lamindb 0.76.3__py3-none-any.whl → 0.76.4__py3-none-any.whl

lamindb/__init__.py

@@ -1,7 +1,6 @@
 """A data framework for biology.
 
-Records
-=======
+Core registries.
 
 .. autosummary::
    :toctree: .
@@ -17,8 +16,7 @@ Records
    FeatureSet
    Param
 
-Key functionality
-=================
+Key functionality.
 
 .. autosummary::
    :toctree: .
@@ -29,8 +27,7 @@ Key functionality
    view
    save
 
-Modules & settings
-==================
+Modules and settings.
 
 .. autosummary::
    :toctree: .
@@ -44,7 +41,7 @@ Modules & settings
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.76.3"
+__version__ = "0.76.4"
 
 import os as _os
 

lamindb/_artifact.py

@@ -366,11 +366,6 @@ def get_artifact_kwargs_from_data(
     else:
         storage = default_storage
 
-    # for now comment out this error to allow creating new versions of stores
-    # in the default folder (.lamindb)
-    #    if key is not None and key.startswith(AUTO_KEY_PREFIX):
-    #        raise ValueError(f"Key cannot start with {AUTO_KEY_PREFIX}")
-
     log_storage_hint(
         check_path_in_storage=check_path_in_storage,
         storage=storage,
@@ -542,10 +537,10 @@ def __init__(artifact: Artifact, *args, **kwargs):
         else VisibilityChoice.default.value
     )
     format = kwargs.pop("format") if "format" in kwargs else None
+    _is_internal_call = kwargs.pop("_is_internal_call", False)
     skip_check_exists = (
         kwargs.pop("skip_check_exists") if "skip_check_exists" in kwargs else False
     )
-    _uid = kwargs.pop("_uid", None)
     if "default_storage" in kwargs:
         default_storage = kwargs.pop("default_storage")
     else:
@@ -561,9 +556,6 @@ def __init__(artifact: Artifact, *args, **kwargs):
     if "is_new_version_of" in kwargs:
         logger.warning("`is_new_version_of` will be removed soon, please use `revises`")
         revises = kwargs.pop("is_new_version_of")
-    assert not (  # noqa: S101
-        revises is not None and _uid is not None
-    ), "Can not init with both `revises` and `_uid`"
     if not len(kwargs) == 0:
         raise ValueError(
             "Only data, key, run, description, version, revises, visibility"
@@ -579,15 +571,29 @@ def __init__(artifact: Artifact, *args, **kwargs):
         raise ValueError(
             f"`key` is {key}, but `revises.key` is '{revises.key}'\n\n Either do *not* pass `key`.\n\n{note}"
         )
-    if _uid is not None:
-        provisional_uid, revises = _uid, None
-    else:
-        provisional_uid, revises = create_uid(revises=revises, version=version)
     if revises is not None:
         if not isinstance(revises, Artifact):
             raise TypeError("`revises` has to be of type `Artifact`")
         if description is None:
             description = revises.description
+    if key is not None and AUTO_KEY_PREFIX in key:
+        raise ValueError(
+            f"Do not pass key that contains a managed storage path in `{AUTO_KEY_PREFIX}`"
+        )
+    # below is for internal calls that require defining the storage location
+    # ahead of constructing the Artifact
+    if isinstance(data, (str, Path)) and AUTO_KEY_PREFIX in str(data):
+        if _is_internal_call:
+            is_automanaged_path = True
+            user_provided_key = key
+            key = None
+        else:
+            raise ValueError(
+                f"Do not pass path inside the `{AUTO_KEY_PREFIX}` directory."
+            )
+    else:
+        is_automanaged_path = False
+    provisional_uid, revises = create_uid(revises=revises, version=version)
     kwargs_or_artifact, privates = get_artifact_kwargs_from_data(
         data=data,
         key=key,
@@ -615,16 +621,29 @@ def __init__(artifact: Artifact, *args, **kwargs):
     else:
         kwargs = kwargs_or_artifact
 
+    if data is not None:
+        artifact._local_filepath = privates["local_filepath"]
+        artifact._cloud_filepath = privates["cloud_filepath"]
+        artifact._memory_rep = privates["memory_rep"]
+        artifact._to_store = not privates["check_path_in_storage"]
+
+    if is_automanaged_path and _is_internal_call:
+        kwargs["_key_is_virtual"] = True
+        assert AUTO_KEY_PREFIX in kwargs["key"]  # noqa: S101
+        uid = kwargs["key"].replace(AUTO_KEY_PREFIX, "").replace(kwargs["suffix"], "")
+        kwargs["key"] = user_provided_key
+        if revises is not None:
+            assert uid.startswith(revises.stem_uid)  # noqa: S101
+        if len(uid) == 16:
+            if revises is None:
+                uid += "0000"
+            else:
+                uid, revises = create_uid(revises=revises, version=version)
+        kwargs["uid"] = uid
+
     # only set key now so that we don't do a look-up on it in case revises is passed
     if revises is not None:
         kwargs["key"] = revises.key
-    # in case we have a new version of a folder with a different hash, print a
-    # warning that the old version can't be recovered
-    if revises is not None and revises.n_objects is not None and revises.n_objects > 1:
-        logger.warning(
-            f"artifact version {version} will _update_ the state of folder {revises.path} - "
-            "to _retain_ the old state by duplicating the entire folder, do _not_ pass `revises`"
-        )
 
     kwargs["type"] = type
     kwargs["version"] = version
@@ -643,12 +662,6 @@ def __init__(artifact: Artifact, *args, **kwargs):
 
     add_transform_to_kwargs(kwargs, kwargs["run"])
 
-    if data is not None:
-        artifact._local_filepath = privates["local_filepath"]
-        artifact._cloud_filepath = privates["cloud_filepath"]
-        artifact._memory_rep = privates["memory_rep"]
-        artifact._to_store = not privates["check_path_in_storage"]
-
     super(Artifact, artifact).__init__(**kwargs)
 
 
@@ -943,10 +956,9 @@ def open(
                 if self.hash != hash:
                     from ._record import init_self_from_db
 
-                    logger.warning(
-                        "The hash of the tiledbsoma store has changed, creating a new version of the artifact."
-                    )
-                    new_version = Artifact(filepath, revises=self).save()
+                    new_version = Artifact(
+                        filepath, revises=self, _is_internal_call=True
+                    ).save()
                     init_self_from_db(self, new_version)
 
                     if localpath != filepath and localpath.exists():
@@ -1174,3 +1186,4 @@ Artifact._delete_skip_storage = _delete_skip_storage
 Artifact._save_skip_storage = _save_skip_storage
 Artifact.path = path
 Artifact.backed = backed
+Artifact.view_lineage = HasFeatures.view_lineage

lamindb/_can_validate.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Iterable, Literal
+from typing import TYPE_CHECKING, Literal
 
 import lamindb_setup as ln_setup
 import numpy as np
@@ -79,6 +79,19 @@ def _check_organism_db(organism: Record, using_key: str | None):
                 )
 
 
+def _concat_lists(values: ListLike) -> list[str]:
+    """Concatenate a list of lists of strings into a single list."""
+    if len(values) > 0 and isinstance(values, (list, pd.Series)):
+        try:
+            if isinstance(values[0], list):
+                if isinstance(values, pd.Series):
+                    values = values.tolist()
+                values = sum([v for v in values if isinstance(v, list)], [])
+        except KeyError:
+            pass
+    return values
+
+
 def _inspect(
     cls,
     values: ListLike,
@@ -94,6 +107,7 @@ def _inspect(
 
     if isinstance(values, str):
         values = [values]
+    values = _concat_lists(values)
 
     field = get_name_field(cls, field=field)
     queryset = _queryset(cls, using_key)
@@ -184,6 +198,7 @@ def _validate(
     return_str = True if isinstance(values, str) else False
     if isinstance(values, str):
         values = [values]
+    values = _concat_lists(values)
 
     field = get_name_field(cls, field=field)
 
@@ -229,7 +244,7 @@ def _validate(
 @doc_args(CanValidate.standardize.__doc__)
 def standardize(
     cls,
-    values: Iterable,
+    values: ListLike,
     field: str | StrField | None = None,
     *,
     return_field: str = None,
@@ -295,7 +310,7 @@ def remove_synonym(self, synonym: str | ListLike):
 
 def _standardize(
     cls,
-    values: Iterable,
+    values: ListLike,
     field: str | StrField | None = None,
     *,
     return_field: str = None,
@@ -315,6 +330,7 @@ def _standardize(
     return_str = True if isinstance(values, str) else False
     if isinstance(values, str):
         values = [values]
+    values = _concat_lists(values)
 
     field = get_name_field(cls, field=field)
     return_field = get_name_field(
@@ -416,7 +432,7 @@ def _standardize(
 
 
 def _add_or_remove_synonyms(
-    synonym: str | Iterable,
+    synonym: str | ListLike,
     record: Record,
     action: Literal["add", "remove"],
     force: bool = False,

lamindb/_curate.py

@@ -144,6 +144,7 @@ class DataFrameCurator(BaseCurator):
         organism: str | None = None,
         sources: dict[str, Record] | None = None,
         exclude: dict | None = None,
+        check_valid_keys: bool = True,
     ) -> None:
         from lamindb.core._settings import settings
 
@@ -163,6 +164,8 @@ class DataFrameCurator(BaseCurator):
             exclude = {}
         self._exclude = exclude
         self._non_validated = None
+        if check_valid_keys:
+            self._check_valid_keys()
         self._save_columns()
 
     @property
@@ -191,14 +194,25 @@ class DataFrameCurator(BaseCurator):
             using_key=using_key or self._using_key,
         )
 
+    def _check_valid_keys(self, extra: set = None) -> None:
+        if extra is None:
+            extra = set()
+        for name, d in {
+            "categoricals": self._fields,
+            "sources": self._sources,
+            "exclude": self._exclude,
+        }.items():
+            if not isinstance(d, dict):
+                raise TypeError(f"{name} must be a dictionary!")
+            valid_keys = set(self._df.columns) | {"columns"} | extra
+            nonval_keys = [key for key in d.keys() if key not in valid_keys]
+            if len(nonval_keys) > 0:
+                raise ValueError(
+                    f"the following keys passed to {name} are not allowed: {nonval_keys}"
+                )
+
     def _save_columns(self, validated_only: bool = True, **kwargs) -> None:
         """Save column name records."""
-        missing_columns = set(self.fields.keys()) - set(self._df.columns)
-        if missing_columns:
-            raise ValueError(
-                f"Columns {missing_columns} are not found in the data object!"
-            )
-
         # Always save features specified as the fields keys
         update_registry(
             values=list(self.fields.keys()),
@@ -426,8 +440,10 @@ class AnnDataCurator(DataFrameCurator):
             organism=organism,
             sources=sources,
             exclude=exclude,
+            check_valid_keys=False,
         )
         self._obs_fields = categoricals
+        self._check_valid_keys(extra={"var_index"})
 
     @property
     def var_index(self) -> FieldAttr:
@@ -633,6 +649,7 @@ class MuDataCurator:
                 verbosity=verbosity,
                 sources=self._sources.get(modality),
                 exclude=self._exclude.get(modality),
+                check_valid_keys=False,
                 **self._kwargs,
             )
             for modality in self._modalities

lamindb/_finish.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
 import os
+import re
 import shutil
-import subprocess
 from datetime import datetime, timezone
 from typing import TYPE_CHECKING
 
@@ -18,12 +18,81 @@ if TYPE_CHECKING:
     from ._query_set import QuerySet
 
 
+# this is from the get_title function in nbproject
+# should be moved into lamindb sooner or later
+def prepare_notebook(
+    nb,
+    strip_title: bool = False,
+) -> str | None:
+    """Strip title from the notebook if requested."""
+    title_found = False
+    for cell in nb.cells:
+        cell.metadata.clear()  # strip cell metadata
+        if not title_found and cell["cell_type"] == "markdown":
+            lines = cell["source"].split("\n")
+            for i, line in enumerate(lines):
+                if line.startswith("# "):
+                    line.lstrip("#").strip(" .").strip()
+                    title_found = True
+                    if strip_title:
+                        lines.pop(i)
+                        cell["source"] = "\n".join(lines)
+    return None
+
+
+def notebook_to_report(notebook_path: Path, output_path: Path) -> None:
+    import nbformat
+    import traitlets.config as config
+    from nbconvert import HTMLExporter
+
+    with open(notebook_path, encoding="utf-8") as f:
+        notebook = nbformat.read(f, as_version=4)
+    prepare_notebook(notebook, strip_title=True)
+    notebook.metadata.clear()  # strip notebook metadata
+    # if we were to export as ipynb, the following two lines would do it
+    # with open(output_path, "w", encoding="utf-8") as f:
+    #     nbformat.write(notebook, f)
+    # instead we need all this code
+    c = config.Config()
+    c.HTMLExporter.preprocessors = []
+    c.HTMLExporter.exclude_input_prompt = True
+    c.HTMLExporter.exclude_output_prompt = True
+    c.HTMLExporter.anchor_link_text = " "
+    html_exporter = HTMLExporter(config=c)
+    html, _ = html_exporter.from_notebook_node(notebook)
+    output_path.write_text(html, encoding="utf-8")
+
+
+def notebook_to_script(
+    transform: Transform, notebook_path: Path, script_path: Path
+) -> None:
+    import jupytext
+
+    notebook = jupytext.read(notebook_path)
+    py_content = jupytext.writes(notebook, fmt="py:percent")
+    # remove global metadata header
+    py_content = re.sub(r"^# ---\n.*?# ---\n\n", "", py_content, flags=re.DOTALL)
+    # replace title
+    py_content = py_content.replace(f"# # {transform.name}", "# # transform.name")
+    script_path.write_text(py_content)
+
+
+def script_to_notebook(transform: Transform, notebook_path: Path) -> None:
+    import jupytext
+
+    # get title back
+    py_content = transform.source_code.replace(
+        "# # transform.name", f"# # {transform.name}"
+    )
+    notebook = jupytext.reads(py_content, fmt="py:percent")
+    jupytext.write(notebook, notebook_path)
+
+
 def save_context_core(
     *,
     run: Run,
     transform: Transform,
     filepath: Path,
-    transform_family: QuerySet | None = None,
     finished_at: bool = False,
     from_cli: bool = False,
 ) -> str | None:
@@ -36,19 +105,17 @@ def save_context_core(
     # for scripts, things are easy
     is_consecutive = True
     is_notebook = transform.type == "notebook"
-    _source_code_artifact_path = filepath
+    source_code_path = filepath
     # for notebooks, we need more work
     if is_notebook:
         try:
-            import nbstripout
+            import jupytext
             from nbproject.dev import (
                 check_consecutiveness,
                 read_notebook,
             )
         except ImportError:
-            logger.error(
-                "install nbproject & nbstripout: pip install nbproject nbstripout"
-            )
+            logger.error("install nbproject & jupytext: pip install nbproject jupytext")
             return None
         notebook_content = read_notebook(filepath)  # type: ignore
         is_consecutive = check_consecutiveness(
@@ -62,66 +129,30 @@ def save_context_core(
                 response = "n"
             if response != "y":
                 return "aborted-non-consecutive"
-        # convert the notebook file to html
-        # log_level is set to 40 to silence the nbconvert logging
-        subprocess.run(
-            [
-                "jupyter",
-                "nbconvert",
-                "--to",
-                "html",
-                filepath.as_posix(),
-                "--Application.log_level=40",
-            ],
-            check=True,
+        # write the report
+        report_path = ln_setup.settings.storage.cache_dir / filepath.name.replace(
+            ".ipynb", ".html"
         )
-        # move the temporary file into the cache dir in case it's accidentally
-        # in an existing storage location -> we want to move associated
-        # artifacts into default storage and not register them in an existing
-        # location
-        report_path_orig = filepath.with_suffix(".html")  # current location
-        report_path = ln_setup.settings.storage.cache_dir / report_path_orig.name
-        # don't use Path.rename here because of cross-device link error
-        # https://laminlabs.slack.com/archives/C04A0RMA0SC/p1710259102686969
-        shutil.move(
-            report_path_orig,  # type: ignore
-            report_path,
+        notebook_to_report(filepath, report_path)
+        # write the source code
+        source_code_path = ln_setup.settings.storage.cache_dir / filepath.name.replace(
+            ".ipynb", ".py"
         )
-        # strip the output from the notebook to create the source code file
-        # first, copy the notebook file to a temporary file in the cache
-        _source_code_artifact_path = ln_setup.settings.storage.cache_dir / filepath.name
-        shutil.copy2(filepath, _source_code_artifact_path)  # copy
-        subprocess.run(
-            [
-                "nbstripout",
-                _source_code_artifact_path,
-                "--extra-keys",
-                "metadata.version metadata.kernelspec metadata.language_info metadata.pygments_lexer metadata.name metadata.file_extension",
-            ],
-            check=True,
-        )
-    # find initial versions of source codes and html reports
-    prev_report = None
-    prev_source = None
-    if transform_family is None:
-        transform_family = transform.versions
-    if len(transform_family) > 0:
-        for prev_transform in transform_family.order_by("-created_at"):
-            if (
-                prev_transform.latest_run is not None
-                and prev_transform.latest_run.report_id is not None
-            ):
-                prev_report = prev_transform.latest_run.report
-            if prev_transform._source_code_artifact_id is not None:
-                prev_source = prev_transform._source_code_artifact
+        notebook_to_script(transform, filepath, source_code_path)
     ln.settings.creation.artifact_silence_missing_run_warning = True
-
     # track source code
-    if transform._source_code_artifact_id is not None:
+    hash, _ = hash_file(source_code_path)  # ignore hash_type for now
+    if (
+        transform._source_code_artifact_id is not None
+        or transform.source_code is not None
+    ):
         # check if the hash of the transform source code matches
         # (for scripts, we already run the same logic in track() - we can deduplicate the call at some point)
-        hash, _ = hash_file(_source_code_artifact_path)  # ignore hash_type for now
-        if hash != transform._source_code_artifact.hash:
+        if transform.hash is not None:
+            condition = hash != transform.hash
+        else:
+            condition = hash != transform._source_code_artifact.hash
+        if condition:
             if os.getenv("LAMIN_TESTING") is None:
                 # in test, auto-confirm overwrite
                 response = input(
@@ -131,11 +162,8 @@ def save_context_core(
             else:
                 response = "y"
             if response == "y":
-                transform._source_code_artifact.replace(_source_code_artifact_path)
-                transform._source_code_artifact.save(upload=True)
-                logger.success(
-                    f"replaced transform._source_code_artifact: {transform._source_code_artifact}"
-                )
+                transform.source_code = source_code_path.read_text()
+                transform.hash = hash
             else:
                 logger.warning(
                     "Please re-run `ln.context.track()` to make a new version"
@@ -144,19 +172,8 @@ def save_context_core(
         else:
             logger.important("source code is already saved")
     else:
-        _source_code_artifact = ln.Artifact(
-            _source_code_artifact_path,
-            description=f"Source of transform {transform.uid}",
-            version=transform.version,
-            revises=prev_source,
-            visibility=0,  # hidden file
-            run=False,
-        )
-        _source_code_artifact.save(upload=True, print_progress=False)
-        transform._source_code_artifact = _source_code_artifact
-        logger.debug(
-            f"saved transform._source_code_artifact: {transform._source_code_artifact}"
-        )
+        transform.source_code = source_code_path.read_text()
+        transform.hash = hash
 
     # track environment
     env_path = ln_setup.settings.storage.cache_dir / f"run_env_pip_{run.uid}.txt"
@@ -211,7 +228,6 @@ def save_context_core(
             report_file = ln.Artifact(
                 report_path,
                 description=f"Report of run {run.uid}",
-                revises=prev_report,
                 visibility=0,  # hidden file
                 run=False,
             )

lamindb/_query_set.py

@@ -132,7 +132,7 @@ class RecordsList(UserList):
         return one_helper(self)
 
 
-class QuerySet(models.QuerySet, CanValidate):
+class QuerySet(models.QuerySet):
     """Sets of records returned by queries.
 
     See Also:
@@ -301,42 +301,50 @@ class QuerySet(models.QuerySet, CanValidate):
         else:
             raise ValueError("Record isn't subclass of `lamindb.core.IsVersioned`")
 
-    @doc_args(Record.search.__doc__)
-    def search(self, string: str, **kwargs):
-        """{}"""  # noqa: D415
-        from ._record import _search
 
-        return _search(cls=self, string=string, **kwargs)
+# -------------------------------------------------------------------------------------
+# CanValidate
+# -------------------------------------------------------------------------------------
 
-    @doc_args(Record.lookup.__doc__)
-    def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
-        """{}"""  # noqa: D415
-        from ._record import _lookup
 
-        return _lookup(cls=self, field=field, **kwargs)
+@doc_args(Record.search.__doc__)
+def search(self, string: str, **kwargs):
+    """{}"""  # noqa: D415
+    from ._record import _search
 
-    @doc_args(CanValidate.validate.__doc__)
-    def validate(self, values: ListLike, field: str | StrField | None = None, **kwargs):
-        """{}"""  # noqa: D415
-        from ._can_validate import _validate
+    return _search(cls=self, string=string, **kwargs)
 
-        return _validate(cls=self, values=values, field=field, **kwargs)
 
-    @doc_args(CanValidate.inspect.__doc__)
-    def inspect(self, values: ListLike, field: str | StrField | None = None, **kwargs):
-        """{}"""  # noqa: D415
-        from ._can_validate import _inspect
+@doc_args(Record.lookup.__doc__)
+def lookup(self, field: StrField | None = None, **kwargs) -> NamedTuple:
+    """{}"""  # noqa: D415
+    from ._record import _lookup
 
-        return _inspect(cls=self, values=values, field=field, **kwargs)
+    return _lookup(cls=self, field=field, **kwargs)
 
-    @doc_args(CanValidate.standardize.__doc__)
-    def standardize(
-        self, values: Iterable, field: str | StrField | None = None, **kwargs
-    ):
-        """{}"""  # noqa: D415
-        from ._can_validate import _standardize
 
-        return _standardize(cls=self, values=values, field=field, **kwargs)
+@doc_args(CanValidate.validate.__doc__)
+def validate(self, values: ListLike, field: str | StrField | None = None, **kwargs):
+    """{}"""  # noqa: D415
+    from ._can_validate import _validate
+
+    return _validate(cls=self, values=values, field=field, **kwargs)
+
+
+@doc_args(CanValidate.inspect.__doc__)
+def inspect(self, values: ListLike, field: str | StrField | None = None, **kwargs):
+    """{}"""  # noqa: D415
+    from ._can_validate import _inspect
+
+    return _inspect(cls=self, values=values, field=field, **kwargs)
+
+
+@doc_args(CanValidate.standardize.__doc__)
+def standardize(self, values: Iterable, field: str | StrField | None = None, **kwargs):
+    """{}"""  # noqa: D415
+    from ._can_validate import _standardize
+
+    return _standardize(cls=self, values=values, field=field, **kwargs)
 
 
 models.QuerySet.df = QuerySet.df
@@ -345,10 +353,10 @@ models.QuerySet.first = QuerySet.first
 models.QuerySet.one = QuerySet.one
 models.QuerySet.one_or_none = QuerySet.one_or_none
 models.QuerySet.latest_version = QuerySet.latest_version
-models.QuerySet.search = QuerySet.search
-models.QuerySet.lookup = QuerySet.lookup
-models.QuerySet.validate = QuerySet.validate
-models.QuerySet.inspect = QuerySet.inspect
-models.QuerySet.standardize = QuerySet.standardize
+models.QuerySet.search = search
+models.QuerySet.lookup = lookup
+models.QuerySet.validate = validate
+models.QuerySet.inspect = inspect
+models.QuerySet.standardize = standardize
 models.QuerySet._delete_base_class = models.QuerySet.delete
 models.QuerySet.delete = QuerySet.delete

lamindb/_record.py

@@ -57,7 +57,7 @@ def suggest_records_with_similar_names(record: Record, kwargs) -> bool:
     if kwargs.get("name") is None:
         return False
     queryset = _search(
-        record.__class__, kwargs["name"], field="name", truncate_words=True, limit=20
+        record.__class__, kwargs["name"], field="name", truncate_words=True, limit=3
     )
     if not queryset.exists():  # empty queryset
         return False
@@ -586,7 +586,8 @@ def delete(self) -> None:
     # but that's for another time
     if isinstance(self, IsVersioned) and self.is_latest:
         new_latest = (
-            self.__class__.filter(is_latest=False, uid__startswith=self.stem_uid)
+            self.__class__.objects.using(self._state.db)
+            .filter(is_latest=False, uid__startswith=self.stem_uid)
             .order_by("-created_at")
             .first()
         )

lamindb/_transform.py

@@ -37,8 +37,7 @@ def __init__(transform: Transform, *args, **kwargs):
             "Only name, key, version, type, revises, reference, "
             f"reference_type can be passed, but you passed: {kwargs}"
         )
-    # Transform allows passing a uid, all others don't
-    if uid is None and key is not None:
+    if revises is None and key is not None:
         revises = Transform.filter(key=key).order_by("-created_at").first()
     if revises is not None and key is not None and revises.key != key:
         note = message_update_key_in_version_family(

lamindb/core/__init__.py

@@ -10,8 +10,6 @@ Registries:
    QuerySet
    QueryManager
    RecordsList
-   HasFeatures
-   HasParams
    FeatureManager
    ParamManager
    LabelManager

lamindb/core/_context.py

@@ -414,6 +414,10 @@ class Context:
         if transform is None:
             if uid is None:
                 uid = f"{stem_uid}{get_uid_ext(version)}"
+            # note that here we're not passing revises because we're not querying it
+            # hence, we need to do a revision family lookup based on key
+            # hence, we need key to be not None
+            assert key is not None  # noqa: S101
             transform = Transform(
                 uid=uid,
                 version=version,
@@ -422,8 +426,7 @@ class Context:
                 reference=transform_ref,
                 reference_type=transform_ref_type,
                 type=transform_type,
-            )
-            transform.save()
+            ).save()
             self._logging_message += f"created Transform('{transform.uid}')"
         else:
             uid = transform.uid
@@ -449,29 +452,36 @@ class Context:
                     "updated transform name, "  # white space on purpose
                 )
             # check whether transform source code was already saved
-            if transform._source_code_artifact_id is not None:
-                response = None
+            if (
+                transform._source_code_artifact_id is not None
+                or transform.source_code is not None
+            ):
+                bump_revision = False
                 if is_run_from_ipython:
-                    response = "y"  # auto-bump version
+                    bump_revision = True
                 else:
                     hash, _ = hash_file(self._path)  # ignore hash_type for now
-                    if hash != transform._source_code_artifact.hash:
-                        response = "y"  # auto-bump version
+                    if transform.hash is not None:
+                        condition = hash != transform.hash
+                    else:
+                        condition = hash != transform._source_code_artifact.hash
+                    if condition:
+                        bump_revision = True
                     else:
                         self._logging_message += f"loaded Transform('{transform.uid}')"
-                if response is not None:
+                if bump_revision:
                     change_type = (
                         "Re-running saved notebook"
                         if is_run_from_ipython
                         else "Source code changed"
                     )
                     suid, vuid = (
-                        uid[: Transform._len_stem_uid],
-                        uid[Transform._len_stem_uid :],
+                        uid[:-4],
+                        uid[-4:],
                     )
                     new_vuid = increment_base62(vuid)
                     raise UpdateContext(
-                        f"{change_type}, bump version by setting:\n\n"
+                        f"{change_type}, bump revision by setting:\n\n"
                         f'ln.context.uid = "{suid}{new_vuid}"'
                     )
             else:

lamindb/core/_label_manager.py

@@ -118,13 +118,11 @@ def validate_labels(labels: QuerySet | list | dict):
 
 
 class LabelManager:
-    """Label manager (:attr:`~lamindb.core.HasFeatures.labels`).
+    """Label manager.
 
     This allows to manage untyped labels :class:`~lamindb.ULabel` and arbitrary
     typed labels (e.g., :class:`~bionty.CellLine`) and associate labels
     with features.
-
-    See :class:`~lamindb.core.HasFeatures` for more information.
     """
 
     def __init__(self, host: Artifact | Collection):

lamindb/core/storage/_anndata_accessor.py

@@ -10,7 +10,7 @@ import numpy as np
 import pandas as pd
 from anndata import AnnData
 from anndata import __version__ as anndata_version
-from anndata._core.index import Index, _normalize_indices
+from anndata._core.index import _normalize_indices
 from anndata._core.views import _resolve_idx
 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
@@ -29,6 +29,11 @@ if TYPE_CHECKING:
 
 anndata_version_parse = version.parse(anndata_version)
 
+if anndata_version_parse < version.parse("0.9.0"):
+    from anndata._core.index import Index
+else:
+    from anndata.compat import Index
+
 if anndata_version_parse < version.parse("0.10.0"):
     if anndata_version_parse < version.parse("0.9.1"):
         logger.warning(

lamindb/core/storage/_tiledbsoma.py

@@ -2,11 +2,11 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING, Literal
 
-from anndata import AnnData
+from anndata import AnnData, read_h5ad
 from lamin_utils import logger
 from lamindb_setup import settings as setup_settings
 from lamindb_setup.core._settings_storage import get_storage_region
-from lamindb_setup.core.upath import create_path
+from lamindb_setup.core.upath import LocalPathClasses, create_path
 from lnschema_core import Artifact, Run
 
 if TYPE_CHECKING:
@@ -23,7 +23,12 @@ def _read_adata_h5ad_zarr(objpath: UPath):
     if objpath.is_dir():
         adata = read_adata_zarr(objpath)
     else:
-        adata = read_adata_h5ad(objpath)
+        # read only local in backed for now
+        # in principle possible to read remote in backed also
+        if isinstance(objpath, LocalPathClasses):
+            adata = read_h5ad(objpath.as_posix(), backed="r")
+        else:
+            adata = read_adata_h5ad(objpath)
     return adata
 
 
@@ -85,27 +90,24 @@ def save_tiledbsoma_experiment(
 ) -> Artifact:
     """Write `AnnData` to `tiledbsoma.Experiment`.
 
-    Reads `AnnData` objects, writes them to `tiledbsoma.Experiment`, creates `lamindb.Artifact`
-    and saves the artifact.
-    Note that this function adds `lamin_run_uid` column to `obs` of in-memory `AnnData` objects
-    when it writes to a new store or appends to a store that has this column in `obs`.
+    Reads `AnnData` objects, writes them to `tiledbsoma.Experiment`, creates & saves an {class}`~lamindb.Artifact`.
+
+    Populates a column `lamin_run_uid` column in `obs` with the current `run.uid`.
 
-    See also `tiledbsoma.io.from_anndata
+    Is based on `tiledbsoma.io.from_anndata
     <https://tiledbsoma.readthedocs.io/en/latest/_autosummary/tiledbsoma.io.from_anndata.html>`__.
 
     Args:
         adatas: `AnnData` objects to write, in-memory or on-disk.
-        key: A relative path within default storage.
+        key: An optional key to reference the artifact.
         description: A description.
         run: The run that creates the artifact.
         revises: `lamindb.Artifact` with `tiledbsoma.Experiment` to append to.
-            Triggers a revision (a new untagged version).
         measurement_name: The name of the measurement to store data in `tiledbsoma.Experiment`.
         obs_id_name: Which `AnnData` `obs` column to use for append mode.
         var_id_name: Which `AnnData` `var` column to use for append mode.
         append_obsm_varm: Whether to append `obsm` and `varm` in append mode .
-        **kwargs: Additional keyword arguments passed to `tiledbsoma.io.from_anndata` that
-            writes `adatas`.
+        **kwargs: Keyword arguments passed to `tiledbsoma.io.from_anndata`.
     """
     try:
         import tiledbsoma as soma
@@ -120,14 +122,12 @@ def save_tiledbsoma_experiment(
     run = get_run(run)
 
     appending = revises is not None
-
     if appending:
-        _uid = None
         storepath = revises.path
     else:
-        _uid, _ = create_uid(n_full_id=20)
+        uid, _ = create_uid(n_full_id=20)
         storage_key = auto_storage_key_from_artifact_uid(
-            _uid, ".tiledbsoma", is_dir=True
+            uid, ".tiledbsoma", is_dir=True
         )
         storepath = setup_settings.storage.root / storage_key
 
@@ -162,7 +162,8 @@ def save_tiledbsoma_experiment(
                 adata.obs["lamin_run_uid"] = run.uid
         adata_objects.append(adata)
 
-    if appending or len(adata_objects) > 1:
+    registration_mapping = kwargs.get("registration_mapping", None)
+    if registration_mapping is None and (appending or len(adata_objects) > 1):
         registration_mapping = soma_io.register_anndatas(
             experiment_uri=storepath if appending else None,
             adatas=adata_objects,
@@ -172,8 +173,6 @@ def save_tiledbsoma_experiment(
             append_obsm_varm=append_obsm_varm,
             context=ctx,
         )
-    else:
-        registration_mapping = None
 
     for adata_obj in adata_objects:
         soma_io.from_anndata(
@@ -188,5 +187,10 @@ def save_tiledbsoma_experiment(
         )
 
     return Artifact(
-        storepath, key=key, description=description, run=run, revises=revises, _uid=_uid
+        storepath,
+        key=key,
+        description=description,
+        run=run,
+        revises=revises,
+        _is_internal_call=True,
     ).save()

lamindb/core/versioning.py

@@ -99,6 +99,10 @@ def create_uid(
     n_full_id: int = 20,
     revises: IsVersioned | None = None,
 ) -> tuple[str, IsVersioned | None]:
+    """This also updates revises in case it's not the latest version.
+
+    This is why it returns revises.
+    """
     if revises is not None:
         if not revises.is_latest:
             # need one more request

lamindb/integrations/_vitessce.py

@@ -56,22 +56,12 @@ def save_vitessce_config(
                 raise ValueError("Each file must have a 'url' key.")
             s3_path = file["url"]
             s3_path_last_element = s3_path.split("/")[-1]
-            # note 1: the following parses the stem uid of the artifact from the S3 path
-            # there might be a better way of doing this in case the vitessce config
-            # gets updated in the future; but given these paths are set in stone
-            # this should be more robust than it looks
-            #
-            # note 2: what's not great is the fact that people might use composite suffixes we don't recognize
-            # I don't know what to do about it other than documenting it clearly
-            # https://github.com/laminlabs/lamindb/blob/main/lamindb/core/storage/_valid_suffixes.py
-            # https://docs.lamin.ai/lamindb.core.storage.valid_suffixes
-            #
             # now start with attempting to strip the composite suffix candidates
             for suffix in valid_composite_zarr_suffixes:
                 s3_path_last_element = s3_path_last_element.replace(suffix, "")
             # in case there was no hit, strip plain ".zarr"
             artifact_stem_uid = s3_path_last_element.replace(".zarr", "")
-            # if there is still a "." in string, we
+            # if there is still a "." in string, raise an error
             if "." in artifact_stem_uid:
                 raise ValueError(
                     f"Suffix should be '.zarr' or one of {valid_composite_zarr_suffixes}. Inspect your path {s3_path}"

{lamindb-0.76.3.dist-info → lamindb-0.76.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.3
+Version: 0.76.4
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,22 +9,22 @@ 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==0.73.3
-Requires-Dist: lamindb_setup==0.76.7
+Requires-Dist: lnschema_core==0.73.5
+Requires-Dist: lamindb_setup==0.76.8
 Requires-Dist: lamin_utils==0.13.4
-Requires-Dist: lamin_cli==0.16.2
+Requires-Dist: lamin_cli==0.17.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
-Requires-Dist: anndata>=0.8.0,<=0.10.8
+Requires-Dist: anndata>=0.8.0,<=0.10.9
 Requires-Dist: scipy<1.13.0rc1
 Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.49.0 ; extra == "bionty"
+Requires-Dist: bionty==0.49.1 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -38,7 +38,7 @@ 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==0.10.4 ; extra == "jupyter"
-Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
+Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb

{lamindb-0.76.3.dist-info → lamindb-0.76.4.dist-info}/RECORD

@@ -1,30 +1,30 @@
-lamindb/__init__.py,sha256=iZlJlG4hUmSRNZvau2bAEG2Z9B-qnWWNazYYw5m3ciM,2351
-lamindb/_artifact.py,sha256=6iD2qzZxWUHPiItUdEJt9BDbYVv6HF3bgpW2ZDjMf7s,44093
-lamindb/_can_validate.py,sha256=ne8-9sAG9vXnMXZqso6mYMt-xDg16h-gq6yHJXKFpuI,17690
+lamindb/__init__.py,sha256=faIPIM0ynMz0AU9pziDSQJT-rQhUXqpJ3PWRlmijqbs,2319
+lamindb/_artifact.py,sha256=QjCge5kaAcfhGv84s299OT99LmHTSYDxgzw5kN-x3-8,44416
+lamindb/_can_validate.py,sha256=9di9FLmC2m3dpT42sceF34UEFzQITi2e_hjVMa8DIc4,18261
 lamindb/_collection.py,sha256=F_VgpLBprrzUQ-tPngWvO9vFd7jX66MVwIi031JOris,14871
-lamindb/_curate.py,sha256=_VISRycaPaburnJKuFM5XpEWqNGozdUcwBGMj_knZpM,58041
+lamindb/_curate.py,sha256=gCbDiqhsJzVZZ6BuEoFXUpsNOffpUNDlrX1dJiOqJJo,58753
 lamindb/_feature.py,sha256=nZhtrH0ssoNls-hV-dkwfK9sKypg2El59R9qfarxfUE,5340
 lamindb/_feature_set.py,sha256=DmAy96V_RyV0yiyvWOCHgustXPsCaMwn4TrWwh2qDd8,8104
 lamindb/_filter.py,sha256=9QHa9J-_6QeYPQATZpTun2VGiFofwzB0Km-KnKajHcM,663
-lamindb/_finish.py,sha256=Yytv26ruL7EFxKewOrgqJxDircZVCpHOkwUjqdh4oMY,9411
+lamindb/_finish.py,sha256=NEZmTW7sWzwi-QYTwVgoOeeD-pZxWBrZOITK_YoJreU,9434
 lamindb/_from_values.py,sha256=8kYpR8Q85EOaTcsPGjVHeZh29fGVgum5OEQf4Hsz_80,13533
 lamindb/_is_versioned.py,sha256=5lAnhTboltFkZCKVRV1uxkm0OCjJz_HKi3yQq_vEuMs,1306
 lamindb/_parents.py,sha256=eMavdd6IO6STOVJSlR2TzdRtx6sKYDKsMOtlR3DZlgQ,15599
 lamindb/_query_manager.py,sha256=Ipe85HL31DDwMbC8CN_1Svbwk48a_DUh_INGQdZL08I,4222
-lamindb/_query_set.py,sha256=rykST1bxbk2_dt8Rx1TGTEHzXUc1yyc0rZWHO6bRGBA,12667
-lamindb/_record.py,sha256=MDLvcsZ23lZkThnrYQtj_uW-1BnxCPpyJ5mKl9KPs4A,21199
+lamindb/_query_set.py,sha256=BiGvEiaBSd9aV28EAy83Q8h6RLsYMDjfxLOljAcyMaM,12692
+lamindb/_record.py,sha256=53_0oU6v45V5gIDJgkAUSX7iIV5Si_4cuOWUHJa8JVo,21241
 lamindb/_run.py,sha256=5M_r1zGDv9HlqbqRKTWCYCOtENovJ-8mQ4kY7XqcLaU,1888
 lamindb/_save.py,sha256=Fu7Z84btKOXfTfpunKLni21s5ER2zIllqg5e3nPq-0A,10910
 lamindb/_storage.py,sha256=GBVChv-DHVMNEBJL5l_JT6B4RDhZ6NnwgzmUICphYKk,413
-lamindb/_transform.py,sha256=Ck674iuKIp9HDpHuyFFM2xKJcFAUvQDRTnEdnx00Rq0,4114
+lamindb/_transform.py,sha256=Rgj8uq6t4NpyP7DtQ-0IRJs7vSEKHyWftY5dvwKNFgs,4063
 lamindb/_ulabel.py,sha256=XDSdZBXX_ki5s1vOths3MjF2x5DPggBR_PV_KF4SGyg,1611
 lamindb/_utils.py,sha256=LGdiW4k3GClLz65vKAVRkL6Tw-Gkx9DWAdez1jyA5bE,428
 lamindb/_view.py,sha256=4Ln2ItTb3857PAI-70O8eJYqoTJ_NNFc7E_wds6OGns,2412
-lamindb/core/__init__.py,sha256=Nq-YbQT8X0KXoGXgctr9lm8H7J6sZeBBJ3hixGq0iuQ,1523
-lamindb/core/_context.py,sha256=FamAbmq3VZYrgwZkaRtkBY3f5YepLtlblh8wyv4a1OQ,19546
+lamindb/core/__init__.py,sha256=hxPWM_Jnrllx0G_6itEGU2meXwptkkgiL9zsBvlhHM4,1495
+lamindb/core/_context.py,sha256=U-vmMH4s0ZfvS6KBRj5mOsOFuvcioJ7FgUdn0OOkLvA,19972
 lamindb/core/_data.py,sha256=eocOXsZGu62LPtz6yIlvHhPSJTf3yF2ITZTffyflWYI,16269
 lamindb/core/_feature_manager.py,sha256=94tX6gq_Rx7fkDARQBxB2z92qUDpHocFSAdKv5izMT4,32490
-lamindb/core/_label_manager.py,sha256=jSLvxAuTuOYosSh_QJhIz3bqnbmWKP43y5abVMb-hOQ,9240
+lamindb/core/_label_manager.py,sha256=zCE-PS1Y5ALpzoSOx1P6ZTFVPgFNRAmmyTQF0e8QBXA,9131
 lamindb/core/_mapped_collection.py,sha256=1XzratL2IvRleqioNhWo26Lsuqkev8-HEImmHQxw9Kw,23266
 lamindb/core/_settings.py,sha256=GGEB8BU5GinIfD4ktr1Smp6GPHGaInu46MhP4EecZDY,5950
 lamindb/core/_sync_git.py,sha256=qc0yfPyKeG4uuNT_3qsv-mkIMqhLFqfXNeNVO49vV00,4547
@@ -33,15 +33,15 @@ lamindb/core/exceptions.py,sha256=TKyt1JOUwWIHbkCQjir_LQadf8960eQ95RWhSpz5_Bk,12
 lamindb/core/fields.py,sha256=47Jmh3efUr5ZscgimR_yckY-I3cNf8ScLutbwKCK3j4,162
 lamindb/core/schema.py,sha256=KiYQn_8fokSMztTNDe6qUocZzKXWxU32H-YChNJv51A,1877
 lamindb/core/types.py,sha256=uVBqSVLoQaTkqP9nqsJhwU6yYnx8H5e6-ZxrB6vpOOw,265
-lamindb/core/versioning.py,sha256=__SOHhk5OjMJgAUjixzp0GFcQrpjm8sBUXC9Fouk2AE,5162
+lamindb/core/versioning.py,sha256=GYhgSA6IOlWMMNfctZu7U_jIvmQP2gdvsZxn4bTanOc,5277
 lamindb/core/datasets/__init__.py,sha256=zRP98oqUAaXhqWyKMiH0s_ImVIuNeziQQ2kQ_t0f-DI,1353
 lamindb/core/datasets/_core.py,sha256=CgVF_pXuBXLElzubDMsl1DbpYOnXCY0HleITVvBKih4,19873
 lamindb/core/datasets/_fake.py,sha256=BZF9R_1iF0HDnvtZNqL2FtsjSMuqDIfuFxnw_LJYIh4,953
 lamindb/core/storage/__init__.py,sha256=x-Bpxv1rx6uGog-chI0fdpt0UhkXQkwoQqye0TNk0WQ,514
-lamindb/core/storage/_anndata_accessor.py,sha256=jmEZeeZlt8-qBXRkU0tTA-t6dVEb_dH86wc1ok0jSRY,24030
+lamindb/core/storage/_anndata_accessor.py,sha256=F3ze8ICG7K4BKueg-766olnoEA8Eh8gVrvDSSE2FX-M,24160
 lamindb/core/storage/_anndata_sizes.py,sha256=aXO3OB--tF5MChenSsigW6Q-RuE8YJJOUTVukkLrv9A,1029
 lamindb/core/storage/_backed_access.py,sha256=YcWCeT2eligJGsBdjJS_-4el_eC9J088jxUWG9lsleM,3231
-lamindb/core/storage/_tiledbsoma.py,sha256=_ObAT3pIx0OA5uq55v6aWnIeyTTKjetjV3Gkk4oDWR0,6851
+lamindb/core/storage/_tiledbsoma.py,sha256=OVDjvu4lRovRtWcn9Tu3N5tA-zbF8snsjkR4DOXOTTc,7001
 lamindb/core/storage/_valid_suffixes.py,sha256=vUSeQ4s01rdhD_vSd6wKmFBsgMJAKkBMnL_T9Y1znMg,501
 lamindb/core/storage/_zarr.py,sha256=5ceEz6YIvgvUnVVNWhK5Z4W0WfrvyvY82Yna5jSX1_E,3661
 lamindb/core/storage/objects.py,sha256=OzvBCS-Urz5mr-O95qYt6RGBDDX5HmjfRRKWPPDn1ZE,1797
@@ -50,10 +50,10 @@ lamindb/core/subsettings/__init__.py,sha256=KFHPzIE7f7Bj4RgMjGQF4CjTdHVG_VNFBrCn
 lamindb/core/subsettings/_creation_settings.py,sha256=54mfMH_osC753hpxcl7Dq1rwBD2LHnWveXtQpkLBITE,1194
 lamindb/core/subsettings/_transform_settings.py,sha256=4YbCuZtJo6zdytl6UQR4GvdDkTtT6SRBqVzofGzNOt8,583
 lamindb/integrations/__init__.py,sha256=RWGMYYIzr8zvmNPyVB4m-p4gMDhxdRbjES2Ed23OItw,215
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 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
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