easylink 0.1.12__tar.gz → 0.1.13__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (195) hide show
  1. {easylink-0.1.12 → easylink-0.1.13}/.github/CODEOWNERS +1 -1
  2. {easylink-0.1.12 → easylink-0.1.13}/CHANGELOG.rst +4 -0
  3. {easylink-0.1.12 → easylink-0.1.13}/Makefile +5 -2
  4. {easylink-0.1.12 → easylink-0.1.13}/PKG-INFO +1 -1
  5. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/01_step.drawio.png +0 -0
  6. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/02_default_implementation.drawio.png +0 -0
  7. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/03_slots.drawio.png +0 -0
  8. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/04_data_dependency.drawio.png +0 -0
  9. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/05_pipeline_schema.drawio.png +0 -0
  10. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/06_default_input.drawio.png +0 -0
  11. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/07_cloneable_section.drawio.png +0 -0
  12. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/08_cloneable_section_expanded.drawio.png +0 -0
  13. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/09_loopable_section.drawio.png +0 -0
  14. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/10_loopable_section_expanded.drawio.png +0 -0
  15. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/11_cloneable_section_splitter.drawio.png +0 -0
  16. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/12_cloneable_section_splitter_expanded.drawio.png +0 -0
  17. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/13_autoparallel_section.drawio.png +0 -0
  18. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/14_choice_section.drawio.png +0 -0
  19. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/15_choice_section_expanded.drawio.png +0 -0
  20. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/16_step_hierarchy.drawio.png +0 -0
  21. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/17_draws.drawio.png +0 -0
  22. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/18_schema_to_pipeline.drawio.png +0 -0
  23. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/19_schema_to_pipeline_combined.drawio.png +0 -0
  24. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/clustering_pass_sub_steps.drawio.png +0 -0
  25. easylink-0.1.13/docs/source/concepts/pipeline_schema/images/entity_resolution_pipeline_schema.drawio.png +0 -0
  26. easylink-0.1.13/docs/source/concepts/pipeline_schema/index.rst +751 -0
  27. easylink-0.1.13/src/easylink/_version.py +1 -0
  28. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/PKG-INFO +1 -1
  29. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/SOURCES.txt +21 -0
  30. easylink-0.1.12/docs/source/concepts/pipeline_schema/index.rst +0 -47
  31. easylink-0.1.12/src/easylink/_version.py +0 -1
  32. {easylink-0.1.12 → easylink-0.1.13}/.bandit +0 -0
  33. {easylink-0.1.12 → easylink-0.1.13}/.flake8 +0 -0
  34. {easylink-0.1.12 → easylink-0.1.13}/.github/pull_request_template.md +0 -0
  35. {easylink-0.1.12 → easylink-0.1.13}/.github/workflows/deploy.yml +0 -0
  36. {easylink-0.1.12 → easylink-0.1.13}/.github/workflows/update_readme.yml +0 -0
  37. {easylink-0.1.12 → easylink-0.1.13}/.gitignore +0 -0
  38. {easylink-0.1.12 → easylink-0.1.13}/.readthedocs.yml +0 -0
  39. {easylink-0.1.12 → easylink-0.1.13}/Jenkinsfile +0 -0
  40. {easylink-0.1.12 → easylink-0.1.13}/README.rst +0 -0
  41. {easylink-0.1.12 → easylink-0.1.13}/docs/Makefile +0 -0
  42. {easylink-0.1.12 → easylink-0.1.13}/docs/nitpick-exceptions +0 -0
  43. {easylink-0.1.12 → easylink-0.1.13}/docs/source/_static/style.css +0 -0
  44. {easylink-0.1.12 → easylink-0.1.13}/docs/source/_templates/layout.html +0 -0
  45. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/cli.rst +0 -0
  46. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/configuration.rst +0 -0
  47. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/graph_components.rst +0 -0
  48. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/implementation.rst +0 -0
  49. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/index.rst +0 -0
  50. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/pipeline.rst +0 -0
  51. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/pipeline_graph.rst +0 -0
  52. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/pipeline_schema.rst +0 -0
  53. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/pipeline_schema_constants/development.rst +0 -0
  54. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/pipeline_schema_constants/index.rst +0 -0
  55. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/pipeline_schema_constants/testing.rst +0 -0
  56. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/rule.rst +0 -0
  57. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/runner.rst +0 -0
  58. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/step.rst +0 -0
  59. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/aggregator_utils.rst +0 -0
  60. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/data_utils.rst +0 -0
  61. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/general_utils.rst +0 -0
  62. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/index.rst +0 -0
  63. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/paths.rst +0 -0
  64. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/splitter_utils.rst +0 -0
  65. {easylink-0.1.12 → easylink-0.1.13}/docs/source/api_reference/utilities/validation_utils.rst +0 -0
  66. {easylink-0.1.12 → easylink-0.1.13}/docs/source/concepts/index.rst +0 -0
  67. {easylink-0.1.12 → easylink-0.1.13}/docs/source/conf.py +0 -0
  68. {easylink-0.1.12 → easylink-0.1.13}/docs/source/glossary.rst +0 -0
  69. {easylink-0.1.12 → easylink-0.1.13}/docs/source/index.rst +0 -0
  70. {easylink-0.1.12 → easylink-0.1.13}/docs/source/user_guide/cli.rst +0 -0
  71. {easylink-0.1.12 → easylink-0.1.13}/docs/source/user_guide/index.rst +0 -0
  72. {easylink-0.1.12 → easylink-0.1.13}/docs/source/user_guide/tutorials/getting_started.rst +0 -0
  73. {easylink-0.1.12 → easylink-0.1.13}/docs/source/user_guide/tutorials/index.rst +0 -0
  74. {easylink-0.1.12 → easylink-0.1.13}/pyproject.toml +0 -0
  75. {easylink-0.1.12 → easylink-0.1.13}/python_versions.json +0 -0
  76. {easylink-0.1.12 → easylink-0.1.13}/pytype.cfg +0 -0
  77. {easylink-0.1.12 → easylink-0.1.13}/setup.cfg +0 -0
  78. {easylink-0.1.12 → easylink-0.1.13}/setup.py +0 -0
  79. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/__about__.py +0 -0
  80. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/__init__.py +0 -0
  81. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/cli.py +0 -0
  82. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/configuration.py +0 -0
  83. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/graph_components.py +0 -0
  84. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/images/spark_cluster/Dockerfile +0 -0
  85. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/images/spark_cluster/README.md +0 -0
  86. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/implementation.py +0 -0
  87. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/implementation_metadata.yaml +0 -0
  88. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/pipeline.py +0 -0
  89. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/pipeline_graph.py +0 -0
  90. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/pipeline_schema.py +0 -0
  91. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/pipeline_schema_constants/__init__.py +0 -0
  92. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/pipeline_schema_constants/development.py +0 -0
  93. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/pipeline_schema_constants/testing.py +0 -0
  94. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/rule.py +0 -0
  95. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/runner.py +0 -0
  96. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/step.py +0 -0
  97. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/README.md +0 -0
  98. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/build-containers-local.sh +0 -0
  99. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/build-containers-remote.sh +0 -0
  100. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/input_data/create_input_files.ipynb +0 -0
  101. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/input_data/input_file_1.csv +0 -0
  102. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/input_data/input_file_1.parquet +0 -0
  103. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/input_data/input_file_2.csv +0 -0
  104. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/input_data/input_file_2.parquet +0 -0
  105. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/python_pandas/README.md +0 -0
  106. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/python_pandas/dummy_step.py +0 -0
  107. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/python_pandas/python_pandas.def +0 -0
  108. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/python_pyspark/README.md +0 -0
  109. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/python_pyspark/dummy_step.py +0 -0
  110. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/python_pyspark/python_pyspark.def +0 -0
  111. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/r/README.md +0 -0
  112. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/r/dummy_step.R +0 -0
  113. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/r/r-image.def +0 -0
  114. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/steps/dev/test.py +0 -0
  115. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/__init__.py +0 -0
  116. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/aggregator_utils.py +0 -0
  117. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/data_utils.py +0 -0
  118. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/general_utils.py +0 -0
  119. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/paths.py +0 -0
  120. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/spark.smk +0 -0
  121. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/splitter_utils.py +0 -0
  122. {easylink-0.1.12 → easylink-0.1.13}/src/easylink/utilities/validation_utils.py +0 -0
  123. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/dependency_links.txt +0 -0
  124. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/entry_points.txt +0 -0
  125. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/not-zip-safe +0 -0
  126. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/requires.txt +0 -0
  127. {easylink-0.1.12 → easylink-0.1.13}/src/easylink.egg-info/top_level.txt +0 -0
  128. {easylink-0.1.12 → easylink-0.1.13}/tests/__init__.py +0 -0
  129. {easylink-0.1.12 → easylink-0.1.13}/tests/conftest.py +0 -0
  130. {easylink-0.1.12 → easylink-0.1.13}/tests/e2e/test_easylink_run.py +0 -0
  131. {easylink-0.1.12 → easylink-0.1.13}/tests/e2e/test_step_types.py +0 -0
  132. {easylink-0.1.12 → easylink-0.1.13}/tests/integration/test_snakemake.py +0 -0
  133. {easylink-0.1.12 → easylink-0.1.13}/tests/integration/test_snakemake_slurm.py +0 -0
  134. {easylink-0.1.12 → easylink-0.1.13}/tests/integration/test_snakemake_spark.py +0 -0
  135. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/common/environment_local.yaml +0 -0
  136. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/common/input_data.yaml +0 -0
  137. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/common/pipeline.yaml +0 -0
  138. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/e2e/environment_slurm.yaml +0 -0
  139. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/e2e/pipeline.yaml +0 -0
  140. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/e2e/pipeline_expanded.yaml +0 -0
  141. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/integration/environment_spark_slurm.yaml +0 -0
  142. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/integration/pipeline.yaml +0 -0
  143. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/integration/pipeline_spark.yaml +0 -0
  144. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/environment_minimum.yaml +0 -0
  145. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/environment_spark_slurm.yaml +0 -0
  146. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline.yaml +0 -0
  147. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_bad_combined_implementations.yaml +0 -0
  148. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_bad_implementation.yaml +0 -0
  149. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_bad_loop_formatting.yaml +0 -0
  150. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_bad_step.yaml +0 -0
  151. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_bad_type_key.yaml +0 -0
  152. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_combine_bad_implementation_names.yaml +0 -0
  153. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_combine_bad_topology.yaml +0 -0
  154. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_combine_two_steps.yaml +0 -0
  155. {easylink-0.1.12 → easylink-0.1.13}/tests/specifications/unit/pipeline_combine_with_extra_node.yaml +0 -0
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  171. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/__init__.py +0 -0
  172. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/conftest.py +0 -0
  173. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/rule_strings/aggregation_rule.txt +0 -0
  174. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/rule_strings/checkpoint_rule.txt +0 -0
  175. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/rule_strings/embarrassingly_parallel_rule.txt +0 -0
  176. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/rule_strings/implemented_rule_local.txt +0 -0
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  181. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/rule_strings/validation_rule.txt +0 -0
  182. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_cli.py +0 -0
  183. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_config.py +0 -0
  184. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_data_utils.py +0 -0
  185. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_general_utils.py +0 -0
  186. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_graph_components.py +0 -0
  187. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_implementation.py +0 -0
  188. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_pipeline.py +0 -0
  189. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_pipeline_graph.py +0 -0
  190. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_pipeline_schema.py +0 -0
  191. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_rule.py +0 -0
  192. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_runner.py +0 -0
  193. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_step.py +0 -0
  194. {easylink-0.1.12 → easylink-0.1.13}/tests/unit/test_validations.py +0 -0
  195. {easylink-0.1.12 → easylink-0.1.13}/update_readme.py +0 -0
{easylink-0.1.12 → easylink-0.1.13}/.github/CODEOWNERS RENAMED
@@ -1,2 +1,2 @@
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  # default owners
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- * @aflaxman @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier @zmbc
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+ * @aflaxman @albrja @hussain-jafari @patricktnast @rmudambi @stevebachmeier @tylerdy @zmbc
{easylink-0.1.12 → easylink-0.1.13}/CHANGELOG.rst RENAMED
@@ -1,3 +1,7 @@
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+ **0.1.13 - 4/21/25**
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+
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+ - remove graphviz from doc build install
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+
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  **0.1.12 - 4/1/25**
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  - Propagate embarrassingly parallel splitters and aggregators to leaf steps
{easylink-0.1.12 → easylink-0.1.13}/Makefile RENAMED
@@ -14,6 +14,9 @@ PACKAGE_NAME = easylink
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  include $(MAKE_INCLUDES)/base.mk
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  include $(MAKE_INCLUDES)/test.mk
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+ install: ENV_REQS?=dev
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  install:
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- conda install -y python-graphviz
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- $(MAKE) -f $(MAKE_INCLUDES)/base.mk install
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+ # Don't install Graphviz for docs. This could break if we add doctests which require graphviz!
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+ # Note that installing the python package graphviz doesn't actually require the graphviz system package.
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+ $(if $(filter-out docs,${ENV_REQS}),conda install -y python-graphviz,)
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+ $(MAKE) -f $(MAKE_INCLUDES)/base.mk install ENV_REQS=${ENV_REQS}
{easylink-0.1.12 → easylink-0.1.13}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: easylink
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- Version: 0.1.12
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+ Version: 0.1.13
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  Summary: Research repository for the EasyLink ER ecosystem project.
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  Home-page: https://github.com/ihmeuw/easylink
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  Author: The EasyLink developers