lamindb 0.74.1__py3-none-any.whl → 0.74.3__py3-none-any.whl

lamindb/core/_run_context.py

@@ -43,7 +43,7 @@ def get_uid_ext(version: str) -> str:
     # merely zero-padding the nbproject version such that the base62 encoding is
     # at least 4 characters long doesn't yields sufficiently diverse hashes and
     # leads to collisions; it'd be nice because the uid_ext would be ordered
-    return encodebytes(hashlib.md5(version.encode()).digest())[:4]
+    return encodebytes(hashlib.md5(version.encode()).digest())[:4]  # noqa: S324
 
 
 def update_stem_uid_or_version(
@@ -113,7 +113,7 @@ def get_notebook_name_colab() -> str:
 
     ip = gethostbyname(gethostname())  # 172.28.0.12
     try:
-        name = get(f"http://{ip}:9000/api/sessions").json()[0]["name"]
+        name = get(f"http://{ip}:9000/api/sessions").json()[0]["name"]  # noqa: S113
     except Exception:
         logger.warning(
             "could not get notebook name from Google Colab, using: notebook.ipynb"

lamindb/core/_settings.py

@@ -108,7 +108,8 @@ class Settings:
         For example: `ln.sync_git_repo = https://github.com/laminlabs/redun-lamin`
         """
         self._sync_git_repo = sanitize_git_repo_url(value)
-        assert self._sync_git_repo.startswith("https://")
+        if not self._sync_git_repo.startswith("https://"):  # pragma: nocover
+            raise ValueError("git repository URL must start with 'https://'.")
 
     @property
     def storage(self) -> StorageSettings:

lamindb/core/_sync_git.py

@@ -24,8 +24,7 @@ def get_git_repo_from_remote() -> Path:
         f"running outside of synched git repo, cloning {repo_url} into {repo_dir}"
     )
     result = subprocess.run(
-        f"git clone --depth 10 {repo_url}.git",
-        shell=True,
+        ["git", "clone", "--depth", "10", f"{repo_url}.git"],
         capture_output=True,
         cwd=setup_settings.storage.cache_dir,
     )
@@ -36,8 +35,7 @@ def get_git_repo_from_remote() -> Path:
 
 def check_local_git_repo() -> bool:
     result = subprocess.run(
-        "git config --get remote.origin.url",
-        shell=True,
+        ["git", "config", "--get remote.origin.url"],
         capture_output=True,
     )
     result_str = result.stdout.decode().strip()
@@ -55,10 +53,9 @@ def check_local_git_repo() -> bool:
 
 
 def get_git_commit_hash(blob_hash: str, repo_dir: Path | None = None) -> str | None:
-    command = f"git log --find-object={blob_hash} --pretty=format:%H"
+    command = ["git", "log", f"--find-object={blob_hash}", "--pretty=format:%H"]
     result = subprocess.run(
         command,
-        shell=True,
         capture_output=True,
         cwd=repo_dir,
     )
@@ -68,7 +65,7 @@ def get_git_commit_hash(blob_hash: str, repo_dir: Path | None = None) -> str | N
     if commit_hash == "" or result.returncode == 1:
         return None
     else:
-        assert (
+        assert (  # noqa: S101
             len(commit_hash) == 40
         ), f"commit hash |{commit_hash}| is not 40 characters long"
         return commit_hash
@@ -82,21 +79,34 @@ def get_filepath_within_git_repo(
     # from anywhere in the repo, hence, let's get the root
     repo_root = (
         subprocess.run(
-            "git rev-parse --show-toplevel",
-            shell=True,
+            ["git", "rev-parse", "--show-toplevel"],
             capture_output=True,
             cwd=repo_dir,
         )
         .stdout.decode()
         .strip()
     )
-    command = f"git ls-tree -r {commit_hash} | grep -E {blob_hash}"
+    # Run the git commands separately to circumvent spawning a shell
+    git_command = ["git", "ls-tree", "-r", commit_hash]
+    git_process = subprocess.Popen(
+        git_command,
+        stdout=subprocess.PIPE,
+        cwd=repo_root,
+    )
+
+    grep_command = ["grep", "-E", blob_hash]
     result = subprocess.run(
-        command,
-        shell=True,
+        grep_command,
+        stdin=git_process.stdout,
         capture_output=True,
         cwd=repo_root,
     )
+
+    # Close the stdout to allow git_process to receive a SIGPIPE if grep_command exits
+    git_process.stdout.close()
+    git_process.wait()
+
+    command = " ".join(git_command) + " | " + " ".join(grep_command)
     if result.returncode != 0 and result.stderr.decode() != "":
         raise RuntimeError(f"{command}\n{result.stderr.decode()}")
     if len(result.stdout.decode()) == 0:

lamindb/core/_track_environment.py

@@ -15,7 +15,11 @@ def track_environment(run: Run) -> None:
     # create a requirements.txt
     # we don't create a conda environment.yml mostly for its slowness
     try:
-        result = subprocess.run(f"pip freeze > {str(filepath)}", shell=True)
+        with open(filepath, "w") as f:
+            result = subprocess.run(
+                ["pip", "freeze"],
+                stdout=f,
+            )
     except OSError as e:
         result = None
         logger.warning(f"could not run pip freeze with error {e}")

lamindb/core/datasets/_core.py

@@ -185,8 +185,6 @@ def anndata_mouse_sc_lymph_node(
 
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
-        auto_save_parents = bt.settings.auto_save_parents
-        bt.settings.auto_save_parents = False
         # strain
         bt.ExperimentalFactor.from_public(ontology_id="EFO:0004472").save()
         # developmental stage
@@ -215,7 +213,6 @@ def anndata_mouse_sc_lymph_node(
             labels += [ln.ULabel(name=name) for name in adata.obs[col]]
         ln.save(labels)
         ln.settings.verbosity = verbosity
-        bt.settings.auto_save_parents = auto_save_parents
 
     return adata
 
@@ -313,8 +310,6 @@ def anndata_human_immune_cells(
 
         verbosity = ln.settings.verbosity
         ln.settings.verbosity = "error"
-        auto_save_parents = bt.settings.auto_save_parents
-        bt.settings.auto_save_parents = False
         ln.save(
             bt.Gene.from_values(
                 adata.var.index, field="ensembl_gene_id", organism="human"
@@ -331,7 +326,6 @@ def anndata_human_immune_cells(
         bt.ExperimentalFactor.from_public(ontology_id="EFO:0008913").save()
         ln.save([ln.ULabel(name=name) for name in adata.obs.donor.unique()])
         ln.settings.verbosity = verbosity
-        bt.settings.auto_save_parents = auto_save_parents
     return adata
 
 

lamindb/core/fields.py

@@ -1,6 +1,6 @@
 """Fields.
 
-The field accessor of a :class:`~lamindb.core.Registry`:
+The field accessor of a :class:`~lamindb.core.Record`:
 
 .. autosummary::
    :toctree: .

lamindb/core/schema.py

@@ -1,10 +1,10 @@
 from __future__ import annotations
 
 from django.db.models import ManyToManyField
-from lnschema_core.models import Feature, FeatureSet, LinkORM, Registry
+from lnschema_core.models import Feature, FeatureSet, LinkORM, Record
 
 
-def dict_schema_name_to_model_name(orm: type[Registry]) -> dict[str, Registry]:
+def dict_schema_name_to_model_name(orm: type[Record]) -> dict[str, Record]:
     d: dict = {
         i.related_model.__get_name_with_schema__(): i.related_model
         for i in orm._meta.related_objects
@@ -21,9 +21,9 @@ def dict_schema_name_to_model_name(orm: type[Registry]) -> dict[str, Registry]:
 
 
 def dict_related_model_to_related_name(
-    orm: type[Registry], links: bool = False
+    orm: type[Record], links: bool = False
 ) -> dict[str, str]:
-    def include(model: Registry):
+    def include(model: Record):
         return not links != issubclass(model, LinkORM)
 
     related_objects = orm._meta.related_objects + orm._meta.many_to_many
@@ -39,7 +39,7 @@ def dict_related_model_to_related_name(
     return d
 
 
-def get_related_name(features_type: type[Registry]) -> str:
+def get_related_name(features_type: type[Record]) -> str:
     candidates = [
         field.related_name
         for field in FeatureSet._meta.related_objects
@@ -49,7 +49,7 @@ def get_related_name(features_type: type[Registry]) -> str:
         raise ValueError(
             f"Can't create feature sets from {features_type.__name__} because it's not"
             " related to it!\nYou need to create a link model between FeatureSet and"
-            " your Registry in your custom schema.\nTo do so, add a"
+            " your Record in your custom schema.\nTo do so, add a"
             " line:\nfeature_sets = models.ManyToMany(FeatureSet,"
             " related_name='mythings')\n"
         )

lamindb/core/storage/_backed_access.py

@@ -28,6 +28,8 @@ if TYPE_CHECKING:
     from pathlib import Path
 
     from fsspec.core import OpenFile
+    from tiledbsoma import Collection as SOMACollection
+    from tiledbsoma import Experiment as SOMAExperiment
 
 anndata_version_parse = version.parse(anndata_version)
 
@@ -100,7 +102,7 @@ def _records_to_df(obj):
         return obj
 
 
-class AccessRegistry:
+class AccessRecord:
     def __init__(self):
         self._registry = {}
         self._openers = {}
@@ -141,7 +143,7 @@ class AccessRegistry:
 
 
 # storage specific functions should be registered and called through the registry
-registry = AccessRegistry()
+registry = AccessRecord()
 
 
 @registry.register_open("h5py")
@@ -207,8 +209,10 @@ def safer_read_partial(elem, indices):
             try:
                 ds = CSRDataset(elem)
                 result = _subset_sparse(ds, indices)
-            except Exception:
-                pass
+            except Exception as e:
+                logger.debug(
+                    f"Encountered an exception while attempting to subset a sparse dataset by indices.\n{e}"
+                )
         if result is None:
             raise ValueError(
                 "Can not get a subset of the element of type"
@@ -305,8 +309,10 @@ if ZARR_INSTALLED:
                 try:
                     ds = CSRDataset(elem)
                     return _subset_sparse(ds, indices)
-                except Exception:
-                    pass
+                except Exception as e:
+                    logger.debug(
+                        f"Encountered an exception while attempting to subset a sparse dataset by indices.\n{e}"
+                    )
             raise ValueError(
                 "Can not get a subset of the element of type"
                 f" {type(elem).__name__} with an empty spec."
@@ -734,24 +740,62 @@ class BackedAccessor:
 
 def backed_access(
     artifact_or_filepath: Artifact | Path, using_key: str | None = None
-) -> AnnDataAccessor | BackedAccessor:
+) -> AnnDataAccessor | BackedAccessor | SOMACollection | SOMAExperiment:
     if isinstance(artifact_or_filepath, Artifact):
         filepath = filepath_from_artifact(artifact_or_filepath, using_key=using_key)
     else:
         filepath = artifact_or_filepath
     name = filepath.name
+    suffix = filepath.suffix
+
+    if name == "soma" or suffix == ".tiledbsoma":
+        try:
+            import tiledbsoma as soma
+        except ImportError as e:
+            raise ImportError(
+                "Please install tiledbsoma: pip install tiledbsoma"
+            ) from e
+        filepath_str = filepath.as_posix()
+        if filepath.protocol == "s3":
+            from lamindb_setup.core._settings_storage import get_storage_region
+
+            region = get_storage_region(filepath_str)
+            tiledb_config = {"vfs.s3.region": region}
+            storage_options = filepath.storage_options
+            if "key" in storage_options:
+                tiledb_config["vfs.s3.aws_access_key_id"] = storage_options["key"]
+            if "secret" in storage_options:
+                tiledb_config["vfs.s3.aws_secret_access_key"] = storage_options[
+                    "secret"
+                ]
+            if "token" in storage_options:
+                tiledb_config["vfs.s3.aws_session_token"] = storage_options["token"]
+            ctx = soma.SOMATileDBContext(tiledb_config=tiledb_config)
+            # this is a strange bug
+            # for some reason iterdir futher gives incorrect results
+            # if cache is not invalidated
+            # instead of obs and ms it gives ms and ms in the list of names
+            filepath.fs.invalidate_cache()
+        else:
+            ctx = None
 
-    if filepath.suffix in (".h5", ".hdf5", ".h5ad"):
+        soma_objects = [obj.name for obj in filepath.iterdir()]
+        if "obs" in soma_objects and "ms" in soma_objects:
+            SOMAType = soma.Experiment
+        else:
+            SOMAType = soma.Collection
+        return SOMAType.open(filepath_str, context=ctx)
+    elif suffix in {".h5", ".hdf5", ".h5ad"}:
         conn, storage = registry.open("h5py", filepath)
-    elif filepath.suffix == ".zarr":
+    elif suffix == ".zarr":
         conn, storage = registry.open("zarr", filepath)
     else:
         raise ValueError(
-            "object should have .h5, .hdf5, .h5ad, .zarr suffix, not"
-            f" {filepath.suffix}."
+            "object should have .h5, .hdf5, .h5ad, .zarr, .tiledbsoma suffix, not"
+            f" {suffix}."
         )
 
-    if filepath.suffix == ".h5ad":
+    if suffix == ".h5ad":
         return AnnDataAccessor(conn, storage, name)
     else:
         if get_spec(storage).encoding_type == "anndata":

lamindb/core/storage/paths.py

@@ -47,7 +47,7 @@ def auto_storage_key_from_artifact(artifact: Artifact):
 
 
 def auto_storage_key_from_artifact_uid(uid: str, suffix: str, is_dir: bool) -> str:
-    assert isinstance(suffix, str)
+    assert isinstance(suffix, str)  # noqa: S101 Suffix cannot be None.
     if is_dir:
         uid_storage = uid[:16]  # 16 chars, leave 4 chars for versioning
     else:

lamindb/core/versioning.py

@@ -97,7 +97,7 @@ def get_uid_from_old_version(
     version: str | None = None,
     using_key: str | None = None,
 ) -> tuple[str, str]:
-    """{}."""
+    """{}"""  # noqa: D415
     msg = ""
     if is_new_version_of.version is None:
         previous_version = "1"

lamindb/integrations/_vitessce.py

@@ -39,9 +39,10 @@ def save_vitessce_config(vitessce_config: VitessceConfig, description: str) -> A
             if "url" not in file:
                 raise ValueError("Each file must have a 'url' key.")
             filename = file["url"].split("/")[-1]
-            assert filename.endswith(
-                (".anndata.zarr", ".spatialdata.zarr", ".ome.zarr")
-            )
+            if not filename.endswith((".anndata.zarr", ".zarr", ".ome.zarr")):
+                logger.warning(
+                    "filename should end with '.anndata.zarr', '.zarr', or '.ome.zarr'."
+                )
             filestem = (
                 filename.replace(".anndata.zarr", "")
                 .replace(".spatialdata.zarr", "")

{lamindb-0.74.1.dist-info → lamindb-0.74.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.74.1
+Version: 0.74.3
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,10 +9,10 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.70.0
-Requires-Dist: lamindb_setup==0.73.2
+Requires-Dist: lnschema_core==0.70.5
+Requires-Dist: lamindb_setup==0.74.2
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.14.0
+Requires-Dist: lamin_cli==0.15.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -23,10 +23,8 @@ Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: psutil
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.44.0 ; extra == "bionty"
-Requires-Dist: pandas<2 ; extra == "dev"
+Requires-Dist: bionty==0.44.3 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -39,7 +37,7 @@ Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
-Requires-Dist: nbproject==0.10.3 ; extra == "jupyter"
+Requires-Dist: nbproject==0.10.4 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"

lamindb-0.74.3.dist-info/RECORD

@@ -0,0 +1,57 @@
+lamindb/__init__.py,sha256=VfwmNQfCefzn3jsRS2l3fnV7jub1RpMj4aVCFh09vxI,2249
+lamindb/_artifact.py,sha256=pdSMBuZnlr-Jfot8p90x7TEbto-viXyryax5p1FljEs,40133
+lamindb/_can_validate.py,sha256=CUu-lBY9XnSYGWiazYhLMW5H0LuuR86mVbU7UnIZTVU,15010
+lamindb/_collection.py,sha256=P4UjZxC2OcViTmqSeW3NIiXU3C0ZF5BF9P6YcchS2Zg,14617
+lamindb/_curate.py,sha256=i3pqkNvgXtOXXmw7zPgnr7BT3KnZDBw8DyxuyPkhwbo,44898
+lamindb/_feature.py,sha256=hLj5KDhIVkZrIa7IbiHGyUBGZS7PeDNxKsNK1EadBAc,7377
+lamindb/_feature_set.py,sha256=nsiT9mKfEJdh2yqihOawfFL0mkHRNi5-9vxRllv5NAM,8137
+lamindb/_filter.py,sha256=Ed9k-LOkr1BwqeHpvaEe0w27cG7Bu0BaXPDA0OIzUpQ,1410
+lamindb/_finish.py,sha256=FRGN2cmBbZqmxr803YIpGGUaqst8xBTi3kmliV5oJo4,10504
+lamindb/_from_values.py,sha256=SGTQNb0M1h3icuYsfIIjqI7xNy3i3Frw_-PAl5MXMBo,13860
+lamindb/_is_versioned.py,sha256=8pXW2gkLTZsTxRERuWZLidiagNIC8evmCmnbztWkVQ4,1343
+lamindb/_parents.py,sha256=Zgi9Lmw9td18Y0QJ96rYaBrjSaZ8XGcseWdbJkpJhFU,15061
+lamindb/_query_manager.py,sha256=6_ZqQr0SKTYsbMtJd5BmaMoyASIVel5v2F1KMgacWlU,4252
+lamindb/_query_set.py,sha256=LM5NsAWy5FCZZSxX1VbE20RdA5nsyk4_5p4abuMjdcI,11662
+lamindb/_record.py,sha256=5B0mMvEoZ0gZ6MALy6bsbDOVU47pkVEhRCBVwVJnNwg,19150
+lamindb/_run.py,sha256=xj3ER4F_yWvuNw1mr0XU-QuIPi5hBO7Ue0ygBgJQ6mc,1887
+lamindb/_save.py,sha256=xs1ZdTYGd78zA3XqXhiwZ_QKAogLdHCQv1EBVFDWCis,11020
+lamindb/_storage.py,sha256=GBVChv-DHVMNEBJL5l_JT6B4RDhZ6NnwgzmUICphYKk,413
+lamindb/_transform.py,sha256=E9C7psuOnsNrUQpWRuGgEUM8_pc7YhDn7n4ieHzB4X0,3169
+lamindb/_ulabel.py,sha256=XDSdZBXX_ki5s1vOths3MjF2x5DPggBR_PV_KF4SGyg,1611
+lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
+lamindb/_view.py,sha256=_sAcSD06bC92R_LLDcHMhO0IfOqybBXXRYxOXvm1Juc,2322
+lamindb/core/__init__.py,sha256=HtyYVFrS6RclSk7gZty9vgXU0k2_oZiqFPfqghBc4Fc,1415
+lamindb/core/_data.py,sha256=yk2ozTt-mNIA8bWllmcC__WgFukj03fZU41rr_ultlM,16264
+lamindb/core/_feature_manager.py,sha256=EvMoY9EAFGdbRkDR44YMJBMWBEt9IbtfZ0RHmiv0D58,31910
+lamindb/core/_label_manager.py,sha256=udG70H1FucAr4lmtFMgAcMJiAcYvoZIyT034NO93YF8,9265
+lamindb/core/_mapped_collection.py,sha256=SGUsR6RbjNzUOq6A6wTa4M4GkLMuP4Z70WOeF39WPCU,19618
+lamindb/core/_run_context.py,sha256=w_LdfwYTncCZmh4agNPey37UdKrzSglLfLUNBe5z1mw,18421
+lamindb/core/_settings.py,sha256=sDfIfq9H7H8nUE51FJF4EO_Zihlxh44S3GbaliHKJY4,6108
+lamindb/core/_sync_git.py,sha256=qc0yfPyKeG4uuNT_3qsv-mkIMqhLFqfXNeNVO49vV00,4547
+lamindb/core/_track_environment.py,sha256=STzEVUzOeUEWdX7WDJUkKH4u08k7eupRX6AXQwoVt14,828
+lamindb/core/exceptions.py,sha256=bbm-PeSy24qFcqh2HpucZWpwGAvk-TL_3FUoAPb3e3E,867
+lamindb/core/fields.py,sha256=47Jmh3efUr5ZscgimR_yckY-I3cNf8ScLutbwKCK3j4,162
+lamindb/core/schema.py,sha256=sNrzWnqeyh9Ppr7yImlSAXiHb_VJdB5DWuO-QERxQGY,1847
+lamindb/core/types.py,sha256=xeQF2x40p2pR9eIVQrXT74RrS810z2fbjmTRTSQUqPM,230
+lamindb/core/versioning.py,sha256=lz1JP3K-0npeSTZPY7kMVXqOOcB8IEGmdG0Si3kSdN8,4956
+lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
+lamindb/core/datasets/_core.py,sha256=NhMELgF4aR9HAlU37BF3FkPLobxinRbMJ8s6XwgIqEM,19549
+lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
+lamindb/core/storage/__init__.py,sha256=5LUFQKRr2BX24d-yWBezhTXBV83sShcOvPj5Y5u6qIg,441
+lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
+lamindb/core/storage/_backed_access.py,sha256=4VmnqGd5DH6xJ5UQ7JMiQ2dfs-uLBnVlJXkZB8GcJHI,26624
+lamindb/core/storage/_valid_suffixes.py,sha256=J08aglC9oo35pzahj0SQXW9IHib8Asp4dc11co-2uys,212
+lamindb/core/storage/_zarr.py,sha256=5ceEz6YIvgvUnVVNWhK5Z4W0WfrvyvY82Yna5jSX1_E,3661
+lamindb/core/storage/objects.py,sha256=OzvBCS-Urz5mr-O95qYt6RGBDDX5HmjfRRKWPPDn1ZE,1797
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