linkml-store 0.2.9__py3-none-any.whl → 0.2.10rc1__py3-none-any.whl

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Files changed (26) hide show
  1. linkml_store/api/collection.py +2 -2
  2. linkml_store/api/database.py +1 -12
  3. linkml_store/api/stores/duckdb/duckdb_collection.py +25 -23
  4. linkml_store/api/stores/duckdb/duckdb_database.py +2 -2
  5. linkml_store/api/stores/filesystem/filesystem_database.py +1 -1
  6. linkml_store/api/stores/mongodb/mongodb_collection.py +39 -25
  7. linkml_store/api/stores/neo4j/neo4j_database.py +1 -1
  8. linkml_store/api/stores/solr/solr_collection.py +102 -19
  9. linkml_store/cli.py +1 -2
  10. linkml_store/index/implementations/llm_indexer.py +0 -1
  11. linkml_store/index/indexer.py +2 -1
  12. linkml_store/inference/implementations/llm_inference_engine.py +2 -4
  13. linkml_store/inference/inference_config.py +1 -1
  14. linkml_store/inference/inference_engine.py +1 -1
  15. linkml_store/plotting/__init__.py +5 -0
  16. linkml_store/plotting/cli.py +172 -0
  17. linkml_store/plotting/heatmap.py +356 -0
  18. linkml_store/utils/dat_parser.py +1 -1
  19. linkml_store/utils/enrichment_analyzer.py +7 -7
  20. linkml_store/utils/llm_utils.py +1 -1
  21. linkml_store/utils/object_utils.py +9 -3
  22. {linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/METADATA +1 -1
  23. {linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/RECORD +26 -23
  24. {linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/WHEEL +1 -1
  25. {linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/LICENSE +0 -0
  26. {linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/entry_points.txt +0 -0
{linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/RECORD RENAMED
@@ -1,65 +1,68 @@
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  linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
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  linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
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  linkml_store/api/client.py,sha256=I2kCSMQ-HS0EByJHfewsRbunNYfuZ9JoZv8AXj7Ho48,12970
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- linkml_store/api/collection.py,sha256=OQnqAKdnFlnDRnySfgdh20txKgTLqTtHLoY3VBrPcEQ,43138
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+ linkml_store/api/collection.py,sha256=zmMGequFf9WmoNgkd1_cuydInRe_aTqJvmuybizKjO8,43118
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  linkml_store/api/config.py,sha256=pOz210JIwkEEXtfjcsZBp1UEedkBu8RkH62Qa1b4exI,5777
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- linkml_store/api/database.py,sha256=r7F8i9qqAxRpX58nTfCmcoiUDw7oZ-aL_c4OQjlYsCg,30768
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+ linkml_store/api/database.py,sha256=W0ootSLm4MGTHexR-De_GvBFlsio00KwkoNksSbpmso,30442
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  linkml_store/api/queries.py,sha256=tx9fgGY5fC_2ZbIvg4BqTK_MXJwA_DI4mxr8HdQ6Vos,2075
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  linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  linkml_store/api/stores/chromadb/__init__.py,sha256=e9BkOPuPnVQKA5PRKDulag59yGNHDP3U2_DnPSrFAKM,132
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  linkml_store/api/stores/chromadb/chromadb_collection.py,sha256=RQUZx5oeotkzNihg-dlSevkiTiKY1d9x0bS63HF80W4,4270
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  linkml_store/api/stores/chromadb/chromadb_database.py,sha256=dZA3LQE8-ZMhJQOzsUFyxehnKpFF7adR182aggfkaFY,3205
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  linkml_store/api/stores/duckdb/__init__.py,sha256=rbQSDgNg-fdvi6-pHGYkJTST4p1qXUZBf9sFSsO3KPk,387
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- linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=d5Mp0cKGpMVOrV-YjTSg2DFbKE2INaRBcVAYgz0zdKY,15335
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- linkml_store/api/stores/duckdb/duckdb_database.py,sha256=SB3FoKSXj8SLxGK6zlwKc1SyX1a9JvPPI4HV1jqYnL0,10907
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+ linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=AW7YhHdegHdbcAB1Lnr1WNI9VUAxRyMd3oHMnzfsLuQ,15057
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+ linkml_store/api/stores/duckdb/duckdb_database.py,sha256=R2NB9r5WgYc5CTKaiXwK_BS-C0RO6WLTlG8EooCzTuk,10886
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  linkml_store/api/stores/duckdb/mappings.py,sha256=tDce3W1Apwammhf4LS6cRJ0m4NiJ0eB7vOI_4U5ETY8,148
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  linkml_store/api/stores/filesystem/__init__.py,sha256=rD6nsZLkMphS4EQSrGtjirYD32ENRIqv7Kllm5CLBMY,346
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  linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=9gqY2KRZsn_RWk4eKkxFd3_wcxs5YaXvcBI7GGJBMGE,6751
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- linkml_store/api/stores/filesystem/filesystem_database.py,sha256=e9hSGoaOxr_sG_RhjgzV_yvdQ_xbHHXHJDtufWzAX4E,2883
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+ linkml_store/api/stores/filesystem/filesystem_database.py,sha256=Ich707bWzgeq3tdv37wLLkM4Kb3lr4w3T1iftvbMqdw,2883
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  linkml_store/api/stores/hdf5/__init__.py,sha256=l4cIh3v7P0nPbwGIsfuCMD_serQ8q8c7iuUA9W2Jb4o,97
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  linkml_store/api/stores/hdf5/hdf5_collection.py,sha256=mnpLMYehn3PuaIjp2dXrIWu8jh-bdQ84X2Ku83jMdEY,3805
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  linkml_store/api/stores/hdf5/hdf5_database.py,sha256=EZbjrpaqiNDEFvoD5dZNcGBXA8z6HRNL81emueTZWNw,2714
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  linkml_store/api/stores/mongodb/__init__.py,sha256=OSFCr7RQlDEe-O-Y0P_i912oAMK-L3pC7Cnj7sxlwAk,510
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- linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=39As4FEqj5jQiiDJoIYhuJpUPXXIJalpY6rNBcoMZyo,14397
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+ linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=lR18BdaVUbuJDIltuL42MnGJWyMa28XFi_x1PHb3u0M,14884
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  linkml_store/api/stores/mongodb/mongodb_database.py,sha256=Lr47vVaJv_cgTCc2ArEma9R5T0agR_haaCJB6BageyI,4112
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  linkml_store/api/stores/neo4j/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  linkml_store/api/stores/neo4j/neo4j_collection.py,sha256=a-Az5_ypdBMgeNyhrTW7q-ik-vYPCDDONIK7N_CDA9c,17449
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- linkml_store/api/stores/neo4j/neo4j_database.py,sha256=zanP_uBZO3AH0wuzbu6auK4zcZon_lMreC2vooSZwt8,5571
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+ linkml_store/api/stores/neo4j/neo4j_database.py,sha256=QN6-iSshQwTk0GWDANmSCs8b_Oqd-KI5gI90nq82HWM,5574
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  linkml_store/api/stores/solr/__init__.py,sha256=aAfnaN9mZOiIDj1NYz0Ll9fZF2gG7UU_vhP4SNCL2d8,36
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- linkml_store/api/stores/solr/solr_collection.py,sha256=_KCYOtak-TGLYCV26rRwQeDvbUiO1qkWtzpB8rSFzpw,4849
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+ linkml_store/api/stores/solr/solr_collection.py,sha256=rSCh9wzmP2ijD7St6xjhTKFeKszUBRg5ZvJjvvLkvLE,8869
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  linkml_store/api/stores/solr/solr_database.py,sha256=TFjqbY7jAkdrhAchbNg0E-mChSP7ogNwFExslbvX7Yo,2877
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  linkml_store/api/stores/solr/solr_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  linkml_store/api/types.py,sha256=3aIQtDFMvsSmjuN5qrR2vNK5sHa6yzD_rEOPA6tHwvg,176
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- linkml_store/cli.py,sha256=Cmwpi4FoumzXxSTyB76c6NBfkQeZcXGFK2D0JcTGg5Y,37690
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+ linkml_store/cli.py,sha256=OJbzxNlqHERUMrqMiznRjA_3tp5eXBA3w7cex0nVPhM,37663
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  linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
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  linkml_store/graphs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  linkml_store/graphs/graph_map.py,sha256=bYRxv8n1YPnFqE9d6JKNmRawb8EAhsPlHhBue0gvtZE,712
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  linkml_store/index/__init__.py,sha256=6SQzDe-WZSSqbGNsbCDfyPTyz0s9ISDKw1dm9xgQuT4,1396
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  linkml_store/index/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- linkml_store/index/implementations/llm_indexer.py,sha256=N3LSDcQ0dwbrStMQLd5Ts2ojt5QV06pOmGExncE4WQs,5925
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+ linkml_store/index/implementations/llm_indexer.py,sha256=gGyl4j7AF72CyfJLKAMOUJOPhHwptS_0k8mcJ-t76zU,5911
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  linkml_store/index/implementations/simple_indexer.py,sha256=KnkFJtXTHnwjhD_D6ZK2rFhBID1dgCedcOVPEWAY2NU,1282
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- linkml_store/index/indexer.py,sha256=maETwr-DGKDywCjBK7J7LkbARjNQSosNvOSUJlaAXsQ,7653
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+ linkml_store/index/indexer.py,sha256=YK715LJtoJY0fUaHBsS0kJs-Vs3sOug7biouIsfQsTo,7654
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  linkml_store/inference/__init__.py,sha256=b8NAFNZjOYU_8gOvxdyCyoiHOOl5Ai2ckKs1tv7ZkkY,342
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  linkml_store/inference/evaluation.py,sha256=YDFYaEu2QLSfFq4oyARrnKfTiPLtNF8irhhspgVDfdY,6013
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  linkml_store/inference/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- linkml_store/inference/implementations/llm_inference_engine.py,sha256=dNGcxmDdyRDqZW0DGRty3pCegnG_SothhM1_T7b71fE,5489
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+ linkml_store/inference/implementations/llm_inference_engine.py,sha256=qoMrzsEE5zDTHc6Y1nBQcSOYDjJETRqsZL7Zl7p3hLg,5407
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  linkml_store/inference/implementations/rag_inference_engine.py,sha256=xdf1WJ-e0G34Y_F4h4UzkLNF2TZjSfdNIUiYTP7xiZU,11276
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  linkml_store/inference/implementations/rule_based_inference_engine.py,sha256=0IEY_fsHJPJy6QKbYQU_qE87RRnPOXQxPuJKXCQG8jU,6250
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  linkml_store/inference/implementations/sklearn_inference_engine.py,sha256=_PiZom5i3ki9SmdqwF7SipHeLPK-Ai-vEiiuOfgNWd4,13516
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- linkml_store/inference/inference_config.py,sha256=vSuFy65JhtyAMEt7wh62OQ-VJXL_G8uXFQziLWcOaBA,2283
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- linkml_store/inference/inference_engine.py,sha256=7P9syuIwwBpCUytfqZcCR5ei61ys5LIw8YhO0iIehG4,7191
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+ linkml_store/inference/inference_config.py,sha256=bbYiWf9eYdjEDzpMK-k5AfrhyzZlotVxPLZtjnVsA5Q,2283
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+ linkml_store/inference/inference_engine.py,sha256=r5Adx1ZOfe4eJ9XgMEYgXb9XhSDCzq7t4Sdvn4EXOUQ,7191
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  linkml_store/inference/inference_engine_registry.py,sha256=6o66gvBYBwdeAKm62zqqvfaBlcopVP_cla3L6uXGsHA,3015
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+ linkml_store/plotting/__init__.py,sha256=8Wjpwjhtp1-Ci_B2gRVUZ8EI_hGxpuhXQPlUny5ZWC0,84
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+ linkml_store/plotting/cli.py,sha256=rPTPwracoRq80vjMGeFghUf9r6MMYpibZ62fW85NrsI,7482
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+ linkml_store/plotting/heatmap.py,sha256=uXnIpQyIPHGAk_sgSKKPWZpbBm8nuLEjQrfAJgIsMCc,13594
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  linkml_store/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  linkml_store/utils/change_utils.py,sha256=O2rvSvgTKB60reLLz9mX5OWykAA_m93bwnUh5ZWa0EY,471
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- linkml_store/utils/dat_parser.py,sha256=d3arx8szcylyFHi6H_aqtGgJwYY8F1ahMFEcvg12iUM,3047
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- linkml_store/utils/enrichment_analyzer.py,sha256=b5GcR8UOyvvXiau0Wfh3zQiaSqW6c5bOCzIVtPCpF4Y,7720
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+ linkml_store/utils/dat_parser.py,sha256=BY4QOQ5YSv6u5SIEXN5bLWCjcynBaC9Tndze0FwOP3M,3047
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+ linkml_store/utils/enrichment_analyzer.py,sha256=KLVdw0zqnWKdfCiUwSuBm8f5g5gppiADIysHamMcnSg,7707
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  linkml_store/utils/file_utils.py,sha256=rQ7-XpmI6_Kx_dhEnI98muFRr0MmgI_kZ_9cgJBf_0I,1411
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  linkml_store/utils/format_utils.py,sha256=ZKMNUYOTcKEWx0s5GBZSbe7-ncfHgiQ63jdig2tbxCg,16743
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  linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
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- linkml_store/utils/llm_utils.py,sha256=PClY2FeNuCx8pJzw6KcH4zIWUuYLZtFc6hUA-zCcCsU,3536
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+ linkml_store/utils/llm_utils.py,sha256=N_Xo1CRPYfN1nKw_UUOxGJyl1IK2N8lJ6Zrh8mcZF8g,3536
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  linkml_store/utils/mongodb_utils.py,sha256=Rl1YmMKs1IXwSsJIViSDChbi0Oer5cBnMmjka2TeQS8,4665
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  linkml_store/utils/neo4j_utils.py,sha256=y3KPmDZ8mQmePgg0lUeKkeKqzEr2rV226xxEtHc5pRg,1266
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- linkml_store/utils/object_utils.py,sha256=V0s_ZzqAGkFUfrU-9fAPb5g3snMmgKKhR3SiYZgECXI,6353
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+ linkml_store/utils/object_utils.py,sha256=s6GIcfEODI8oALL_-ohtTlW_jwCRL48KaP1FGp4YS9M,6596
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  linkml_store/utils/pandas_utils.py,sha256=ttkXGCJZcNhmy72SkY4ZfKbC-lyscpI74YLKznJ8AfM,3183
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  linkml_store/utils/patch_utils.py,sha256=q-h_v68okyruzdPTEHCe0WubbQHKpi1qy5bJ9vFWDo8,4823
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  linkml_store/utils/query_utils.py,sha256=HWt46BsGWoIGiNBTtvpXGY6onPRWsQky6eu_9cYqbvo,3440
@@ -76,8 +79,8 @@ linkml_store/webapi/html/database_details.html.j2,sha256=qtXdavbZb0mohiObI9dvJtk
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  linkml_store/webapi/html/databases.html.j2,sha256=a9BCWQYfPeFhdUd31CWhB0yWhTIFXQayO08JgjyqKoc,294
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  linkml_store/webapi/html/generic.html.j2,sha256=KtLaO2HUEF2Opq-OwHKgRKetNWe8IWc6JuIkxRPsywk,1018
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  linkml_store/webapi/main.py,sha256=B0Da575kKR7X88N9ykm99Dem8FyBAW9f-w3A_JwUzfw,29165
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- linkml_store-0.2.9.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
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- linkml_store-0.2.9.dist-info/METADATA,sha256=ZpUTktmtmOmV2-kcqaCP3mvjhNgJNcskKLlVWearjc0,7025
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- linkml_store-0.2.9.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
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- linkml_store-0.2.9.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
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- linkml_store-0.2.9.dist-info/RECORD,,
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+ linkml_store-0.2.10rc1.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
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+ linkml_store-0.2.10rc1.dist-info/METADATA,sha256=ApfUFD87aguIxXb20QF_lPRSxenx0KhkHp9Ruw-l-3Y,7029
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+ linkml_store-0.2.10rc1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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+ linkml_store-0.2.10rc1.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
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+ linkml_store-0.2.10rc1.dist-info/RECORD,,
{linkml_store-0.2.9.dist-info → linkml_store-0.2.10rc1.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: poetry-core 2.1.2
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+ Generator: poetry-core 2.1.3
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  Root-Is-Purelib: true
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  Tag: py3-none-any