linkml-reference-validator 0.1.8__tar.gz → 0.2.0__tar.gz

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Files changed (153) hide show
  1. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/claude.yml +1 -1
  2. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/dragon-ai.yml +2 -2
  3. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/PKG-INFO +1 -1
  4. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.claude/.mcp.json +0 -0
  5. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.claude/settings.json +0 -0
  6. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.copier-answers.yml +0 -0
  7. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.devcontainer/devcontainer.json +0 -0
  8. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.devcontainer/post_create.sh +0 -0
  9. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.editorconfig +0 -0
  10. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/actions/claude-code-action/action.yml +0 -0
  11. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/actions/claude-issue-summarize-action/action.yml +0 -0
  12. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/actions/claude-issue-triage-action/action.yml +0 -0
  13. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/ai-controllers.json +0 -0
  14. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/copilot-instructions.md +0 -0
  15. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/copilot-setup-steps.yml +0 -0
  16. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/dependabot.yml +0 -0
  17. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/claude-code-review.yml +0 -0
  18. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/claude-issue-summarize.yml +0 -0
  19. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/claude-issue-triage.yml +0 -0
  20. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/claude-ontology-review.yml +0 -0
  21. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/deploy-docs.yaml +0 -0
  22. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/main.yaml +0 -0
  23. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/pypi-publish.yaml +0 -0
  24. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.gitignore +0 -0
  25. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.goosehints +0 -0
  26. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.pre-commit-config.yaml +0 -0
  27. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.yamllint.yaml +0 -0
  28. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/AGENTS.md +0 -0
  29. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/BUG_GEO_ACCESSION_TO_UID.md +0 -0
  30. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/BUG_ZENODO_DOI_AND_URL_HANDLING.md +0 -0
  31. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/CLAUDE.md +0 -0
  32. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/CLI-ISSUES.md +0 -0
  33. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/CODE_OF_CONDUCT.md +0 -0
  34. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/CONTRIBUTING.md +0 -0
  35. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/FEATURE_REQUEST_REPAIR.md +0 -0
  36. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/LICENSE +0 -0
  37. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/README.md +0 -0
  38. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/REVIEW2.md +0 -0
  39. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/REVIEW3.md +0 -0
  40. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/ai.just +0 -0
  41. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/copilot-instructions.md +0 -0
  42. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/about.md +0 -0
  43. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/concepts/content-types.md +0 -0
  44. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/concepts/editorial-conventions.md +0 -0
  45. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/concepts/how-it-works.md +0 -0
  46. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/elements/.gitkeep +0 -0
  47. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/add-reference-source.md +0 -0
  48. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/repair-validation-errors.md +0 -0
  49. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/skip-unsupported-references.md +0 -0
  50. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/use-local-files-and-urls.md +0 -0
  51. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/validate-clinical-trials.md +0 -0
  52. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/validate-dois.md +0 -0
  53. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/validate-entrez.md +0 -0
  54. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/validate-obo-files.md +0 -0
  55. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/validate-titles.md +0 -0
  56. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/how-to/validate-urls.md +0 -0
  57. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/index.md +0 -0
  58. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/notebooks/01_getting_started.ipynb +0 -0
  59. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/notebooks/02_advanced_usage.ipynb +0 -0
  60. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/notebooks/03_python_api.ipynb +0 -0
  61. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/notebooks/04_obo_validation.ipynb +0 -0
  62. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/notebooks/05_geo_validation.ipynb +0 -0
  63. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/quickstart.md +0 -0
  64. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/reference/cli.md +0 -0
  65. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/setup-guide.md +0 -0
  66. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/templates-linkml/README.md +0 -0
  67. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/todo.md +0 -0
  68. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/troubleshooting.md +0 -0
  69. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/docs/tutorials/complete-workflow.md +0 -0
  70. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/examples/README.md +0 -0
  71. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/justfile +0 -0
  72. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/mkdocs.yml +0 -0
  73. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/mypy.ini +0 -0
  74. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/notebooks/01_getting_started.ipynb +0 -0
  75. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/notebooks/02_advanced_usage.ipynb +0 -0
  76. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/notebooks/03_python_api.ipynb +0 -0
  77. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/notebooks/README.md +0 -0
  78. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/project/README.md +0 -0
  79. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/project.justfile +0 -0
  80. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/pyproject.toml +0 -0
  81. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/pytest.ini +0 -0
  82. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/__init__.py +0 -0
  83. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/_version.py +0 -0
  84. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/cli/__init__.py +0 -0
  85. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/cli/cache.py +0 -0
  86. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/cli/lookup.py +0 -0
  87. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/cli/repair.py +0 -0
  88. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/cli/shared.py +0 -0
  89. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/cli/validate.py +0 -0
  90. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/__init__.py +0 -0
  91. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/reference_fetcher.py +0 -0
  92. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/__init__.py +0 -0
  93. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/base.py +0 -0
  94. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/clinicaltrials.py +0 -0
  95. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/doi.py +0 -0
  96. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/entrez.py +0 -0
  97. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/file.py +0 -0
  98. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/json_api.py +0 -0
  99. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/loader.py +0 -0
  100. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/pmid.py +0 -0
  101. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/url.py +0 -0
  102. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/sources/utils.py +0 -0
  103. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/etl/text_extractor.py +0 -0
  104. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/field_detection.py +0 -0
  105. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/models.py +0 -0
  106. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/plugins/REVIEW.md +0 -0
  107. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/plugins/__init__.py +0 -0
  108. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/plugins/reference_validation_plugin.py +0 -0
  109. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/validation/__init__.py +0 -0
  110. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/validation/fuzzy_text_utils.py +0 -0
  111. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/validation/repairer.py +0 -0
  112. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/src/linkml_reference_validator/validation/supporting_text_validator.py +0 -0
  113. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/__init__.py +0 -0
  114. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/conftest.py +0 -0
  115. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/data/test_data_invalid.yaml +0 -0
  116. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/data/test_data_valid.yaml +0 -0
  117. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/data/test_schema.yaml +0 -0
  118. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/CLINICALTRIALS_NCT00000001.md +0 -0
  119. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/GEO_GSE12345.md +0 -0
  120. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMC_TEST001.md +0 -0
  121. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMC_TEST001.txt +0 -0
  122. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMC_TEST002.md +0 -0
  123. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMC_TEST002.txt +0 -0
  124. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMID_TEST001.md +0 -0
  125. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMID_TEST001.txt +0 -0
  126. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMID_TEST002.md +0 -0
  127. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMID_TEST002.txt +0 -0
  128. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMID_TEST003.md +0 -0
  129. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/PMID_TEST003.txt +0 -0
  130. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/fixtures/sample.obo +0 -0
  131. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_cli.py +0 -0
  132. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_cli_lookup.py +0 -0
  133. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_cli_repair.py +0 -0
  134. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_clinicaltrials_integration.py +0 -0
  135. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_e2e_integration.py +0 -0
  136. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_field_detection.py +0 -0
  137. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_fuzzy_suggestions.py +0 -0
  138. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_geo_integration.py +0 -0
  139. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_json_api_source.py +0 -0
  140. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_models.py +0 -0
  141. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_optional_linkml_dependency.py +0 -0
  142. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_plugin_integration.py +0 -0
  143. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_pmc_fulltext.py +0 -0
  144. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_real_validation.py +0 -0
  145. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_reference_fetcher.py +0 -0
  146. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_repair.py +0 -0
  147. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_source_utils.py +0 -0
  148. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_sources.py +0 -0
  149. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_supporting_text_validator.py +0 -0
  150. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_text_extractor.py +0 -0
  151. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_title_validation.py +0 -0
  152. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/tests/test_validation_config.py +0 -0
  153. {linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/uv.lock +0 -0
{linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/claude.yml RENAMED
@@ -31,7 +31,7 @@ jobs:
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  - name: Install uv
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- uses: astral-sh/setup-uv@v5
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{linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/.github/workflows/dragon-ai.yml RENAMED
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  - name: Check for qualifying mention
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- uses: actions/github-script@v6
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  with:
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{linkml_reference_validator-0.1.8 → linkml_reference_validator-0.2.0}/PKG-INFO RENAMED
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  Name: linkml_reference_validator
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- Version: 0.1.8
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+ Version: 0.2.0
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  Summary: Validation of supporting text from references and publications
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  Author-email: Chris Mungall <cjmungall@lbl.gov>
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  License-Expression: Apache-2.0