linkml-store 0.2.5__py3-none-any.whl → 0.2.9__py3-none-any.whl

linkml_store/utils/vector_utils.py

@@ -8,6 +8,7 @@ logger = logging.getLogger(__name__)
 
 LOL = List[List[float]]
 
+
 def pairwise_cosine_similarity(vector1: np.array, vector2: np.array) -> float:
     """
     Calculate the cosine similarity between two vectors.
@@ -34,7 +35,7 @@ def pairwise_cosine_similarity(vector1: np.array, vector2: np.array) -> float:
     dot_product = np.dot(vector1, vector2)
     norm1 = np.linalg.norm(vector1)
     norm2 = np.linalg.norm(vector2)
-    return dot_product / (norm1 * norm2)
+    return float(dot_product / (norm1 * norm2))
 
 
 def compute_cosine_similarity_matrix(list1: LOL, list2: LOL) -> np.ndarray:
@@ -77,9 +78,7 @@ def top_matches(cosine_similarity_matrix: np.ndarray) -> Tuple[np.ndarray, np.nd
     return top_match_indices, top_match_values
 
 
-def top_n_matches(
-    cosine_similarity_matrix: np.ndarray, n: int = 10
-) -> Tuple[np.ndarray, np.ndarray]:
+def top_n_matches(cosine_similarity_matrix: np.ndarray, n: int = 10) -> Tuple[np.ndarray, np.ndarray]:
     # Find the indices that would sort each row in descending order
     sorted_indices = np.argsort(-cosine_similarity_matrix, axis=1)
 
@@ -136,10 +135,7 @@ def mmr_diversified_search(
                     max_sim_to_selected = max(
                         [
                             np.dot(document_vectors[idx], document_vectors[s])
-                            / (
-                                np.linalg.norm(document_vectors[idx])
-                                * np.linalg.norm(document_vectors[s])
-                            )
+                            / (np.linalg.norm(document_vectors[idx]) * np.linalg.norm(document_vectors[s]))
                             for s in selected_indices
                         ]
                     )
@@ -160,6 +156,3 @@ def mmr_diversified_search(
         selected_indices.add(best_index)
 
     return result_indices
-
-
-

{linkml_store-0.2.5.dist-info → linkml_store-0.2.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: linkml-store
-Version: 0.2.5
+Version: 0.2.9
 Summary: linkml-store
 License: MIT
 Author: Author 1
@@ -24,6 +24,7 @@ Provides-Extra: map
 Provides-Extra: mongodb
 Provides-Extra: neo4j
 Provides-Extra: pyarrow
+Provides-Extra: rdf
 Provides-Extra: renderer
 Provides-Extra: scipy
 Provides-Extra: tests
@@ -34,12 +35,12 @@ Requires-Dist: duckdb (>=0.10.1)
 Requires-Dist: duckdb-engine (>=0.11.2)
 Requires-Dist: fastapi ; extra == "fastapi"
 Requires-Dist: frictionless ; extra == "frictionless"
-Requires-Dist: gcsfs
 Requires-Dist: google-cloud-bigquery ; extra == "bigquery"
 Requires-Dist: h5py ; extra == "h5py"
 Requires-Dist: jinja2 (>=3.1.4,<4.0.0)
 Requires-Dist: jsonlines (>=4.0.0,<5.0.0)
 Requires-Dist: jsonpatch (>=1.33)
+Requires-Dist: lightrdf ; extra == "rdf"
 Requires-Dist: linkml (>=1.8.0) ; extra == "validation"
 Requires-Dist: linkml-runtime (>=1.8.0)
 Requires-Dist: linkml_map ; extra == "map"
@@ -54,7 +55,7 @@ Requires-Dist: plotly ; extra == "analytics"
 Requires-Dist: py2neo ; extra == "neo4j"
 Requires-Dist: pyarrow ; extra == "pyarrow"
 Requires-Dist: pydantic (>=2.0.0,<3.0.0)
-Requires-Dist: pymongo ; extra == "mongodb"
+Requires-Dist: pymongo (>=4.11,<5.0) ; extra == "mongodb"
 Requires-Dist: pystow (>=0.5.4,<0.6.0)
 Requires-Dist: python-dotenv (>=1.0.1,<2.0.0)
 Requires-Dist: ruff (>=0.6.2) ; extra == "tests"

{linkml_store-0.2.5.dist-info → linkml_store-0.2.9.dist-info}/RECORD

@@ -1,71 +1,73 @@
 linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
 linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
-linkml_store/api/client.py,sha256=RfroZ4LRxeTCM0Z15mUsCDkt4IwwY-W9D-jiZoFmXbs,12785
-linkml_store/api/collection.py,sha256=CGvWxH7HRhjDt9Cp3SGdMqyhYx7Q4fRKUtAJV74_l0g,39711
+linkml_store/api/client.py,sha256=I2kCSMQ-HS0EByJHfewsRbunNYfuZ9JoZv8AXj7Ho48,12970
+linkml_store/api/collection.py,sha256=OQnqAKdnFlnDRnySfgdh20txKgTLqTtHLoY3VBrPcEQ,43138
 linkml_store/api/config.py,sha256=pOz210JIwkEEXtfjcsZBp1UEedkBu8RkH62Qa1b4exI,5777
-linkml_store/api/database.py,sha256=yqLmJJGS8VHOJwmsPhxmvEHLPsfJVYYOxIZJtQ_Q9sE,29460
+linkml_store/api/database.py,sha256=r7F8i9qqAxRpX58nTfCmcoiUDw7oZ-aL_c4OQjlYsCg,30768
 linkml_store/api/queries.py,sha256=tx9fgGY5fC_2ZbIvg4BqTK_MXJwA_DI4mxr8HdQ6Vos,2075
 linkml_store/api/stores/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/api/stores/chromadb/__init__.py,sha256=e9BkOPuPnVQKA5PRKDulag59yGNHDP3U2_DnPSrFAKM,132
 linkml_store/api/stores/chromadb/chromadb_collection.py,sha256=RQUZx5oeotkzNihg-dlSevkiTiKY1d9x0bS63HF80W4,4270
 linkml_store/api/stores/chromadb/chromadb_database.py,sha256=dZA3LQE8-ZMhJQOzsUFyxehnKpFF7adR182aggfkaFY,3205
 linkml_store/api/stores/duckdb/__init__.py,sha256=rbQSDgNg-fdvi6-pHGYkJTST4p1qXUZBf9sFSsO3KPk,387
-linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=Rkbm_uIVIRj5576lEolsyY_3Um1h8Lf3RHn8Fy3LIgU,7036
-linkml_store/api/stores/duckdb/duckdb_database.py,sha256=GH9bcOfHpNp6r-Eu1C3W0xuYcLsqGFDH1Sh4weifGaQ,9923
+linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=d5Mp0cKGpMVOrV-YjTSg2DFbKE2INaRBcVAYgz0zdKY,15335
+linkml_store/api/stores/duckdb/duckdb_database.py,sha256=SB3FoKSXj8SLxGK6zlwKc1SyX1a9JvPPI4HV1jqYnL0,10907
 linkml_store/api/stores/duckdb/mappings.py,sha256=tDce3W1Apwammhf4LS6cRJ0m4NiJ0eB7vOI_4U5ETY8,148
-linkml_store/api/stores/filesystem/__init__.py,sha256=KjvCjdttwqMHNeGyL-gr59zRz0--HFEWWUNNCJ5hITs,347
+linkml_store/api/stores/filesystem/__init__.py,sha256=rD6nsZLkMphS4EQSrGtjirYD32ENRIqv7Kllm5CLBMY,346
 linkml_store/api/stores/filesystem/filesystem_collection.py,sha256=9gqY2KRZsn_RWk4eKkxFd3_wcxs5YaXvcBI7GGJBMGE,6751
 linkml_store/api/stores/filesystem/filesystem_database.py,sha256=e9hSGoaOxr_sG_RhjgzV_yvdQ_xbHHXHJDtufWzAX4E,2883
 linkml_store/api/stores/hdf5/__init__.py,sha256=l4cIh3v7P0nPbwGIsfuCMD_serQ8q8c7iuUA9W2Jb4o,97
 linkml_store/api/stores/hdf5/hdf5_collection.py,sha256=mnpLMYehn3PuaIjp2dXrIWu8jh-bdQ84X2Ku83jMdEY,3805
 linkml_store/api/stores/hdf5/hdf5_database.py,sha256=EZbjrpaqiNDEFvoD5dZNcGBXA8z6HRNL81emueTZWNw,2714
 linkml_store/api/stores/mongodb/__init__.py,sha256=OSFCr7RQlDEe-O-Y0P_i912oAMK-L3pC7Cnj7sxlwAk,510
-linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=unN0v7RYlGIiJxEhbNRxZ86TVQ4ELlAsNWTwEbg7E_g,6831
-linkml_store/api/stores/mongodb/mongodb_database.py,sha256=Y9MIV0KSRGCyopz8vGEivhSuvF0vZLCDJd29cdqMIX8,3857
+linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=39As4FEqj5jQiiDJoIYhuJpUPXXIJalpY6rNBcoMZyo,14397
+linkml_store/api/stores/mongodb/mongodb_database.py,sha256=Lr47vVaJv_cgTCc2ArEma9R5T0agR_haaCJB6BageyI,4112
 linkml_store/api/stores/neo4j/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/api/stores/neo4j/neo4j_collection.py,sha256=a-Az5_ypdBMgeNyhrTW7q-ik-vYPCDDONIK7N_CDA9c,17449
 linkml_store/api/stores/neo4j/neo4j_database.py,sha256=zanP_uBZO3AH0wuzbu6auK4zcZon_lMreC2vooSZwt8,5571
 linkml_store/api/stores/solr/__init__.py,sha256=aAfnaN9mZOiIDj1NYz0Ll9fZF2gG7UU_vhP4SNCL2d8,36
-linkml_store/api/stores/solr/solr_collection.py,sha256=ZlxC3JbVaHfSA4HuTeJTsp6qe48tHS6Fgel5jsqXcsM,4727
+linkml_store/api/stores/solr/solr_collection.py,sha256=_KCYOtak-TGLYCV26rRwQeDvbUiO1qkWtzpB8rSFzpw,4849
 linkml_store/api/stores/solr/solr_database.py,sha256=TFjqbY7jAkdrhAchbNg0E-mChSP7ogNwFExslbvX7Yo,2877
 linkml_store/api/stores/solr/solr_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/api/types.py,sha256=3aIQtDFMvsSmjuN5qrR2vNK5sHa6yzD_rEOPA6tHwvg,176
-linkml_store/cli.py,sha256=RgRdO4isZgt3KOtGMqpMY3fHwKCTMGyfzHaa1SK3vhA,31264
+linkml_store/cli.py,sha256=Cmwpi4FoumzXxSTyB76c6NBfkQeZcXGFK2D0JcTGg5Y,37690
 linkml_store/constants.py,sha256=x4ZmDsfE9rZcL5WpA93uTKrRWzCD6GodYXviVzIvR38,112
 linkml_store/graphs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/graphs/graph_map.py,sha256=bYRxv8n1YPnFqE9d6JKNmRawb8EAhsPlHhBue0gvtZE,712
 linkml_store/index/__init__.py,sha256=6SQzDe-WZSSqbGNsbCDfyPTyz0s9ISDKw1dm9xgQuT4,1396
 linkml_store/index/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/index/implementations/llm_indexer.py,sha256=ja7UXhQj7F0g6HiRIJ8EBPuM86nOgr49jkh7eh_nCHs,5644
+linkml_store/index/implementations/llm_indexer.py,sha256=N3LSDcQ0dwbrStMQLd5Ts2ojt5QV06pOmGExncE4WQs,5925
 linkml_store/index/implementations/simple_indexer.py,sha256=KnkFJtXTHnwjhD_D6ZK2rFhBID1dgCedcOVPEWAY2NU,1282
-linkml_store/index/indexer.py,sha256=e5dsjh2wjOTDRsfClKJAFTbcK1UC7BOGkUCOfDg9omI,7635
+linkml_store/index/indexer.py,sha256=maETwr-DGKDywCjBK7J7LkbARjNQSosNvOSUJlaAXsQ,7653
 linkml_store/inference/__init__.py,sha256=b8NAFNZjOYU_8gOvxdyCyoiHOOl5Ai2ckKs1tv7ZkkY,342
 linkml_store/inference/evaluation.py,sha256=YDFYaEu2QLSfFq4oyARrnKfTiPLtNF8irhhspgVDfdY,6013
 linkml_store/inference/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-linkml_store/inference/implementations/llm_inference_engine.py,sha256=iSxiboYpgB0_yL4zlHIJx2ZbvDrJC8JioewTKgLUS0U,5443
-linkml_store/inference/implementations/rag_inference_engine.py,sha256=R3Dz-DyNx7UU3ZaV1n9homxC2nUAT5JZnd4IRkIFftk,11326
+linkml_store/inference/implementations/llm_inference_engine.py,sha256=dNGcxmDdyRDqZW0DGRty3pCegnG_SothhM1_T7b71fE,5489
+linkml_store/inference/implementations/rag_inference_engine.py,sha256=xdf1WJ-e0G34Y_F4h4UzkLNF2TZjSfdNIUiYTP7xiZU,11276
 linkml_store/inference/implementations/rule_based_inference_engine.py,sha256=0IEY_fsHJPJy6QKbYQU_qE87RRnPOXQxPuJKXCQG8jU,6250
-linkml_store/inference/implementations/sklearn_inference_engine.py,sha256=Sdi7CoRK3qoLJu3prgLy1Ck_zQ1gHWRKFybHe7XQ4_g,13192
-linkml_store/inference/inference_config.py,sha256=EFGdigxWsfTPREbgqyJVRShN0JktCEmFLLoECrLfXSg,2282
+linkml_store/inference/implementations/sklearn_inference_engine.py,sha256=_PiZom5i3ki9SmdqwF7SipHeLPK-Ai-vEiiuOfgNWd4,13516
+linkml_store/inference/inference_config.py,sha256=vSuFy65JhtyAMEt7wh62OQ-VJXL_G8uXFQziLWcOaBA,2283
 linkml_store/inference/inference_engine.py,sha256=7P9syuIwwBpCUytfqZcCR5ei61ys5LIw8YhO0iIehG4,7191
 linkml_store/inference/inference_engine_registry.py,sha256=6o66gvBYBwdeAKm62zqqvfaBlcopVP_cla3L6uXGsHA,3015
 linkml_store/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/utils/change_utils.py,sha256=O2rvSvgTKB60reLLz9mX5OWykAA_m93bwnUh5ZWa0EY,471
+linkml_store/utils/dat_parser.py,sha256=d3arx8szcylyFHi6H_aqtGgJwYY8F1ahMFEcvg12iUM,3047
+linkml_store/utils/enrichment_analyzer.py,sha256=b5GcR8UOyvvXiau0Wfh3zQiaSqW6c5bOCzIVtPCpF4Y,7720
 linkml_store/utils/file_utils.py,sha256=rQ7-XpmI6_Kx_dhEnI98muFRr0MmgI_kZ_9cgJBf_0I,1411
-linkml_store/utils/format_utils.py,sha256=sjpdJJ8Ww2ilm03mQt_v4QkZvQMymqUeTiPS3U1ViKM,11067
+linkml_store/utils/format_utils.py,sha256=ZKMNUYOTcKEWx0s5GBZSbe7-ncfHgiQ63jdig2tbxCg,16743
 linkml_store/utils/io.py,sha256=JHUrWDtlZC2jtN_PQZ4ypdGIyYlftZEN3JaCvEPs44w,884
-linkml_store/utils/llm_utils.py,sha256=51AiwMeXm2FpiD-9AywKcbZzlUMqXRAjDFJEp5Ia0LA,3494
+linkml_store/utils/llm_utils.py,sha256=PClY2FeNuCx8pJzw6KcH4zIWUuYLZtFc6hUA-zCcCsU,3536
 linkml_store/utils/mongodb_utils.py,sha256=Rl1YmMKs1IXwSsJIViSDChbi0Oer5cBnMmjka2TeQS8,4665
 linkml_store/utils/neo4j_utils.py,sha256=y3KPmDZ8mQmePgg0lUeKkeKqzEr2rV226xxEtHc5pRg,1266
 linkml_store/utils/object_utils.py,sha256=V0s_ZzqAGkFUfrU-9fAPb5g3snMmgKKhR3SiYZgECXI,6353
-linkml_store/utils/pandas_utils.py,sha256=djiFPO3YbgRVo2XAZuKCtgH8QVLuUyPIsfS8e-0umsU,3182
+linkml_store/utils/pandas_utils.py,sha256=ttkXGCJZcNhmy72SkY4ZfKbC-lyscpI74YLKznJ8AfM,3183
 linkml_store/utils/patch_utils.py,sha256=q-h_v68okyruzdPTEHCe0WubbQHKpi1qy5bJ9vFWDo8,4823
 linkml_store/utils/query_utils.py,sha256=HWt46BsGWoIGiNBTtvpXGY6onPRWsQky6eu_9cYqbvo,3440
 linkml_store/utils/schema_utils.py,sha256=iJiZxo5NGr7v87h4DV6V9DrDOZHSswMRuf0N4V2rVtg,646
 linkml_store/utils/sklearn_utils.py,sha256=itPpcrsbbyOazdjmivaaZ1lyZeytm0a0hJ2AS8ziUgg,7590
-linkml_store/utils/sql_utils.py,sha256=T41w_vsc3SauTJQkDMwid_nOtKW1YOKyUuaxEf470hk,5938
+linkml_store/utils/sql_utils.py,sha256=GF4s51BP3WmnYuBgtUiwo3uXvYX_ypyrknk4a6tIoSE,6210
 linkml_store/utils/stats_utils.py,sha256=4KqBb1bqDgAmq-1fJLLu5B2paPgoZZc3A-gnyVam4bI,1799
-linkml_store/utils/vector_utils.py,sha256=Q1RlpDzavJAM9-H2m2XNU5BNUcfZkpIWeEZii2hK0PQ,5449
+linkml_store/utils/vector_utils.py,sha256=ZJPRWz64jHMbH5sV1CaCZAAvA_kS1gTjhjnwLRXjKT8,5354
 linkml_store/webapi/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 linkml_store/webapi/html/__init__.py,sha256=hwp5eeBJKH65Bvv1x9Z4vsT1tLSYtb9Dq4I9r1kL1q0,69
 linkml_store/webapi/html/base.html.j2,sha256=hoiV2uaSxxrQp7VuAZBOHueH7czyJMYcPBRN6dZFYhk,693
@@ -74,8 +76,8 @@ linkml_store/webapi/html/database_details.html.j2,sha256=qtXdavbZb0mohiObI9dvJtk
 linkml_store/webapi/html/databases.html.j2,sha256=a9BCWQYfPeFhdUd31CWhB0yWhTIFXQayO08JgjyqKoc,294
 linkml_store/webapi/html/generic.html.j2,sha256=KtLaO2HUEF2Opq-OwHKgRKetNWe8IWc6JuIkxRPsywk,1018
 linkml_store/webapi/main.py,sha256=B0Da575kKR7X88N9ykm99Dem8FyBAW9f-w3A_JwUzfw,29165
-linkml_store-0.2.5.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
-linkml_store-0.2.5.dist-info/METADATA,sha256=3Jd0dGNsKk0FI3ab6aPRMYq4bV9rJr7jzCz99h6srsw,6971
-linkml_store-0.2.5.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-linkml_store-0.2.5.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
-linkml_store-0.2.5.dist-info/RECORD,,
+linkml_store-0.2.9.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
+linkml_store-0.2.9.dist-info/METADATA,sha256=ZpUTktmtmOmV2-kcqaCP3mvjhNgJNcskKLlVWearjc0,7025
+linkml_store-0.2.9.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+linkml_store-0.2.9.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
+linkml_store-0.2.9.dist-info/RECORD,,

{linkml_store-0.2.5.dist-info → linkml_store-0.2.9.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.1
+Generator: poetry-core 2.1.2
 Root-Is-Purelib: true
 Tag: py3-none-any