  86. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon.ico +0 -0
  87. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/favicon_io.zip +0 -0
  88. {pymetadata-0.5.2 → pymetadata-0.5.4}/docs/images/favicon/pymetadata-100x100-300dpi.png +0 -0
  89. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.10.md +0 -0
  90. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.11.md +0 -0
  91. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.12.md +0 -0
  92. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.13.md +0 -0
  93. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.14.md +0 -0
  94. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.15.md +0 -0
  95. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.16.md +0 -0
  96. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.2.md +0 -0
  97. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.3.md +0 -0
  98. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.4.md +0 -0
  99. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.5.md +0 -0
  100. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.6.md +0 -0
  101. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.7.md +0 -0
  102. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.8.md +0 -0
  103. {pymetadata-0.5.2 → pymetadata-0.5.4}/release-notes/0.0.9.md +0 -0
  104. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/cache.py +0 -0
  105. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/console.py +0 -0
  106. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/__init__.py +0 -0
  107. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/creator.py +0 -0
  108. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/synonym.py +0 -0
  109. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/core/xref.py +0 -0
  110. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/__init__.py +0 -0
  111. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/omex_example.py +0 -0
  112. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/test_from_files.omex +0 -0
  113. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/test_from_omex.omex +0 -0
  114. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/README.md +0 -0
  115. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/manifest.xml +0 -0
  116. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/models/omex_comp.xml +0 -0
  117. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/models/omex_comp_flat.xml +0 -0
  118. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/results/testomex/models/omex_minimal.xml +0 -0
  119. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/examples/test.omex +0 -0
  120. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/identifiers/__init__.py +0 -0
  121. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/identifiers/miriam.py +0 -0
  122. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/log.py +0 -0
  123. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/metadata/__init__.py +0 -0
  124. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/omex.py +0 -0
  125. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/omex_v2.py +0 -0
  126. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/ontologies/__init__.py +0 -0
  127. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/ontologies/ols.py +0 -0
  128. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/py.typed +0 -0
  129. {pymetadata-0.5.2 → pymetadata-0.5.4}/src/pymetadata/resources/ontologies/README.md +0 -0
  130. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/core/test_creator.py +0 -0
  131. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/BIOMD0000000001.omex +0 -0
  132. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CombineArchiveShowCase.omex +0 -0
  133. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CombineArchiveShowCase_manifest.xml +0 -0
  134. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CompModels.omex +0 -0
  135. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/CompModels_manifest.xml +0 -0
  136. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/data/omex/iCGB21FR.omex +0 -0
  137. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_chebi.py +0 -0
  138. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_ols.py +0 -0
  139. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_omex.py +0 -0
  140. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_ontology.py +0 -0
  141. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_registry.py +0 -0
  142. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_sbo_kisao.py +0 -0
  143. {pymetadata-0.5.2 → pymetadata-0.5.4}/tests/test_unichem.py +0 -0
  144. {pymetadata-0.5.2 → pymetadata-0.5.4}/tox.ini +0 -0
@@ -1,5 +1,5 @@
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  [tool.bumpversion]
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- current_version = "0.5.2"
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+ current_version = "0.5.4"
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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}"]
@@ -117,7 +117,7 @@ Unit tests and benchmarks
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  pymetadata uses `pytest <http://docs.pytest.org/en/latest/>`_ for its
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  unit-tests and new features should in general always come with new
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- tests that make sure that the code runs as intended.
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+ tests that make sure that the code runs as intended.
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  To run all tests do::
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@@ -7,7 +7,7 @@ about: Report a bug to help improve this project
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  Before you create a new problem report, please look through the list of existing open
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  and closed issues to see if there are similar ones.
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-
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+
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  https://github.com/matthiaskoenig/pymetadata/issues
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  -->
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  name: CI-CD
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- on: [ push, pull_request ]
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  jobs:
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  test:
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  runs-on: ${{ matrix.os }}
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  name: MyPy
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- on: [ push, pull_request ]
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  mypy:
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  runs-on: ubuntu-latest
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  enable-cache: true
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  - name: Test with tox
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  run:
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- uvx --with tox-uv tox -e mypy
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+ uvx --with tox-uv tox -e mypy
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  name: Ruff
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- on: [ push, pull_request ]
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  jobs:
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  ruff:
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  runs-on: ubuntu-latest
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  steps:
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  - uses: actions/checkout@v4
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- - uses: astral-sh/ruff-action@v3
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+ - uses: astral-sh/ruff-action@v3
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+ # This is run as a precondition to commits, run manually via `pre-commit run`
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+
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+ # When adding new hooks, it may make sense to once run
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+ # `pre-commit run --all-files` as by default only changed files are checked
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+ repos:
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+ - repo: https://github.com/pre-commit/pre-commit-hooks
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+ rev: v5.0.0
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+ hooks:
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+ - id: check-yaml
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+ description: Check yaml files for parseable syntax
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+ - id: check-added-large-files
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+ description: Prevent large files from being committed
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+ - id: check-merge-conflict
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+ description: Check for files that contain merge conflict strings
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+ - id: check-symlinks
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+ description: Check for symlinks which do not point to anything
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+ - id: trailing-whitespace
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+ description: Trim trailing whitespaces
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+ - id: end-of-file-fixer
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+ description: Fix empty lines at ends of files
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+ - id: detect-private-key
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+ description: Detects the presence of private keys
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+
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+ - repo: https://github.com/astral-sh/ruff-pre-commit
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+ # Ruff version.
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+ rev: v0.8.6
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+ hooks:
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+ # Run the linter.
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+ - id: ruff
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+ types_or: [ python, pyi ]
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+ args: [ --fix ]
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+ # Run the formatter.
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+ - id: ruff-format
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+ types_or: [ python, pyi ]
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+ 3.13
@@ -47,4 +47,4 @@ docstring-code-format = false
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  docstring-code-line-length = "dynamic"
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  [lint.pydocstyle]
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- convention = "google" # Accepts: "google", "numpy", or "pep257".
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+ convention = "google" # Accepts: "google", "numpy", or "pep257".
@@ -4,4 +4,4 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
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  The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pymetadata
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- Version: 0.5.2
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+ Version: 0.5.4
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  Summary: pymetadata are python utilities for working with metadata.
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  Author-email: Matthias König <konigmatt@googlemail.com>
6
6
  Maintainer-email: Matthias König <konigmatt@googlemail.com>
@@ -27,7 +27,6 @@ Requires-Dist: pydantic>=2.10.4
27
27
  Requires-Dist: requests>=2.32.3
28
28
  Requires-Dist: rich>=13.9.4
29
29
  Requires-Dist: xmltodict>=0.14.2
30
- Requires-Dist: zeep>=4.3.1
31
30
  Provides-Extra: dev
32
31
  Requires-Dist: bump-my-version>=0.29.0; extra == 'dev'
33
32
  Requires-Dist: mypy>=1.9.0; extra == 'dev'
@@ -49,15 +48,15 @@ Description-Content-Type: text/markdown
49
48
  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
50
49
 
51
50
  pymetadata is a collection of python utilities for working with
52
- metadata in the context of COMBINE standards with source code available from
51
+ metadata in the context of COMBINE standards with source code available from
53
52
  [https://github.com/matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata).
54
53
 
55
54
  Features include among others
56
55
 
57
- - COMBINE archive version 1 support (OMEX)
56
+ - [core](src/pymetadata/core)COMBINE archive version 1 support (OMEX)
58
57
  - annotation classes and helpers
59
58
  - SBO and KISAO ontology enums
60
-
59
+
61
60
  If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
62
61
 
63
62
  # Documentation
@@ -75,10 +74,10 @@ Contributions are always welcome! Please read the [contributing guidelines](http
75
74
  - Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
76
75
 
77
76
  # Funding
78
- Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
77
+ Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
79
78
 
80
79
  # Installation
81
- `pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
80
+ `pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
82
81
  can be installed via
83
82
 
84
83
  ```bash
@@ -8,15 +8,15 @@
8
8
  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5308801.svg)](https://doi.org/10.5281/zenodo.5308801)
9
9
 
10
10
  pymetadata is a collection of python utilities for working with
11
- metadata in the context of COMBINE standards with source code available from
11
+ metadata in the context of COMBINE standards with source code available from
12
12
  [https://github.com/matthiaskoenig/pymetadata](https://github.com/matthiaskoenig/pymetadata).
13
13
 
14
14
  Features include among others
15
15
 
16
- - COMBINE archive version 1 support (OMEX)
16
+ - [core](src/pymetadata/core)COMBINE archive version 1 support (OMEX)
17
17
  - annotation classes and helpers
18
18
  - SBO and KISAO ontology enums
19
-
19
+
20
20
  If you have any questions or issues please [open an issue](https://github.com/matthiaskoenig/pymetadata/issues).
21
21
 
22
22
  # Documentation
@@ -34,10 +34,10 @@ Contributions are always welcome! Please read the [contributing guidelines](http
34
34
  - Documentation: [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/)
35
35
 
36
36
  # Funding
37
- Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
37
+ Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).
38
38
 
39
39
  # Installation
40
- `pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
40
+ `pymetadata` is available from [pypi](https://pypi.python.org/pypi/pymetadata) and
41
41
  can be installed via
42
42
 
43
43
  ```bash
@@ -3,15 +3,14 @@
3
3
  ## make release
4
4
  * update ontologies via `ontology.update_ontology_files()`
5
5
  * update release notes in `release-notes` with commit
6
- * make sure all tests run (`tox run-parallel`)
6
+ * make sure all tests run (`tox -p`)
7
7
  * check formating and linting (`ruff check`)
8
- * test bump version (`uv run bump-my-version bump [major|minor|patch] --dry-run -vv`)
9
- * bump version (`bump-my-version bump [major|minor|patch]`)
8
+ * test bump version (`uvx bump-my-version bump [major|minor|patch] --dry-run -vv`)
9
+ * bump version (`uvx bump-my-version bump [major|minor|patch]`)
10
10
  * `git push --tags` (triggers release)
11
11
  * `git push`
12
-
13
12
  * test installation in virtualenv from pypi
14
- ```
13
+ ```bash
15
14
  uv venv --python 3.13
16
15
  uv pip install pymetadata
17
16
  ```
@@ -39,6 +38,8 @@ tox run-parallel
39
38
  ```
40
39
 
41
40
  # Setup pre-commit
42
- pip install pre-commit
41
+ ```bash
42
+ uv pip install pre-commit
43
43
  pre-commit install
44
44
  pre-commit run
45
+ ```
@@ -13,7 +13,7 @@ of ATP in the cytoplasm, blood in a cardiac cavity, the glucokinase reaction).
13
13
 
14
14
 
15
15
 
16
- **entity**
16
+ **entity**
17
17
  OPB: https://bioportal.bioontology.org/ontologies/OPB
18
18
  Ontology of Physics for Biology
19
19
 
@@ -31,6 +31,6 @@ aborption rate: "Material flow rate"
31
31
  Property first; entity second
32
32
 
33
33
 
34
- **Properties of processes**
34
+ **Properties of processes**
35
35
  - describe process: source, sink & mediator; flow of material from one pool to another
36
36
  - to describe the source: stomach; sink
@@ -1 +1 @@
1
- {"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}
1
+ {"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}
@@ -40,7 +40,6 @@ dependencies = [
40
40
  "lxml>=5.3",
41
41
  "rich>=13.9.4",
42
42
  "requests>=2.32.3",
43
- "zeep>=4.3.1",
44
43
  "pronto>=2.5.8",
45
44
  "fastobo>=0.12.3",
46
45
  "jinja2>=3.1.5",
@@ -1,4 +1,3 @@
1
1
  # Release notes for pymetadata 0.0.17
2
2
 
3
3
  - SBO and KISAO helper functions
4
-
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.0.18
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.0.19
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.0.20
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.0.21
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.0.22
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.1.0
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.1
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.2.10
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.2
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.3
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.4
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.5
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,11 +1,11 @@
1
1
  # Release notes for pymetadata 0.2.6
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
7
7
  - bugfix SBML detection in omex
8
- -
8
+ -
9
9
 
10
10
  ## Fixes
11
11
 
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.7
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.8
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,6 +1,6 @@
1
1
  # Release notes for pymetadata 0.2.9
2
2
 
3
- We are pleased to release the next version of pymetadata including the
3
+ We are pleased to release the next version of pymetadata including the
4
4
  following changes:
5
5
 
6
6
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.0
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.1
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.10
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.11
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.2
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.3
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.4
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.5
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.6
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.7
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.8
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.3.9
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.4.0
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.4.1
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.4.2
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features & fixes
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.4.3
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features & fixes
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.4.4
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features & fixes
@@ -1,7 +1,7 @@
1
1
  # Release notes for pymetadata 0.5.0
2
2
  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
3
3
 
4
- We are pleased to release the next version of pymetadata including the
4
+ We are pleased to release the next version of pymetadata including the
5
5
  following changes:
6
6
 
7
7
  ## Features & fixes
@@ -1,7 +1,7 @@
1
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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- We are pleased to release the next version of pymetadata including the
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+ We are pleased to release the next version of pymetadata including the
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  following changes:
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  ## Features & fixes
@@ -1,11 +1,11 @@
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  # Release notes for pymetadata 0.5.2
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  ![pymetadata](https://github.com/matthiaskoenig/pymetadata/raw/develop/docs/images/favicon/pymetadata-100x100-300dpi.png)
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- We are pleased to release the next version of pymetadata including the
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+ We are pleased to release the next version of pymetadata including the
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  following changes:
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  ## Features & fixes
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  - Speedup CI-CD with uv
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- - Markdown README
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+ - Markdown README
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  Your pymetadata team