linkml-store 0.2.6__py3-none-any.whl → 0.2.10rc1__py3-none-any.whl

linkml_store/utils/format_utils.py

@@ -1,5 +1,6 @@
 import csv
 import gzip
+import hashlib
 import io
 import json
 import logging
@@ -29,13 +30,24 @@ class Format(Enum):
     JSONL = "jsonl"
     YAML = "yaml"
     YAMLL = "yamll"
+    TOML = "toml"
     TSV = "tsv"
     CSV = "csv"
     XML = "xml"
+    TURTLE = "turtle"
+    RDFXML = "rdfxml"
+    TEXT = "text"
+    TEXTLINES = "textlines"
     OBO = "obo"
+    FASTA = "fasta"
+    GMT = "gmt"
+    DAT = "dat"
+    MARKDOWN = "markdown"
     PKL = "pkl"
     PYTHON = "python"
     PARQUET = "parquet"
+    HDF5 = "hdf5"
+    NETCDF = "netcdf"
     FORMATTED = "formatted"
     TABLE = "table"
     XLSX = "xlsx"
@@ -55,7 +67,12 @@ class Format(Enum):
             ".yamll": cls.YAMLL,
             ".tsv": cls.TSV,
             ".csv": cls.CSV,
+            ".txt": cls.TEXT,
             ".xml": cls.XML,
+            ".owx": cls.XML,
+            ".owl": cls.RDFXML,
+            ".ttl": cls.TURTLE,
+            ".md": cls.MARKDOWN,
             ".py": cls.PYTHON,
             ".parquet": cls.PARQUET,
             ".pq": cls.PARQUET,
@@ -122,12 +139,25 @@ def clean_nested_structure(obj):
     else:
         return clean_pandas_value(obj)
 
+
 def process_file(
-    f: IO, format: Format, expected_type: Optional[Type] = None, header_comment_token: Optional[str] = None
+    f: IO,
+    format: Format,
+    expected_type: Optional[Type] = None,
+    header_comment_token: Optional[str] = None,
+    format_options: Optional[Dict[str, Any]] = None,
 ) -> List[Dict[str, Any]]:
     """
     Process a single file and return a list of objects.
+
+    :param f: The file object.
+    :param format: The format of the file.
+    :param expected_type: The expected type of the objects.
+    :param header_comment_token: Token used for header comments to be skipped
+    :return:
     """
+    if format_options is None:
+        format_options = {}
     if format == Format.YAMLL:
         format = Format.YAML
         expected_type = list
@@ -142,6 +172,14 @@ def process_file(
             objs = [obj for obj in objs if obj is not None]
         else:
             objs = yaml.safe_load(f)
+    elif format == Format.TOML:
+        import toml
+
+        objs = toml.load(f)
+        if not isinstance(objs, list):
+            objs = [objs]
+    elif format == Format.TEXTLINES:
+        objs = f.readlines()
     elif format in [Format.TSV, Format.CSV]:
         if header_comment_token:
             while True:
@@ -160,14 +198,82 @@ def process_file(
     elif format == Format.XLSX:
         xls = pd.ExcelFile(f)
         objs = {sheet: clean_nested_structure(xls.parse(sheet).to_dict(orient="records")) for sheet in xls.sheet_names}
+    elif format == Format.TEXT:
+        txt = f.read()
+        objs = [
+            {
+                "name": Path(f.name).name,
+                "path": f.name,
+                "content": txt,
+                "size": len(txt),
+                "lines": txt.count("\n") + 1,
+                "md5": hashlib.md5(txt.encode()).hexdigest(),
+            }
+        ]
+    elif format == Format.GMT:
+        objs = []
+        lib_name = Path(f.name).name
+        for line in f:
+            parts = line.strip().split("\t")
+            desc = parts[1]
+            objs.append(
+                {
+                    "library": lib_name,
+                    "uid": f"{lib_name}.{parts[0]}",
+                    "name": parts[0],
+                    "description": desc if desc else None,
+                    "genes": parts[2:],
+                }
+            )
+    elif format == Format.FASTA:
+        objs = []
+        current_obj = None
+        for line in f:
+            line = line.strip()
+            if line.startswith(">"):
+                if current_obj:
+                    objs.append(current_obj)
+                current_obj = {"id": line[1:], "sequence": ""}
+            else:
+                current_obj["sequence"] += line
+        if current_obj:
+            objs.append(current_obj)
     elif format == Format.OBO:
         blocks = split_document(f.read(), "\n\n")
         id_pattern = re.compile(r"id: (\S+)")
+
         def get_id(block):
             m = id_pattern.search(block)
             return m.group(1) if m else None
+
         objs = [{"id": get_id(block), "content": block} for block in blocks]
         objs = [obj for obj in objs if obj["id"]]
+    elif format == Format.DAT:
+        from linkml_store.utils.dat_parser import parse_sib_format
+
+        _, objs = parse_sib_format(f.read())
+    elif format in (Format.RDFXML, Format.TURTLE):
+        import lightrdf
+
+        parser = lightrdf.Parser()
+        objs = []
+        ext_fmt = "rdfxml"
+        if format == Format.TURTLE:
+            ext_fmt = "ttl"
+        bytesio = io.BytesIO(f.read().encode("utf-8"))
+        buffer = io.BufferedReader(bytesio)
+        for s, p, o in parser.parse(buffer, base_iri=None, format=ext_fmt):
+            obj = {
+                "subject": s,
+                "predicate": p,
+                "object": o,
+            }
+            if format_options.get("pivot", False):
+                obj = {
+                    "subject": s,
+                    p: o,
+                }
+            objs.append(obj)
     elif format == Format.PARQUET:
         import pyarrow.parquet as pq
 
@@ -202,6 +308,7 @@ def load_objects(
     :param compression: The compression type. Supports 'gz' for gzip and 'tgz' for tar.gz.
     :param expected_type: The target type to load the objects into, e.g. list
     :param header_comment_token: Token used for header comments to be skipped
+    :param select_query: JSONPath query to select specific objects from the loaded data.
     :return: A list of dictionaries representing the loaded objects.
     """
     if isinstance(file_path, Path):
@@ -290,7 +397,8 @@ def write_output(
 
 
 def render_output(
-    data: Union[List[Dict[str, Any]], Dict[str, Any], pd.DataFrame], format: Optional[Union[Format, str]] = Format.YAML
+    data: Union[List[Dict[str, Any]], Dict[str, Any], pd.DataFrame, List[BaseModel]],
+    format: Optional[Union[Format, str]] = Format.YAML,
 ) -> str:
     """
     Render output data in JSON, JSONLines, YAML, CSV, or TSV format.
@@ -323,6 +431,12 @@ def render_output(
     if isinstance(data, pd.DataFrame):
         data = data.to_dict(orient="records")
 
+    if isinstance(data, BaseModel):
+        data = data.model_dump()
+
+    if data and isinstance(data, list) and isinstance(data[0], BaseModel):
+        data = [d.model_dump() if isinstance(d, BaseModel) else d for d in data]
+
     if isinstance(data, dict) and format in [Format.TSV, Format.CSV]:
         data = [data]
 
@@ -335,8 +449,15 @@ def render_output(
         return "\n".join(json.dumps(obj) for obj in data)
     elif format == Format.PYTHON:
         return str(data)
+    elif format == Format.MARKDOWN:
+
+        def as_markdown(obj: dict):
+            return "## Object\n\n" + "\n".join([f" * {k}: {v}" for k, v in obj.items()])
+
+        return "\n\n".join([as_markdown(obj) for obj in data]) if isinstance(data, list) else as_markdown(data)
     elif format == Format.TABLE:
         from tabulate import tabulate
+
         return tabulate(pd.DataFrame(data), headers="keys", tablefmt="psql")
     elif format == Format.YAML:
         if isinstance(data, list):
@@ -401,4 +522,4 @@ def split_document(doc: str, delimiter: str):
     :param delimiter: The delimiter.
     :return: The parts of the document.
     """
-    return doc.split(delimiter)
+    return doc.split(delimiter)

linkml_store/utils/llm_utils.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Callable, List, Optional, TYPE_CHECKING
+from typing import TYPE_CHECKING, Callable, List, Optional
 
 if TYPE_CHECKING:
     import tiktoken
@@ -76,6 +76,7 @@ def render_formatted_text(
         return text
     if not values:
         raise ValueError(f"Cannot fit text into token limit: {text_length} > {token_limit}")
+    # remove last element and try again
     return render_formatted_text(render_func, values[0:-1], encoding=encoding, token_limit=token_limit)
 
 
@@ -104,6 +105,7 @@ def get_token_limit(model_name: str) -> int:
 
 def parse_yaml_payload(yaml_str: str, strict=False) -> Optional[dict]:
     import yaml
+
     if "```" in yaml_str:
         yaml_str = yaml_str.split("```")[1].strip()
         if yaml_str.startswith("yaml"):
@@ -114,4 +116,4 @@ def parse_yaml_payload(yaml_str: str, strict=False) -> Optional[dict]:
         if strict:
             raise e
         logger.error(f"Error parsing YAML: {yaml_str}\n{e}")
-        return None
+        return None

linkml_store/utils/object_utils.py

@@ -83,15 +83,21 @@ def object_path_get(obj: Union[BaseModel, Dict[str, Any]], path: str, default_va
     'NA'
     """
     if isinstance(obj, BaseModel):
-        obj = obj.dict()
+        obj = obj.model_dump()
     parts = path.split(".")
     for part in parts:
         if "[" in part:
             key, index = part[:-1].split("[")
             index = int(index)
-            obj = obj[key][index]
+            if key in obj and obj[key] is not None:
+                obj = obj[key][index]
+            else:
+                return default_value
         else:
-            obj = obj.get(part, default_value)
+            if isinstance(obj, list):
+                obj = [v1.get(part, default_value) for v1 in obj]
+            else:
+                obj = obj.get(part, default_value)
     return obj
 
 

linkml_store/utils/pandas_utils.py

@@ -56,7 +56,7 @@ def nested_objects_to_dataframe(data: List[Dict[str, Any]]) -> pd.DataFrame:
 
 
 def facet_summary_to_dataframe_unmelted(
-    facet_summary: Dict[Union[str, Tuple[str, ...]], List[Tuple[Union[str, Tuple[str, ...]], int]]]
+    facet_summary: Dict[Union[str, Tuple[str, ...]], List[Tuple[Union[str, Tuple[str, ...]], int]]],
 ) -> pd.DataFrame:
     rows = []
 

linkml_store/utils/sql_utils.py

@@ -116,7 +116,7 @@ def facet_count_sql(query: Query, facet_column: Union[str, Tuple[str, ...]], mul
         modified_where = " AND ".join(conditions)
 
     def make_col_safe(col):
-        return '"' + quoted_name(col, True) + '"' if ' ' in col else col
+        return '"' + quoted_name(col, True) + '"' if " " in col else col
 
     if isinstance(facet_column, str):
         facet_column = make_col_safe(facet_column)

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.
@@ -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-0.2.6.dist-info → linkml_store-0.2.10rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: linkml-store
-Version: 0.2.6
+Version: 0.2.10rc1
 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
@@ -39,6 +40,7 @@ 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"

{linkml_store-0.2.6.dist-info → linkml_store-0.2.10rc1.dist-info}/RECORD

@@ -1,71 +1,76 @@
 linkml_store/__init__.py,sha256=jlU6WOUAn8cKIhzbTULmBTWpW9gZdEt7q_RI6KZN1bY,118
 linkml_store/api/__init__.py,sha256=3CelcFEFz0y3MkQAzhQ9JxHIt1zFk6nYZxSmYTo8YZE,226
-linkml_store/api/client.py,sha256=-XX1H5dIPBCPwU3lgZLtb7JXmUQR_c-FYGSKEW1idr8,12970
-linkml_store/api/collection.py,sha256=Edwyb36D8NJjb-bkDy3O8BJbDVxtSH3yOKI_QW9_cic,41620
+linkml_store/api/client.py,sha256=I2kCSMQ-HS0EByJHfewsRbunNYfuZ9JoZv8AXj7Ho48,12970
+linkml_store/api/collection.py,sha256=zmMGequFf9WmoNgkd1_cuydInRe_aTqJvmuybizKjO8,43118
 linkml_store/api/config.py,sha256=pOz210JIwkEEXtfjcsZBp1UEedkBu8RkH62Qa1b4exI,5777
-linkml_store/api/database.py,sha256=JyQ8SuPrNiltgMH4pdFt4IgGBc9nq3mfRJ5ZUEIDEqA,29696
+linkml_store/api/database.py,sha256=W0ootSLm4MGTHexR-De_GvBFlsio00KwkoNksSbpmso,30442
 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=1Jc770CR3oipfLj9iJn-dbkgtoEObLbylUQCoUWxuzs,7313
-linkml_store/api/stores/duckdb/duckdb_database.py,sha256=idIe89yqrdMKR69Xpi3cd5LStwe6FRBOm4eJGsHfOV0,10904
+linkml_store/api/stores/duckdb/duckdb_collection.py,sha256=AW7YhHdegHdbcAB1Lnr1WNI9VUAxRyMd3oHMnzfsLuQ,15057
+linkml_store/api/stores/duckdb/duckdb_database.py,sha256=R2NB9r5WgYc5CTKaiXwK_BS-C0RO6WLTlG8EooCzTuk,10886
 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/filesystem/filesystem_database.py,sha256=Ich707bWzgeq3tdv37wLLkM4Kb3lr4w3T1iftvbMqdw,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=hKwaHHFxfWqjBNHZpzVuDVruH_SdXzoIKHdePN3JDEg,10447
-linkml_store/api/stores/mongodb/mongodb_database.py,sha256=HfVEEFCuwZ96KO3eWuSGFajRUgZPmeG-fqsrWHZhJng,4077
+linkml_store/api/stores/mongodb/mongodb_collection.py,sha256=lR18BdaVUbuJDIltuL42MnGJWyMa28XFi_x1PHb3u0M,14884
+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/neo4j/neo4j_database.py,sha256=QN6-iSshQwTk0GWDANmSCs8b_Oqd-KI5gI90nq82HWM,5574
 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=rSCh9wzmP2ijD7St6xjhTKFeKszUBRg5ZvJjvvLkvLE,8869
 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=GtbLVMcH6rHEeEMljFGVFd8U5h71WN_ojmIp17UlJxo,31253
+linkml_store/cli.py,sha256=OJbzxNlqHERUMrqMiznRjA_3tp5eXBA3w7cex0nVPhM,37663
 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=gGyl4j7AF72CyfJLKAMOUJOPhHwptS_0k8mcJ-t76zU,5911
 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=YK715LJtoJY0fUaHBsS0kJs-Vs3sOug7biouIsfQsTo,7654
 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=qoMrzsEE5zDTHc6Y1nBQcSOYDjJETRqsZL7Zl7p3hLg,5407
+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/inference_engine.py,sha256=7P9syuIwwBpCUytfqZcCR5ei61ys5LIw8YhO0iIehG4,7191
+linkml_store/inference/implementations/sklearn_inference_engine.py,sha256=_PiZom5i3ki9SmdqwF7SipHeLPK-Ai-vEiiuOfgNWd4,13516
+linkml_store/inference/inference_config.py,sha256=bbYiWf9eYdjEDzpMK-k5AfrhyzZlotVxPLZtjnVsA5Q,2283
+linkml_store/inference/inference_engine.py,sha256=r5Adx1ZOfe4eJ9XgMEYgXb9XhSDCzq7t4Sdvn4EXOUQ,7191
 linkml_store/inference/inference_engine_registry.py,sha256=6o66gvBYBwdeAKm62zqqvfaBlcopVP_cla3L6uXGsHA,3015
+linkml_store/plotting/__init__.py,sha256=8Wjpwjhtp1-Ci_B2gRVUZ8EI_hGxpuhXQPlUny5ZWC0,84
+linkml_store/plotting/cli.py,sha256=rPTPwracoRq80vjMGeFghUf9r6MMYpibZ62fW85NrsI,7482
+linkml_store/plotting/heatmap.py,sha256=uXnIpQyIPHGAk_sgSKKPWZpbBm8nuLEjQrfAJgIsMCc,13594
 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=BY4QOQ5YSv6u5SIEXN5bLWCjcynBaC9Tndze0FwOP3M,3047
+linkml_store/utils/enrichment_analyzer.py,sha256=KLVdw0zqnWKdfCiUwSuBm8f5g5gppiADIysHamMcnSg,7707
 linkml_store/utils/file_utils.py,sha256=rQ7-XpmI6_Kx_dhEnI98muFRr0MmgI_kZ_9cgJBf_0I,1411
-linkml_store/utils/format_utils.py,sha256=hHRFkh3cwb5shM6RO7WWuOXsHHH283M_vZjXRuzbwWI,13035
+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=N_Xo1CRPYfN1nKw_UUOxGJyl1IK2N8lJ6Zrh8mcZF8g,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/object_utils.py,sha256=s6GIcfEODI8oALL_-ohtTlW_jwCRL48KaP1FGp4YS9M,6596
+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=qatmrJR2u4ICaO7QhDRL1ukxJlLv0zYSGgmmFV-hdnU,6210
+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=QcLTUQWm5z1OTtiOl0mXKJyFJcQeCtbcc-GQwHhkUYw,5456
+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 +79,8 @@ 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-0.2.6.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
-linkml_store-0.2.6.dist-info/METADATA,sha256=s5x6OmbGC7oVUpXunjiM42sASvsvKR8XRoJllGqF6ww,6964
-linkml_store-0.2.6.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-linkml_store-0.2.6.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
-linkml_store-0.2.6.dist-info/RECORD,,
+linkml_store-0.2.10rc1.dist-info/LICENSE,sha256=77mDOslUnalYnuq9xQYZKtIoNEzcH9mIjvWHOKjamnE,1086
+linkml_store-0.2.10rc1.dist-info/METADATA,sha256=ApfUFD87aguIxXb20QF_lPRSxenx0KhkHp9Ruw-l-3Y,7029
+linkml_store-0.2.10rc1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+linkml_store-0.2.10rc1.dist-info/entry_points.txt,sha256=gWxVsHqx-t-UKWFHFzawQTvs4is4vC1rCF5AeKyqWWk,101
+linkml_store-0.2.10rc1.dist-info/RECORD,,

{linkml_store-0.2.6.dist-info → linkml_store-0.2.10rc1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.1
+Generator: poetry-core 2.1.3
 Root-Is-Purelib: true
 Tag: py3-none-any