lamindb 0.76.8__py3-none-any.whl → 0.76.9__py3-none-any.whl

lamindb/core/versioning.py

@@ -1,158 +1,158 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Literal
-
-from lamin_utils import logger
-from lamin_utils._base62 import CHARSET_DEFAULT as BASE62_CHARS
-from lamindb_setup.core.upath import LocalPathClasses, UPath
-from lnschema_core import ids
-
-if TYPE_CHECKING:
-    from lnschema_core.models import IsVersioned
-
-
-def message_update_key_in_version_family(
-    *,
-    suid: str,
-    existing_key: str,
-    registry: str,
-    new_key: str,
-) -> str:
-    return f'Or update key "{existing_key}" in your existing family:\n\nln.{registry}.filter(uid__startswith="{suid}").update(key="{new_key}")'
-
-
-def increment_base62(s: str) -> str:
-    # we don't need to throw an error for zzzz because uids are enforced to be unique
-    # on the db level and have an enforced maximum length
-    value = sum(BASE62_CHARS.index(c) * (62**i) for i, c in enumerate(reversed(s)))
-    value += 1
-    result = ""
-    while value:
-        value, remainder = divmod(value, 62)
-        result = BASE62_CHARS[remainder] + result
-    return result.zfill(len(s))
-
-
-def bump_version(
-    version: str,
-    bump_type: str = "minor",
-    behavior: Literal["prompt", "error", "ignore"] = "error",
-) -> str:
-    """Bumps the version number by major or minor depending on the bump_type flag.
-
-    Parameters:
-    version (str): The current version in "MAJOR" or "MAJOR.MINOR" format.
-    bump_type (str): The type of version bump, either 'major' or 'minor'.
-
-    Returns:
-    str: The new version string.
-    """
-    try:
-        # Split the version into major and minor parts if possible
-        parts = version.split(".")
-        major = int(parts[0])
-        minor = int(parts[1]) if len(parts) > 1 else 0
-
-        if bump_type == "major":
-            # Bump the major version and reset the minor version
-            new_version = f"{major + 1}"
-        elif bump_type == "minor":
-            # Bump the minor version
-            new_version = f"{major}.{minor + 1}"
-        else:
-            raise ValueError("bump_type must be 'major' or 'minor'")
-
-    except (ValueError, IndexError):
-        if behavior == "prompt":
-            new_version = input(
-                f"The current version is '{version}' - please type the new version: "
-            )
-        elif behavior == "error":
-            raise ValueError(
-                "Cannot auto-increment non-integer castable version, please provide"
-                " manually"
-            ) from None
-        else:
-            logger.warning("could not auto-increment version, fix '?' manually")
-            new_version = "?"
-    return new_version
-
-
-def set_version(version: str | None = None, previous_version: str | None = None):
-    """(Auto-) set version.
-
-    If `version` is `None`, returns the stored version.
-    Otherwise sets the version to the passed version.
-
-    Args:
-        version: Version string.
-        previous_version: Previous version string.
-    """
-    if version is None and previous_version is not None:
-        version = bump_version(previous_version, bump_type="major")
-    return version
-
-
-def create_uid(
-    *,
-    version: str | None = None,
-    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
-            revises = revises.__class__.objects.get(
-                is_latest=True, uid__startswith=revises.stem_uid
-            )
-            logger.warning(
-                f"didn't pass the latest version in `revises`, retrieved it: {revises}"
-            )
-        suid = revises.stem_uid
-        vuid = increment_base62(revises.uid[-4:])
-    else:
-        suid = ids.base62(n_full_id - 4)
-        vuid = "0000"
-    if version is not None:
-        if not isinstance(version, str):
-            raise ValueError(
-                "`version` parameter must be `None` or `str`, e.g., '0.1', '1', '2',"
-                " etc."
-            )
-        if revises is not None:
-            if version == revises.version:
-                raise ValueError(
-                    f"Please increment the previous version: '{revises.version}'"
-                )
-    return suid + vuid, revises
-
-
-def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
-    if isinstance(old_path, LocalPathClasses):
-        # for local path, the rename target must be full path
-        new_path = old_path.as_posix().replace(old_uid, new_uid)
-    else:
-        # for cloud path, the rename target must be the last part of the path
-        new_path = old_path.name.replace(old_uid, new_uid)
-    return new_path
-
-
-def process_revises(
-    revises: IsVersioned | None,
-    version: str | None,
-    name: str | None,
-    type: type[IsVersioned],
-) -> tuple[str, str, str, IsVersioned | None]:
-    if revises is not None and not isinstance(revises, type):
-        raise TypeError(f"`revises` has to be of type `{type.__name__}`")
-    uid, revises = create_uid(
-        revises=revises, version=version, n_full_id=type._len_full_uid
-    )
-    if revises is not None:
-        if name is None:
-            name = revises.name
-    return uid, version, name, revises
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Literal
+
+from lamin_utils import logger
+from lamin_utils._base62 import CHARSET_DEFAULT as BASE62_CHARS
+from lamindb_setup.core.upath import LocalPathClasses, UPath
+from lnschema_core import ids
+
+if TYPE_CHECKING:
+    from lnschema_core.models import IsVersioned
+
+
+def message_update_key_in_version_family(
+    *,
+    suid: str,
+    existing_key: str,
+    registry: str,
+    new_key: str,
+) -> str:
+    return f'Or update key "{existing_key}" to "{new_key}":\n\nln.{registry}.filter(uid__startswith="{suid}").update(key="{new_key}")\n'
+
+
+def increment_base62(s: str) -> str:
+    # we don't need to throw an error for zzzz because uids are enforced to be unique
+    # on the db level and have an enforced maximum length
+    value = sum(BASE62_CHARS.index(c) * (62**i) for i, c in enumerate(reversed(s)))
+    value += 1
+    result = ""
+    while value:
+        value, remainder = divmod(value, 62)
+        result = BASE62_CHARS[remainder] + result
+    return result.zfill(len(s))
+
+
+def bump_version(
+    version: str,
+    bump_type: str = "minor",
+    behavior: Literal["prompt", "error", "ignore"] = "error",
+) -> str:
+    """Bumps the version number by major or minor depending on the bump_type flag.
+
+    Parameters:
+    version (str): The current version in "MAJOR" or "MAJOR.MINOR" format.
+    bump_type (str): The type of version bump, either 'major' or 'minor'.
+
+    Returns:
+    str: The new version string.
+    """
+    try:
+        # Split the version into major and minor parts if possible
+        parts = version.split(".")
+        major = int(parts[0])
+        minor = int(parts[1]) if len(parts) > 1 else 0
+
+        if bump_type == "major":
+            # Bump the major version and reset the minor version
+            new_version = f"{major + 1}"
+        elif bump_type == "minor":
+            # Bump the minor version
+            new_version = f"{major}.{minor + 1}"
+        else:
+            raise ValueError("bump_type must be 'major' or 'minor'")
+
+    except (ValueError, IndexError):
+        if behavior == "prompt":
+            new_version = input(
+                f"The current version is '{version}' - please type the new version: "
+            )
+        elif behavior == "error":
+            raise ValueError(
+                "Cannot auto-increment non-integer castable version, please provide"
+                " manually"
+            ) from None
+        else:
+            logger.warning("could not auto-increment version, fix '?' manually")
+            new_version = "?"
+    return new_version
+
+
+def set_version(version: str | None = None, previous_version: str | None = None):
+    """(Auto-) set version.
+
+    If `version` is `None`, returns the stored version.
+    Otherwise sets the version to the passed version.
+
+    Args:
+        version: Version string.
+        previous_version: Previous version string.
+    """
+    if version is None and previous_version is not None:
+        version = bump_version(previous_version, bump_type="major")
+    return version
+
+
+def create_uid(
+    *,
+    version: str | None = None,
+    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
+            revises = revises.__class__.objects.get(
+                is_latest=True, uid__startswith=revises.stem_uid
+            )
+            logger.warning(
+                f"didn't pass the latest version in `revises`, retrieved it: {revises}"
+            )
+        suid = revises.stem_uid
+        vuid = increment_base62(revises.uid[-4:])
+    else:
+        suid = ids.base62(n_full_id - 4)
+        vuid = "0000"
+    if version is not None:
+        if not isinstance(version, str):
+            raise ValueError(
+                "`version` parameter must be `None` or `str`, e.g., '0.1', '1', '2',"
+                " etc."
+            )
+        if revises is not None:
+            if version == revises.version:
+                raise ValueError(
+                    f"Please increment the previous version: '{revises.version}'"
+                )
+    return suid + vuid, revises
+
+
+def get_new_path_from_uid(old_path: UPath, old_uid: str, new_uid: str):
+    if isinstance(old_path, LocalPathClasses):
+        # for local path, the rename target must be full path
+        new_path = old_path.as_posix().replace(old_uid, new_uid)
+    else:
+        # for cloud path, the rename target must be the last part of the path
+        new_path = old_path.name.replace(old_uid, new_uid)
+    return new_path
+
+
+def process_revises(
+    revises: IsVersioned | None,
+    version: str | None,
+    name: str | None,
+    type: type[IsVersioned],
+) -> tuple[str, str, str, IsVersioned | None]:
+    if revises is not None and not isinstance(revises, type):
+        raise TypeError(f"`revises` has to be of type `{type.__name__}`")
+    uid, revises = create_uid(
+        revises=revises, version=version, n_full_id=type._len_full_uid
+    )
+    if revises is not None:
+        if name is None:
+            name = revises.name
+    return uid, version, name, revises

lamindb/integrations/__init__.py

@@ -1,12 +1,12 @@
-"""Integrations.
-
-.. autosummary::
-   :toctree: .
-
-   save_vitessce_config
-   save_tiledbsoma_experiment
-"""
-
-from lamindb.core.storage import save_tiledbsoma_experiment
-
-from ._vitessce import save_vitessce_config
+"""Integrations.
+
+.. autosummary::
+   :toctree: .
+
+   save_vitessce_config
+   save_tiledbsoma_experiment
+"""
+
+from lamindb.core.storage import save_tiledbsoma_experiment
+
+from ._vitessce import save_vitessce_config

lamindb/integrations/_vitessce.py

@@ -1,107 +1,107 @@
-from __future__ import annotations
-
-import json
-from datetime import datetime, timezone
-from typing import TYPE_CHECKING
-
-import lamindb_setup as ln_setup
-from lamin_utils import logger
-
-from lamindb._artifact import Artifact
-from lamindb._run import Run
-from lamindb._transform import Transform
-
-if TYPE_CHECKING:
-    from vitessce import VitessceConfig
-
-
-# "unit test": https://github.com/laminlabs/lamindb/blob/main/docs/storage/vitessce.ipynb
-# integration test & context: https://github.com/laminlabs/lamin-spatial/blob/main/docs/vitessce.ipynb
-def save_vitessce_config(
-    vitessce_config: VitessceConfig, description: str | None = None
-) -> Artifact:
-    """Validates and saves a ``VitessceConfig`` object.
-
-    Guide: :doc:`docs:vitessce`.
-
-    Args:
-        vitessce_config (``VitessceConfig``): A `VitessceConfig` object.
-        description: A description for the `VitessceConfig` artifact.
-
-    .. versionchanged:: 0.75.1
-        Now displays the "Vitessce button" on the hub next to the dataset. It additionally keeps displaying it next to the configuration file.
-    .. versionchanged:: 0.70.2
-        No longer saves the dataset. It only saves the `VitessceConfig` object.
-    """
-    # can only import here because vitessce is not a dependency
-    from vitessce import VitessceConfig
-
-    from lamindb.core.storage import VALID_SUFFIXES
-
-    assert isinstance(vitessce_config, VitessceConfig)  # noqa: S101
-    vc_dict = vitessce_config.to_dict()
-    valid_composite_zarr_suffixes = [
-        suffix for suffix in VALID_SUFFIXES.COMPOSITE if suffix.endswith(".zarr")
-    ]
-    # validate
-    dataset_artifacts = []
-    assert vc_dict["datasets"]  # noqa: S101
-    for vitessce_dataset in vc_dict["datasets"]:
-        # didn't find good ways to violate the below, hence using plain asserts
-        # without user feedback
-        assert "files" in vitessce_dataset  # noqa: S101
-        assert vitessce_dataset["files"]  # noqa: S101
-        for file in vitessce_dataset["files"]:
-            if "url" not in file:
-                raise ValueError("Each file must have a 'url' key.")
-            s3_path = file["url"]
-            s3_path_last_element = s3_path.split("/")[-1]
-            # 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, 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}"
-                )
-            artifact = Artifact.filter(uid__startswith=artifact_stem_uid).one_or_none()
-            if artifact is None:
-                raise ValueError(
-                    f"Could not find dataset with stem uid '{artifact_stem_uid}' in lamindb: {vitessce_dataset}. Did you follow https://docs.lamin.ai/vitessce? It appears the AWS S3 path doesn't encode a lamindb uid."
-                )
-            else:
-                dataset_artifacts.append(artifact)
-    # the below will be replaced with a `ln.tracked()` decorator soon
-    with logger.mute():
-        transform = Transform(
-            uid="kup03MJBsIVa0001",
-            name="save_vitessce_config",
-            type="function",
-            version="2",
-        ).save()
-    run = Run(transform=transform).save()
-    if len(dataset_artifacts) > 1:
-        # if we have more datasets, we should create a collection
-        # and attach an action to the collection
-        raise NotImplementedError
-    run.input_artifacts.set(dataset_artifacts)
-    # create a JSON export
-    config_file_local_path = (
-        ln_setup.settings.storage.cache_dir / "config.vitessce.json"
-    )
-    with open(config_file_local_path, "w") as file:
-        json.dump(vc_dict, file)
-    vitessce_config_artifact = Artifact(
-        config_file_local_path, description=description, run=run
-    ).save()
-    # we have one and only one dataset artifact, hence the following line is OK
-    dataset_artifacts[0]._actions.add(vitessce_config_artifact)
-    slug = ln_setup.settings.instance.slug
-    logger.important(
-        f"go to: https://lamin.ai/{slug}/artifact/{vitessce_config_artifact.uid}"
-    )
-    run.finished_at = datetime.now(timezone.utc)
-    run.save()
-    return vitessce_config_artifact
+from __future__ import annotations
+
+import json
+from datetime import datetime, timezone
+from typing import TYPE_CHECKING
+
+import lamindb_setup as ln_setup
+from lamin_utils import logger
+
+from lamindb._artifact import Artifact
+from lamindb._run import Run
+from lamindb._transform import Transform
+
+if TYPE_CHECKING:
+    from vitessce import VitessceConfig
+
+
+# "unit test": https://github.com/laminlabs/lamindb/blob/main/docs/storage/vitessce.ipynb
+# integration test & context: https://github.com/laminlabs/lamin-spatial/blob/main/docs/vitessce.ipynb
+def save_vitessce_config(
+    vitessce_config: VitessceConfig, description: str | None = None
+) -> Artifact:
+    """Validates and saves a ``VitessceConfig`` object.
+
+    Guide: :doc:`docs:vitessce`.
+
+    Args:
+        vitessce_config (``VitessceConfig``): A `VitessceConfig` object.
+        description: A description for the `VitessceConfig` artifact.
+
+    .. versionchanged:: 0.75.1
+        Now displays the "Vitessce button" on the hub next to the dataset. It additionally keeps displaying it next to the configuration file.
+    .. versionchanged:: 0.70.2
+        No longer saves the dataset. It only saves the `VitessceConfig` object.
+    """
+    # can only import here because vitessce is not a dependency
+    from vitessce import VitessceConfig
+
+    from lamindb.core.storage import VALID_SUFFIXES
+
+    assert isinstance(vitessce_config, VitessceConfig)  # noqa: S101
+    vc_dict = vitessce_config.to_dict()
+    valid_composite_zarr_suffixes = [
+        suffix for suffix in VALID_SUFFIXES.COMPOSITE if suffix.endswith(".zarr")
+    ]
+    # validate
+    dataset_artifacts = []
+    assert vc_dict["datasets"]  # noqa: S101
+    for vitessce_dataset in vc_dict["datasets"]:
+        # didn't find good ways to violate the below, hence using plain asserts
+        # without user feedback
+        assert "files" in vitessce_dataset  # noqa: S101
+        assert vitessce_dataset["files"]  # noqa: S101
+        for file in vitessce_dataset["files"]:
+            if "url" not in file:
+                raise ValueError("Each file must have a 'url' key.")
+            s3_path = file["url"]
+            s3_path_last_element = s3_path.split("/")[-1]
+            # 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, 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}"
+                )
+            artifact = Artifact.filter(uid__startswith=artifact_stem_uid).one_or_none()
+            if artifact is None:
+                raise ValueError(
+                    f"Could not find dataset with stem uid '{artifact_stem_uid}' in lamindb: {vitessce_dataset}. Did you follow https://docs.lamin.ai/vitessce? It appears the AWS S3 path doesn't encode a lamindb uid."
+                )
+            else:
+                dataset_artifacts.append(artifact)
+    # the below will be replaced with a `ln.tracked()` decorator soon
+    with logger.mute():
+        transform = Transform(
+            uid="kup03MJBsIVa0001",
+            name="save_vitessce_config",
+            type="function",
+            version="2",
+        ).save()
+    run = Run(transform=transform).save()
+    if len(dataset_artifacts) > 1:
+        # if we have more datasets, we should create a collection
+        # and attach an action to the collection
+        raise NotImplementedError
+    run.input_artifacts.set(dataset_artifacts)
+    # create a JSON export
+    config_file_local_path = (
+        ln_setup.settings.storage.cache_dir / "config.vitessce.json"
+    )
+    with open(config_file_local_path, "w") as file:
+        json.dump(vc_dict, file)
+    vitessce_config_artifact = Artifact(
+        config_file_local_path, description=description, run=run
+    ).save()
+    # we have one and only one dataset artifact, hence the following line is OK
+    dataset_artifacts[0]._actions.add(vitessce_config_artifact)
+    slug = ln_setup.settings.instance.slug
+    logger.important(
+        f"go to: https://lamin.ai/{slug}/artifact/{vitessce_config_artifact.uid}"
+    )
+    run.finished_at = datetime.now(timezone.utc)
+    run.save()
+    return vitessce_config_artifact

lamindb/setup/__init__.py

@@ -1,14 +1,14 @@
-import lamindb_setup as _lamindb_setup
-from lamindb_setup import *  # noqa: F403
-from lamindb_setup import (
-    connect,
-    delete,
-    init,
-    settings,
-)
-
-from . import core
-
-del connect  # we have this at the root level, hence, we don't want it here
-__doc__ = _lamindb_setup.__doc__.replace("lamindb_setup", "lamindb.setup")
-settings.__doc__ = settings.__doc__.replace("lamindb_setup", "lamindb.setup")
+import lamindb_setup as _lamindb_setup
+from lamindb_setup import *  # noqa: F403
+from lamindb_setup import (
+    connect,
+    delete,
+    init,
+    settings,
+)
+
+from . import core
+
+del connect  # we have this at the root level, hence, we don't want it here
+__doc__ = _lamindb_setup.__doc__.replace("lamindb_setup", "lamindb.setup")
+settings.__doc__ = settings.__doc__.replace("lamindb_setup", "lamindb.setup")

lamindb/setup/core/__init__.py

@@ -1,4 +1,4 @@
-import lamindb_setup as _lamindb_setup
-from lamindb_setup.core import *  # noqa: F403
-
-__doc__ = _lamindb_setup.core.__doc__.replace("lamindb_setup", "lamindb.setup")
+import lamindb_setup as _lamindb_setup
+from lamindb_setup.core import *  # noqa: F403
+
+__doc__ = _lamindb_setup.core.__doc__.replace("lamindb_setup", "lamindb.setup")