mhd-model 0.1.41__tar.gz → 0.1.42__tar.gz

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Files changed (104) hide show
  1. {mhd_model-0.1.41 → mhd_model-0.1.42}/PKG-INFO +1 -1
  2. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/__init__.py +1 -1
  3. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/legacy/mhd2announce.py +2 -0
  4. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/ms/mhd2announce.py +8 -3
  5. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.legacy-profile.json +1 -1
  6. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.ms-profile.json +1 -1
  7. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.schema.json +1 -1
  8. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.legacy-profile.json +1 -1
  9. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.ms-profile.json +1 -1
  10. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.schema.json +1 -1
  11. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/PKG-INFO +1 -1
  12. {mhd_model-0.1.41 → mhd_model-0.1.42}/pyproject.toml +2 -2
  13. {mhd_model-0.1.41 → mhd_model-0.1.42}/LICENSE +0 -0
  14. {mhd_model-0.1.41 → mhd_model-0.1.42}/README.md +0 -0
  15. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/__init__.py +0 -0
  16. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/cli.py +0 -0
  17. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/create/__init__.py +0 -0
  18. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/create/announcement.py +0 -0
  19. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/create/create.py +0 -0
  20. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/create/neo4j_input.py +0 -0
  21. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/create/sdrf.py +0 -0
  22. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/validate/__init__.py +0 -0
  23. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/validate/announcement.py +0 -0
  24. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/validate/mhd_file.py +0 -0
  25. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/commands/validate/validate.py +0 -0
  26. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/__init__.py +0 -0
  27. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/__init__.py +0 -0
  28. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/__init__.py +0 -0
  29. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/legacy/__init__.py +0 -0
  30. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/ms/__init__.py +0 -0
  31. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/mhd/__init__.py +0 -0
  32. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/mhd/convertor.py +0 -0
  33. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/neo4j_enabled_data/__init__.py +0 -0
  34. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/neo4j_enabled_data/v0_1/__init__.py +0 -0
  35. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/neo4j_enabled_data/v0_1/legacy/__init__.py +0 -0
  36. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/neo4j_enabled_data/v0_1/legacy/convertor.py +0 -0
  37. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/sdrf/__init__.py +0 -0
  38. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/sdrf/mhd2sdrf.py +0 -0
  39. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/domain_utils.py +0 -0
  40. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/log_utils.py +0 -0
  41. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/mhd_client.py +0 -0
  42. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/__init__.py +0 -0
  43. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/definitions.py +0 -0
  44. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/__init__.py +0 -0
  45. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/__init__.py +0 -0
  46. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/__init__.py +0 -0
  47. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/base/__init__.py +0 -0
  48. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/base/profile.py +0 -0
  49. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/legacy/__init__.py +0 -0
  50. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/legacy/profile.py +0 -0
  51. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/ms/__init__.py +0 -0
  52. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/ms/fields.py +0 -0
  53. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/profiles/ms/profile.py +0 -0
  54. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/validation/__init__.py +0 -0
  55. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/validation/base.py +0 -0
  56. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/validation/definitions.py +0 -0
  57. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/announcement/validation/validator.py +0 -0
  58. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/__init__.py +0 -0
  59. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/__init__.py +0 -0
  60. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/__init__.py +0 -0
  61. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/base.py +0 -0
  62. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/dataset_builder.py +0 -0
  63. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/graph_nodes.py +0 -0
  64. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/graph_validation.py +0 -0
  65. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/profile.py +0 -0
  66. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/base/relationships.py +0 -0
  67. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/legacy/__init__.py +0 -0
  68. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/legacy/graph_validation.py +0 -0
  69. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/legacy/profile.py +0 -0
  70. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/ms/__init__.py +0 -0
  71. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/ms/graph_validation.py +0 -0
  72. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/profiles/ms/profile.py +0 -0
  73. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/__init__.py +0 -0
  74. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/base.py +0 -0
  75. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/profile/__init__.py +0 -0
  76. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/profile/base.py +0 -0
  77. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/profile/definition.py +0 -0
  78. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/utils.py +0 -0
  79. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/dataset/validation/validator.py +0 -0
  80. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/rules/__init__.py +0 -0
  81. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/rules/cv_definitions.py +0 -0
  82. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/rules/managed_cv_terms.py +0 -0
  83. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/rules/predefined_cv_terms.py +0 -0
  84. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/sdrf/__init__.py +0 -0
  85. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/model/v0_1/sdrf/model.py +0 -0
  86. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schema_utils.py +0 -0
  87. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/__init__.py +0 -0
  88. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/__init__.py +0 -0
  89. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/__init__.py +0 -0
  90. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/exceptions.py +0 -0
  91. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/fields.py +0 -0
  92. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/model.py +0 -0
  93. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/validation/__init__.py +0 -0
  94. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/validation/cv_term_helper.py +0 -0
  95. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/validation/definitions.py +0 -0
  96. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/validation/registry.py +0 -0
  97. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/shared/validation/validators.py +0 -0
  98. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/utils.py +0 -0
  99. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/SOURCES.txt +0 -0
  100. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/dependency_links.txt +0 -0
  101. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/entry_points.txt +0 -0
  102. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/requires.txt +0 -0
  103. {mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/top_level.txt +0 -0
  104. {mhd_model-0.1.41 → mhd_model-0.1.42}/setup.cfg +0 -0
{mhd_model-0.1.41 → mhd_model-0.1.42}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mhd-model
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- Version: 0.1.41
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+ Version: 0.1.42
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  Summary: MetabolomicsHub Common Data Model
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  Author-email: MetabolomicsHub Team <help@metabolomicshub.org>
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  License-Expression: Apache-2.0
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/__init__.py RENAMED
@@ -1,7 +1,7 @@
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  import pathlib
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  import sys
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3
 
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- __version__ = "v0.1.41"
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+ __version__ = "v0.1.42"
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  application_root_path = pathlib.Path(__file__).parent.parent
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{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/legacy/mhd2announce.py RENAMED
@@ -349,6 +349,8 @@ def create_announcement_file(
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  repository_identifier=study.repository_identifier,
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  schema_name=announcement_schema_name,
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  profile_uri=announcement_profile_uri,
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+ revision=mhd_dataset.repository_revision,
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+ revision_datetime=mhd_dataset.repository_revision_datetime,
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  mhd_metadata_file_url=AnyUrl(mhd_file_url),
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  dataset_url_list=dataset_url_list,
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  license=study.license,
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/convertors/announcement/v0_1/ms/mhd2announce.py RENAMED
@@ -261,8 +261,12 @@ def create_announcement_file(
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  announcement_profile_uri=ANNOUNCEMENT_FILE_V0_1_LEGACY_PROFILE_NAME,
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  ):
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  mhd_dataset = MhDatasetMsProfile.model_validate(mhd_file)
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- nodes_map = {x.id_: x for x in mhd_dataset.graph.nodes}
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- relationships_map = {x.id_: x for x in mhd_dataset.graph.relationships}
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+ nodes_map: dict[str, IdentifiableMhdModel] = {
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+ x.id_: x for x in mhd_dataset.graph.nodes
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+ }
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+ relationships_map: dict[str, BaseMhdRelationship] = {
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+ x.id_: x for x in mhd_dataset.graph.relationships
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+ }
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  all_nodes_map: dict[str, BaseMhdModel] = {}
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  type_map: dict[str, dict[str, BaseMhdModel]] = {}
@@ -279,7 +283,7 @@ def create_announcement_file(
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  relationship_name_map[rel.relationship_name][rel.id_] = rel
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  if "study" not in type_map:
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- logger.info("Study not found for in input file")
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+ logger.error("Study not found for in the input file")
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  return
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  study: graph_nodes.Study = list(type_map["study"].values())[0]
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@@ -293,6 +297,7 @@ def create_announcement_file(
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  type_map["publication"].values()
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  )
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  for node in graph_publications:
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+ relationships_map.get()
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  item = AnnouncementPublication.model_validate(
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  node.model_dump(by_alias=True)
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  )
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.legacy-profile.json RENAMED
@@ -1287,4 +1287,4 @@
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  ],
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  "title": "AnnouncementLegacyProfile",
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  "type": "object"
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- }
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+ }
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.ms-profile.json RENAMED
@@ -1921,4 +1921,4 @@
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  ],
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  "title": "AnnouncementMsProfile",
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  "type": "object"
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- }
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+ }
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/announcement-v0.1.schema.json RENAMED
@@ -1266,4 +1266,4 @@
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  ],
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  "title": "AnnouncementBaseProfile",
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  "type": "object"
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- }
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+ }
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.legacy-profile.json RENAMED
@@ -4373,4 +4373,4 @@
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  ],
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  "title": "MhDatasetLegacyProfile",
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  "type": "object"
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- }
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+ }
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.ms-profile.json RENAMED
@@ -4373,4 +4373,4 @@
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  ],
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  "title": "MhDatasetMsProfile",
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  "type": "object"
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- }
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+ }
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model/schemas/mhd/common-data-model-v0.1.schema.json RENAMED
@@ -4373,4 +4373,4 @@
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  ],
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  "title": "MhDatasetBaseProfile",
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  "type": "object"
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- }
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+ }
{mhd_model-0.1.41 → mhd_model-0.1.42}/mhd_model.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: mhd-model
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- Version: 0.1.41
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+ Version: 0.1.42
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  Summary: MetabolomicsHub Common Data Model
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  Author-email: MetabolomicsHub Team <help@metabolomicshub.org>
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  License-Expression: Apache-2.0
{mhd_model-0.1.41 → mhd_model-0.1.42}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "mhd-model"
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- version = "0.1.41"
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+ version = "0.1.42"
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  description = "MetabolomicsHub Common Data Model"
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  authors = [{"name"="MetabolomicsHub Team", "email"="help@metabolomicshub.org"}]
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  license = "Apache-2.0"
@@ -62,7 +62,7 @@ test = [
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  [tool.commitizen]
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  name = "cz_conventional_commits"
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  version_provider = "uv"
65
- version = "0.1.41"
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+ version = "0.1.42"
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  tag_format = "v$major.$minor.$patch"
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  version_files = [
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  "pyproject.toml:version",
{mhd_model-0.1.41 → mhd_model-0.1.42}/LICENSE RENAMED
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{mhd_model-0.1.41 → mhd_model-0.1.42}/README.md RENAMED
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{mhd_model-0.1.41 → mhd_model-0.1.42}/setup.cfg RENAMED
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