fairscape-cli 1.2.3__tar.gz → 1.2.4__tar.gz

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Files changed (101) hide show
  1. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/LICENSE +6 -6
  2. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/MANIFEST.in +1 -1
  3. {fairscape_cli-1.2.3/src/fairscape_cli.egg-info → fairscape_cli-1.2.4}/PKG-INFO +1 -1
  4. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/README.md +367 -367
  5. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/pyproject.toml +82 -82
  6. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/setup.cfg +0 -0
  7. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/__init__.py +0 -0
  8. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/__main__.py +31 -31
  9. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/__init__.py +0 -0
  10. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/augment_commands.py +204 -204
  11. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/build_commands.py +778 -778
  12. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/import_commands.py +395 -395
  13. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/publish_commands.py +43 -43
  14. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/rocrate_commands.py +1762 -1762
  15. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/schema_commands.py +472 -472
  16. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/commands/track.py +188 -188
  17. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/config.py +17 -17
  18. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/GenomicData.py +503 -503
  19. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/PhysioNetImporter.py +569 -569
  20. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/__init__.py +0 -0
  21. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/bioproject_fetcher.py +547 -547
  22. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/cell_line_api.py +200 -200
  23. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/generic_data/__init__.py +2 -2
  24. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/generic_data/connectors/__init__.py +3 -3
  25. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/generic_data/connectors/dataverse_connector.py +284 -284
  26. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/generic_data/connectors/figshare_connector.py +115 -115
  27. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/data_fetcher/generic_data/research_data.py +208 -208
  28. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/__init__.py +6 -6
  29. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/evidence_graph/__init__.py +0 -0
  30. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/evidence_graph/graph_builder.py +242 -242
  31. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/evidence_graph/html_builder.py +1029 -1029
  32. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/generate_datasheet.py +65 -65
  33. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/rocrate/__init__.py +14 -14
  34. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/rocrate/datasheet_generator.py +383 -383
  35. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/rocrate/section_generators.py +340 -340
  36. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/rocrate/summary_generator.py +251 -251
  37. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/rocrate/utilities/__init__.py +0 -0
  38. fairscape_cli-1.2.4/src/fairscape_cli/datasheet_builder/templates/.DS_Store +0 -0
  39. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/base.html +740 -740
  40. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/preview.html +679 -679
  41. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/sections/distribution.html +40 -40
  42. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/sections/overview.html +174 -174
  43. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/sections/subcrates.html +309 -309
  44. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/sections/summary.html +70 -70
  45. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/datasheet_builder/templates/sections/use_cases.html +131 -131
  46. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/entailments/__init__.py +0 -0
  47. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/entailments/evi.xml +999 -999
  48. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/entailments/find_outputs.py +183 -183
  49. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/entailments/inverse.py +204 -204
  50. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/jupyter/__init__.py +3 -3
  51. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/jupyter/magic.py +104 -104
  52. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/MLModel.py +60 -60
  53. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/__init__.py +47 -47
  54. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/bagit.py +207 -207
  55. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/base.py +51 -51
  56. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/biochem_entity.py +89 -89
  57. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/computation.py +47 -47
  58. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/dataset.py +187 -187
  59. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/experiment.py +51 -51
  60. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/guid_utils.py +64 -64
  61. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/instrument.py +59 -59
  62. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/pep.py +248 -248
  63. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/rocrate.py +892 -892
  64. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/sample.py +63 -63
  65. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/__init__.py +0 -0
  66. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/__init__.py +0 -0
  67. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/cm4ai_schemas.py +63 -63
  68. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_apms_embedding.json +36 -36
  69. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_apmsloader_ppi_edgelist.json +32 -32
  70. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_apmsloader_ppi_gene_node_attributes.json +38 -38
  71. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_coembedding.json +36 -36
  72. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_hierarchy_cx.json +19 -19
  73. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_hierarchy_ppi_cutoff.json +19 -19
  74. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_image_embedding_emd.json +37 -37
  75. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_image_embedding_labels_prob.json +222 -222
  76. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_imageloader_gene_node_attributes.json +56 -56
  77. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_imageloader_samplescopy.json +74 -74
  78. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/cm4ai_schema_imageloader_uniquecopy.json +55 -55
  79. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/default_schemas/default.py +0 -0
  80. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/tabular.py +582 -582
  81. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/schema/utils.py +142 -142
  82. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/software.py +74 -74
  83. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/models/utils.py +82 -82
  84. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/publish/__init__.py +0 -0
  85. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/publish/publish_tools.py +463 -463
  86. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/tracking/__init__.py +34 -34
  87. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/tracking/config.py +49 -49
  88. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/tracking/io_capture.py +298 -298
  89. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/tracking/metadata_generator.py +302 -302
  90. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/tracking/provenance_tracker.py +452 -452
  91. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/tracking/utils.py +60 -60
  92. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/utils/build_utils.py +571 -571
  93. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/utils/huggingface_utils.py +406 -406
  94. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/utils/merkle.py +189 -189
  95. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli/utils/serialization.py +31 -31
  96. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4/src/fairscape_cli.egg-info}/PKG-INFO +1 -1
  97. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli.egg-info/SOURCES.txt +1 -0
  98. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli.egg-info/dependency_links.txt +0 -0
  99. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli.egg-info/entry_points.txt +0 -0
  100. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli.egg-info/requires.txt +0 -0
  101. {fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/src/fairscape_cli.egg-info/top_level.txt +0 -0
{fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/LICENSE RENAMED
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- Copyright 2023 THE RECTOR AND VISITORS OF THE UNIVERSITY OF VIRGINIA
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-
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- Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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-
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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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-
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+ Copyright 2023 THE RECTOR AND VISITORS OF THE UNIVERSITY OF VIRGINIA
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+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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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.
{fairscape_cli-1.2.3 → fairscape_cli-1.2.4}/MANIFEST.in RENAMED
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- include src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/*.json
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+ include src/fairscape_cli/models/schema/default_schemas/cm4ai_schemas/v0.1.0/*.json
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  recursive-include src/fairscape_cli/datasheet_builder/templates *
{fairscape_cli-1.2.3/src/fairscape_cli.egg-info → fairscape_cli-1.2.4}/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: fairscape-cli
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- Version: 1.2.3
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+ Version: 1.2.4
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  Summary: A utility for packaging objects and validating metadata for FAIRSCAPE
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  Author-email: Max Levinson <mal8ch@virginia.edu>, Justin Niestroy <jniestroy@gmail.com>, Sadnan Al Manir <sadnanalmanir@gmail.com>, Tim Clark <twc8q@virginia.edu>
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  License: Copyright 2023 THE RECTOR AND VISITORS OF THE UNIVERSITY OF VIRGINIA