lamindb 0.57.1__py3-none-any.whl → 0.58.0__py3-none-any.whl

lamindb/__init__.py

@@ -53,7 +53,7 @@ Static classes & modules:
 
 """
 
-__version__ = "0.57.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.58.0"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

lamindb/_dataset.py

@@ -179,10 +179,7 @@ def __init__(
     if file is not None and file.run != run:
         _track_run_input(file, run=run)
     elif files is not None:
-        for file in files:
-            if file.run != run:
-                _track_run_input(file, run=run)
-    # there is not other possibility
+        _track_run_input(files, run=run)
 
 
 @classmethod  # type: ignore
@@ -197,6 +194,8 @@ def from_df(
     modality: Optional[Modality] = None,
     reference: Optional[str] = None,
     reference_type: Optional[str] = None,
+    version: Optional[str] = None,
+    is_new_version_of: Optional["File"] = None,
 ) -> "Dataset":
     """{}"""
     feature_set = FeatureSet.from_df(df, field=field, modality=modality)
@@ -205,7 +204,15 @@ def from_df(
     else:
         feature_sets = {}
     dataset = Dataset(
-        data=df, name=name, run=run, description=description, feature_sets=feature_sets
+        data=df,
+        name=name,
+        run=run,
+        description=description,
+        feature_sets=feature_sets,
+        reference=reference,
+        reference_type=reference_type,
+        version=version,
+        is_new_version_of=is_new_version_of,
     )
     return dataset
 
@@ -222,6 +229,8 @@ def from_anndata(
     modality: Optional[Modality] = None,
     reference: Optional[str] = None,
     reference_type: Optional[str] = None,
+    version: Optional[str] = None,
+    is_new_version_of: Optional["File"] = None,
 ) -> "Dataset":
     """{}"""
     if isinstance(adata, File):
@@ -237,6 +246,10 @@ def from_anndata(
         name=name,
         description=description,
         feature_sets=feature_sets,
+        reference=reference,
+        reference_type=reference_type,
+        version=version,
+        is_new_version_of=is_new_version_of,
     )
     return dataset
 
@@ -244,30 +257,48 @@ def from_anndata(
 # internal function, not exposed to user
 def from_files(files: Iterable[File]) -> Tuple[str, Dict[str, str]]:
     # assert all files are already saved
+    logger.debug("check not saved")
     saved = not any([file._state.adding for file in files])
     if not saved:
         raise ValueError("Not all files are yet saved, please save them")
     # query all feature sets of files
+    logger.debug("file ids")
     file_ids = [file.id for file in files]
     # query all feature sets at the same time rather than making a single query per file
+    logger.debug("feature_set_file_links")
     feature_set_file_links = File.feature_sets.through.objects.filter(
         file_id__in=file_ids
     )
-    feature_set_ids = [link.feature_set_id for link in feature_set_file_links]
-    feature_sets = FeatureSet.filter(id__in=feature_set_ids).all()
     feature_sets_by_slots = defaultdict(list)
+    logger.debug("slots")
     for link in feature_set_file_links:
-        feature_sets_by_slots[link.slot].append(
-            feature_sets.filter(id=link.feature_set_id).one()
-        )
+        feature_sets_by_slots[link.slot].append(link.feature_set_id)
     feature_sets_union = {}
-    for slot, feature_sets_slot in feature_sets_by_slots.items():
-        members = feature_sets_slot[0].members
-        for feature_set in feature_sets_slot[1:]:
-            members = members | feature_set.members
-        feature_sets_union[slot] = FeatureSet(members)
+    logger.debug("union")
+    for slot, feature_set_ids_slot in feature_sets_by_slots.items():
+        feature_set_1 = FeatureSet.filter(id=feature_set_ids_slot[0]).one()
+        related_name = feature_set_1._get_related_name()
+        features_registry = getattr(FeatureSet, related_name).field.model
+        start_time = logger.debug("run filter")
+        # this way of writing the __in statement turned out to be the fastest
+        # evaluated on a link table with 16M entries connecting 500 feature sets with
+        # 60k genes
+        feature_ids = (
+            features_registry.feature_sets.through.objects.filter(
+                featureset_id__in=feature_set_ids_slot
+            )
+            .values(f"{features_registry.__name__.lower()}_id")
+            .distinct()
+        )
+        start_time = logger.debug("done, start evaluate", time=start_time)
+        features = features_registry.filter(id__in=feature_ids)
+        feature_sets_union[slot] = FeatureSet(
+            features, type=feature_set_1.type, modality=feature_set_1.modality
+        )
+        start_time = logger.debug("done", time=start_time)
     # validate consistency of hashes
     # we do not allow duplicate hashes
+    logger.debug("hashes")
     hashes = [file.hash for file in files]
     if len(hashes) != len(set(hashes)):
         seen = set()
@@ -276,7 +307,9 @@ def from_files(files: Iterable[File]) -> Tuple[str, Dict[str, str]]:
             "Please pass files with distinct hashes: these ones are non-unique"
             f" {non_unique}"
         )
+    time = logger.debug("hash")
     hash = hash_set(set(hashes))
+    logger.debug("done", time=time)
     return hash, feature_sets_union
 
 

lamindb/_feature_set.py

@@ -239,11 +239,16 @@ def members(self) -> "QuerySet":
         # this should return a queryset and not a list...
         # need to fix this
         return self._features[1]
+    related_name = self._get_related_name()
+    return self.__getattribute__(related_name).all()
+
+
+def _get_related_name(self: FeatureSet) -> str:
     key_split = self.registry.split(".")
     orm_name_with_schema = f"{key_split[0]}.{key_split[1]}"
     feature_sets_related_models = dict_related_model_to_related_name(self)
     related_name = feature_sets_related_models.get(orm_name_with_schema)
-    return self.__getattribute__(related_name).all()
+    return related_name
 
 
 METHOD_NAMES = [
@@ -266,3 +271,4 @@ for name in METHOD_NAMES:
     attach_func_to_class_method(name, FeatureSet, globals())
 
 setattr(FeatureSet, "members", members)
+setattr(FeatureSet, "_get_related_name", _get_related_name)

lamindb/_file.py

@@ -553,9 +553,19 @@ def from_df(
     description: Optional[str] = None,
     run: Optional[Run] = None,
     modality: Optional[Modality] = None,
+    version: Optional[str] = None,
+    is_new_version_of: Optional["File"] = None,
 ) -> "File":
     """{}"""
-    file = File(data=df, key=key, run=run, description=description, log_hint=False)
+    file = File(
+        data=df,
+        key=key,
+        run=run,
+        description=description,
+        version=version,
+        is_new_version_of=is_new_version_of,
+        log_hint=False,
+    )
     feature_set = FeatureSet.from_df(df, field=field, modality=modality)
     if feature_set is not None:
         file._feature_sets = {"columns": feature_set}
@@ -615,9 +625,19 @@ def from_anndata(
     description: Optional[str] = None,
     run: Optional[Run] = None,
     modality: Optional[Modality] = None,
+    version: Optional[str] = None,
+    is_new_version_of: Optional["File"] = None,
 ) -> "File":
     """{}"""
-    file = File(data=adata, key=key, run=run, description=description, log_hint=False)
+    file = File(
+        data=adata,
+        key=key,
+        run=run,
+        description=description,
+        version=version,
+        is_new_version_of=is_new_version_of,
+        log_hint=False,
+    )
     file._feature_sets = parse_feature_sets_from_anndata(adata, field, modality)
     return file
 

lamindb/_parents.py

@@ -201,13 +201,18 @@ def _get_parents(record: Registry, field: str, distance: int, children: bool = F
     d = 2
     while d < distance:
         condition = f"{key}__{condition}"
-        records = model.filter(**{condition: record.__getattribute__(field)}).all()
+        records = model.filter(**{condition: record.__getattribute__(field)})
 
-        if len(records) == 0:
-            return results
+        try:
+            if not records.exists():
+                return results
 
-        results = results | records
-        d += 1
+            results = results | records.all()
+            d += 1
+        except Exception:
+            # For OperationalError:
+            # SQLite does not support joins containing more than 64 tables
+            return results
     return results
 
 

lamindb/dev/_data.py

@@ -308,24 +308,48 @@ def add_labels(
 
 
 def _track_run_input(
-    data: Data, is_run_input: Optional[bool] = None, run: Optional[Run] = None
+    data: Union[Data, Iterable[Data]],
+    is_run_input: Optional[bool] = None,
+    run: Optional[Run] = None,
 ):
     if run is None:
         run = run_context.run
+    # consider that data is an iterable of Data
+    data_iter: Iterable[Data] = [data] if isinstance(data, Data) else data
     track_run_input = False
+    input_data = []
+    if run is not None:
+        # avoid cycles: data can't be both input and output
+        input_data = [data for data in data_iter if data.run_id != run.id]
+        input_data_ids = [data.id for data in data_iter if data.run_id != run.id]
+    if input_data:
+        data_class_name = input_data[0].__class__.__name__.lower()
+    # let us first look at the case in which the user does not
+    # provide a boolean value for `is_run_input`
+    # hence, we need to determine whether we actually want to
+    # track a run or not
     if is_run_input is None:
-        # we need a global run context for this to work
-        if run is not None:
-            # avoid cycles (a file is both input and output)
-            if data.run != run:
+        # we don't have a run record
+        if run is None:
+            if settings.track_run_inputs:
+                logger.hint(
+                    "you can auto-track this file as a run input by calling"
+                    " `ln.track()`"
+                )
+        # assume we have a run record
+        else:
+            # assume there is non-cyclic candidate input data
+            if input_data:
                 if settings.track_run_inputs:
                     transform_note = ""
-                    if data.transform is not None:
-                        transform_note = (
-                            f", adding parent transform {data.transform.id}"
-                        )
+                    if len(input_data) == 1:
+                        if input_data[0].transform is not None:
+                            transform_note = (
+                                ", adding parent transform"
+                                f" {input_data[0].transform.id}"
+                            )
                     logger.info(
-                        f"adding file {data.id} as input for run"
+                        f"adding {data_class_name} {input_data_ids} as input for run"
                         f" {run.id}{transform_note}"
                     )
                     track_run_input = True
@@ -333,12 +357,6 @@ def _track_run_input(
                     logger.hint(
                         "track this file as a run input by passing `is_run_input=True`"
                     )
-        else:
-            if settings.track_run_inputs:
-                logger.hint(
-                    "you can auto-track this file as a run input by calling"
-                    " `ln.track()`"
-                )
     else:
         track_run_input = is_run_input
     if track_run_input:
@@ -348,12 +366,22 @@ def _track_run_input(
                 " run object via `run.input_files.add(file)`"
             )
         # avoid adding the same run twice
-        # avoid cycles (a file is both input and output)
-        if not data.input_of.contains(run) and data.run != run:
-            run.save()
-            data.input_of.add(run)
-            if data.transform is not None:
-                run.transform.parents.add(data.transform)
+        run.save()
+        if data_class_name == "file":
+            LinkORM = run.input_files.through
+            links = [
+                LinkORM(run_id=run.id, file_id=data_id) for data_id in input_data_ids
+            ]
+        else:
+            LinkORM = run.input_datasets.through
+            links = [
+                LinkORM(run_id=run.id, dataset_id=data_id) for data_id in input_data_ids
+            ]
+        LinkORM.objects.bulk_create(links, ignore_conflicts=True)
+        # generalize below for more than one data batch
+        if len(input_data) == 1:
+            if input_data[0].transform is not None:
+                run.transform.parents.add(input_data[0].transform)
 
 
 @property  # type: ignore

lamindb/dev/datasets/_core.py

@@ -156,7 +156,7 @@ def anndata_mouse_sc_lymph_node(
         populate_registries: pre-populate metadata records to simulate existing registries  # noqa
     """
     filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/E-MTAB-8414.h5ad")
-    adata = ad.read(filepath)
+    adata = ad.read_h5ad(filepath)
 
     # The column names are a bit lengthy, let's abbreviate them:
     adata.obs.columns = (
@@ -253,7 +253,7 @@ def anndata_pbmc68k_reduced() -> ad.AnnData:
     filepath, _ = urlretrieve(
         "https://lamindb-dev-datasets.s3.amazonaws.com/scrnaseq_pbmc68k_tiny.h5ad"
     )
-    return ad.read(filepath)
+    return ad.read_h5ad(filepath)
 
 
 def anndata_file_pbmc68k_test() -> Path:
@@ -283,7 +283,7 @@ def anndata_pbmc3k_processed() -> ad.AnnData:  # pragma: no cover
     filepath, _ = urlretrieve(
         "https://lamindb-test.s3.amazonaws.com/scrnaseq_scanpy_pbmc3k_processed.h5ad"
     )
-    pbmc3k = ad.read(filepath)
+    pbmc3k = ad.read_h5ad(filepath)
     pbmc3k.obs.rename(columns={"louvain": "cell_type"}, inplace=True)
     return pbmc3k
 
@@ -306,8 +306,11 @@ def anndata_human_immune_cells(
         adata.write('human_immune.h5ad')
     """
     filepath, _ = urlretrieve("https://lamindb-test.s3.amazonaws.com/human_immune.h5ad")
-    adata = ad.read(filepath)
+    adata = ad.read_h5ad(filepath)
     adata.var.drop(columns=["gene_symbols", "feature_name"], inplace=True)
+    adata.uns.pop("cell_type_ontology_term_id_colors")
+    adata.uns.pop("title")
+    adata.uns.pop("schema_version")
     adata.obs.columns = adata.obs.columns.str.replace("donor_id", "donor")
     columns = [col for col in adata.obs.columns if "ontology_term" not in col]
     adata.obs = adata.obs[columns]
@@ -378,7 +381,7 @@ def anndata_suo22_Visium10X():  # pragma: no cover
     )
     Path("suo22/").mkdir(exist_ok=True)
     filepath = Path(filepath).rename("suo22/Visium10X_data_LI_subset.h5ad")
-    return ad.read(filepath)
+    return ad.read_h5ad(filepath)
 
 
 def mudata_papalexi21_subset():  # pragma: no cover

lamindb/dev/storage/_backed_access.py

@@ -16,13 +16,22 @@ from anndata._io.h5ad import read_dataframe_legacy as read_dataframe_legacy_h5
 from anndata._io.specs.registry import get_spec, read_elem, read_elem_partial
 from anndata.compat import _read_attr
 from fsspec.core import OpenFile
+from lamin_utils import logger
 from lamindb_setup.dev.upath import UPath, infer_filesystem
 from lnschema_core import File
 from packaging import version
 
 from lamindb.dev.storage.file import filepath_from_file
 
-if version.parse(anndata_version) < version.parse("0.10.0"):
+anndata_version_parse = version.parse(anndata_version)
+
+if anndata_version_parse < version.parse("0.10.0"):
+    if anndata_version_parse < version.parse("0.9.1"):
+        logger.warning(
+            "Full backed capabilities are not available for this version of anndata,"
+            " please install anndata>=0.9.1."
+        )
+
     from anndata._core.sparse_dataset import SparseDataset
 
     # try csr for groups with no encoding_type

{lamindb-0.57.1.dist-info → lamindb-0.58.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.57.1
+Version: 0.58.0
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -8,14 +8,14 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
-Requires-Dist: lnschema_core==0.52.0
+Requires-Dist: lnschema_core==0.52.1
 Requires-Dist: lamindb_setup==0.55.6
-Requires-Dist: lamin_utils==0.11.4
+Requires-Dist: lamin_utils==0.11.5
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
-Requires-Dist: anndata>=0.9.1,<=0.10.1
+Requires-Dist: anndata>=0.8.0,<=0.10.2
 Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
@@ -24,7 +24,7 @@ Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: boto3==1.28.17 ; extra == "aws"
 Requires-Dist: aiobotocore==2.5.4 ; extra == "aws"
 Requires-Dist: fsspec[s3]==2023.9.0 ; extra == "aws"
-Requires-Dist: lnschema_bionty==0.33.0 ; extra == "bionty"
+Requires-Dist: lnschema_bionty==0.34.0 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.57.1.dist-info → lamindb-0.58.0.dist-info}/RECORD

@@ -1,12 +1,12 @@
-lamindb/__init__.py,sha256=wouDbXipZRBI2h6a5u0nS7oDs5Z0C-c6YxIzNeWiGUU,2870
-lamindb/_dataset.py,sha256=mBoeQj7KhMxAnb9wmgu7MXxlbPRGQPsGIcBVaiAZjQ8,13453
+lamindb/__init__.py,sha256=BWW5E_HjLH9kJ3Fo6sUfWV2efj0pytTAYmPxnJ-iheA,2870
+lamindb/_dataset.py,sha256=6CJHTiwe1lWLUfPHQzJpq-hj8zRjNTCWLkPmrtxpP7Q,14712
 lamindb/_delete.py,sha256=wiYmYnvIEHrDdmw1NiXyfCY9mBt-FI5XNFi5jyR_mkA,1968
 lamindb/_feature.py,sha256=5gsa7zsMVVtm1DID4dF3Vwo5llWyY1dH3Hg5hjaIrQk,5554
-lamindb/_feature_set.py,sha256=DWDrLlNfsR726IdGw93CcTxSxrfmZtGSulZKCmUv4MQ,9055
-lamindb/_file.py,sha256=0TIsPvOcWXjtgCwTOoeot1o0Gs8ebkcDFQenMSgxXuM,35818
+lamindb/_feature_set.py,sha256=G63pwauDQ7jg4ydFCQLhu-lgO6tm56iQwUdRuNHeKHY,9233
+lamindb/_file.py,sha256=V85tryLD0HsZiPQV4KNmcs3Gdi0qf8dZu27rl2G9D7E,36218
 lamindb/_filter.py,sha256=fNvPbLeOxYzvNKPcFYiFz3P7bkD5_84Xh8HHAoLNdas,1716
 lamindb/_from_values.py,sha256=GitpmKOqV6YHJggaCnJgGsRIHI_bnuLRVE2oo9W-SgE,11613
-lamindb/_parents.py,sha256=-SRNd4O7TUmCIHYysjS00uK1QKODF4UJSXK_T_1KOEI,13212
+lamindb/_parents.py,sha256=VT_gtomf1Erd_AKLVd1uLwigeDqMHtcaAbma3_AbQAw,13408
 lamindb/_query_manager.py,sha256=MXueabWHqft7GWNkzmWbhfTqdk-0mKU7nWrhXG6wpYQ,3693
 lamindb/_query_set.py,sha256=Lf7vLvOsEfUWRQ3iImSj4eQPmUK1KCgeoKS_m66Lp7o,10279
 lamindb/_registry.py,sha256=_pdlEvAtemiQCzpK2s14MsTKkLqE6ORDjhDs7ABs4i4,14893
@@ -19,7 +19,7 @@ lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_validate.py,sha256=3powFmYcNop2R6ijt2v3I_vPn4TD9ET4DJkW8uzQt_U,13719
 lamindb/_view.py,sha256=bzx6e-Cif2CmDQkOu6jMrq_d5rsu6g7hhdaK_sYBv_Y,2150
 lamindb/dev/__init__.py,sha256=Ja96dxb0t7raGsCr8QxqCabyEzIxeVGlL_IgmhxdsB8,1010
-lamindb/dev/_data.py,sha256=-0Bz2wg98-BTzpV_5lUZCrRk9yeU1xqCUrjELomJb60,13818
+lamindb/dev/_data.py,sha256=6TLM2tVWV7xMYzWNA14EsdyhSoRjK7IK6EU4VuQoC-g,15071
 lamindb/dev/_feature_manager.py,sha256=IojA1TPH3ZPlPghV_d1MIPIxdIcYO15RenI_o7YjmAM,8049
 lamindb/dev/_label_manager.py,sha256=5R2rZzdLgiZHEzXyilSjK3J7kHDHUOhneZJuSh--qQY,7339
 lamindb/dev/_priors.py,sha256=eSZEEijmeFs3zcrU27r3T2sSGdsK-cvy7vl6ukDYaU8,785
@@ -31,18 +31,18 @@ lamindb/dev/hashing.py,sha256=IlNrHy-a9NqB0vfqiwIh4sjt40CvaiZIvfK6gMnkxDo,1381
 lamindb/dev/types.py,sha256=svg5S_aynuGfbEOsbmqkR_gF9d9YMzfOkcvGN37Rzvg,232
 lamindb/dev/versioning.py,sha256=XF7X-Ngat_Ggca7FdtZa5ElOKlOgoxDtxwZlhsCTJZU,2788
 lamindb/dev/datasets/__init__.py,sha256=clbWOmg4K8Rh94OPFtJasNKdtUHHvR_Lx11jZWMqfok,1350
-lamindb/dev/datasets/_core.py,sha256=T1XE9tr3uVLnyA2W9_xuF60EQH3WVaS9GBl69cB-KDQ,18844
+lamindb/dev/datasets/_core.py,sha256=-g7wWWYHrejlkSQS04Xafi_w5OjDv9ItHMUFNdHsXlM,18987
 lamindb/dev/datasets/_fake.py,sha256=S8mNho-oSh1M9x9oOSsUBLLHmBAegsOLlFk6LnF81EA,942
 lamindb/dev/storage/__init__.py,sha256=mFvsMkAHHmO_xTM1UI-WGynDObnH0RCI2TXtFGhYfv8,392
 lamindb/dev/storage/_anndata_sizes.py,sha256=0XVzA6AQeVGPaGPrhGusKyxFgFjeo3qSN29hxb8D5E8,993
-lamindb/dev/storage/_backed_access.py,sha256=wSWIUzb3zsb2seZXMbGPTwG-mzFKepUlbhx4b58ZIHo,21850
+lamindb/dev/storage/_backed_access.py,sha256=IWKLxvSWvzXGgysx1FLhfQ3mEoTxhtQXCvqBxpIpucw,22150
 lamindb/dev/storage/_zarr.py,sha256=7W1Jos1QOOF3f41uML_arQoDTNPZVpRyP2m3SLWaCAo,2766
 lamindb/dev/storage/file.py,sha256=xfeU8X1ty80-PhnHOpupBJfibZKhp6MPLA2IjYdTBoY,7982
 lamindb/dev/storage/object.py,sha256=KGuOwwYuN2yCJxTXn9v0LanC0fjKwy_62P-WksHcf40,1140
 lamindb/setup/__init__.py,sha256=8-0F2C4Glx23-b8-D_1CBGgRBM5PppVhazhoXZYOLsg,275
 lamindb/setup/dev/__init__.py,sha256=tBty426VGF2PGqqt2XuNU-WgvOrbOp1aZBDowjLuzgA,242
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