lamindb 0.70.4__py3-none-any.whl → 0.71.0__py3-none-any.whl

lamindb/__init__.py

@@ -40,7 +40,8 @@ Modules & settings:
 
 """
 
-__version__ = "0.70.4"  # denote a release candidate for 0.1.0 with 0.1rc1
+# denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
+__version__ = "0.71.0"
 
 import os as _os
 

lamindb/_artifact.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import shutil
 from pathlib import Path, PurePath, PurePosixPath
 from typing import TYPE_CHECKING, Any, Mapping
 
@@ -9,9 +10,9 @@ import pandas as pd
 from anndata import AnnData
 from lamin_utils import colors, logger
 from lamindb_setup import settings as setup_settings
-from lamindb_setup._init_instance import register_storage
-from lamindb_setup.core import StorageSettings
+from lamindb_setup._init_instance import register_storage_in_instance
 from lamindb_setup.core._docs import doc_args
+from lamindb_setup.core._settings_storage import init_storage
 from lamindb_setup.core.hashing import b16_to_b64, hash_file, hash_md5s_from_dir
 from lamindb_setup.core.upath import (
     create_path,
@@ -100,12 +101,9 @@ def process_pathlike(
             # for the storage root: the bucket
             if not isinstance(filepath, LocalPathClasses):
                 # for a cloud path, new_root is always the bucket name
-                # we should check this assumption
                 new_root = list(filepath.parents)[-1]
-                new_root_str = new_root.as_posix().rstrip("/")
-                logger.warning(f"generating a new storage location at {new_root_str}")
-                storage_settings = StorageSettings(new_root_str)
-                storage_record = register_storage(storage_settings)
+                storage_settings = init_storage(new_root)
+                storage_record = register_storage_in_instance(storage_settings)
                 use_existing_storage_key = True
                 return storage_record, use_existing_storage_key
             # if the filepath is local
@@ -545,11 +543,13 @@ def __init__(artifact: Artifact, *args, **kwargs):
     skip_check_exists = (
         kwargs.pop("skip_check_exists") if "skip_check_exists" in kwargs else False
     )
-    default_storage = (
-        kwargs.pop("default_storage")
-        if "default_storage" in kwargs
-        else settings._storage_settings.record
-    )
+    if "default_storage" in kwargs:
+        default_storage = kwargs.pop("default_storage")
+    else:
+        if setup_settings.instance.keep_artifacts_local:
+            default_storage = setup_settings.instance.storage_local.record
+        else:
+            default_storage = setup_settings.instance.storage.record
     using_key = (
         kwargs.pop("using_key") if "using_key" in kwargs else settings._using_key
     )
@@ -995,7 +995,14 @@ def _delete_skip_storage(artifact, *args, **kwargs) -> None:
 
 # docstring handled through attach_func_to_class_method
 def save(self, upload: bool | None = None, **kwargs) -> None:
+    state_was_adding = self._state.adding
     access_token = kwargs.pop("access_token", None)
+    local_path = None
+    if upload and setup_settings.instance.keep_artifacts_local:
+        # switch local storage location to cloud
+        local_path = self.path
+        self.storage_id = setup_settings.instance.storage.id
+        self._local_filepath = local_path
 
     self._save_skip_storage(**kwargs)
 
@@ -1011,6 +1018,17 @@ def save(self, upload: bool | None = None, **kwargs) -> None:
     exception = check_and_attempt_clearing(self, using_key)
     if exception is not None:
         raise RuntimeError(exception)
+    if local_path is not None and not state_was_adding:
+        # only move the local artifact to cache if it was not newly created
+        local_path_cache = ln_setup.settings.storage.cache_dir / local_path.name
+        # don't use Path.rename here because of cross-device link error
+        # https://laminlabs.slack.com/archives/C04A0RMA0SC/p1710259102686969
+        shutil.move(
+            local_path,  # type: ignore
+            local_path_cache,
+        )
+        logger.important(f"moved local artifact to cache: {local_path_cache}")
+    return self
 
 
 def _save_skip_storage(file, **kwargs) -> None:

lamindb/_finish.py

@@ -121,7 +121,11 @@ def save_run_context_core(
         # first, copy the notebook file to a temporary file in the cache
         source_code_path = ln_setup.settings.storage.cache_dir / filepath.name
         shutil.copy2(filepath, source_code_path)  # copy
-        subprocess.run(f"nbstripout '{source_code_path}'", shell=True, check=True)
+        subprocess.run(
+            f"nbstripout '{source_code_path}' --extra-keys='metadata.version metadata.kernelspec metadata.language_info metadata.pygments_lexer metadata.name metadata.file_extension'",
+            shell=True,
+            check=True,
+        )
     # find initial versions of source codes and html reports
     prev_report = None
     prev_source = None
@@ -149,7 +153,7 @@ def save_run_context_core(
                 response = "y"
             if response == "y":
                 transform.source_code.replace(source_code_path)
-                transform.source_code.save()
+                transform.source_code.save(upload=True)
             else:
                 logger.warning("Please re-run `ln.track()` to make a new version")
                 return "rerun-the-notebook"
@@ -162,7 +166,7 @@ def save_run_context_core(
             visibility=0,  # hidden file
             run=False,
         )
-        source_code.save()
+        source_code.save(upload=True)
         transform.source_code = source_code
         logger.success(f"saved transform.source_code: {transform.source_code}")
     # track environment
@@ -175,7 +179,7 @@ def save_run_context_core(
             run=False,
         )
         if artifact._state.adding:
-            artifact.save()
+            artifact.save(upload=True)
         run.environment = artifact
         logger.success(f"saved run.environment: {run.environment}")
     # save report file
@@ -187,7 +191,7 @@ def save_run_context_core(
                 "there is already an existing report for this run, replacing it"
             )
             run.report.replace(filepath_html)
-            run.report.save()
+            run.report.save(upload=True)
         else:
             report_file = ln.Artifact(
                 filepath_html,
@@ -196,7 +200,7 @@ def save_run_context_core(
                 visibility=0,  # hidden file
                 run=False,
             )
-            report_file.save()
+            report_file.save(upload=True)
             run.report = report_file
         run.is_consecutive = is_consecutive
         if finished_at:

lamindb/_registry.py

@@ -113,7 +113,7 @@ def __init__(orm: Registry, *args, **kwargs):
                     logger.warning(
                         f"loaded {orm.__class__.__name__} record with same"
                         f" name{version_comment}: '{kwargs['name']}' "
-                        "(disable via ln.settings.upon_create_search_names)"
+                        "(disable via `ln.settings.upon_create_search_names`)"
                     )
                     init_self_from_db(orm, existing_record)
                     return None
@@ -498,7 +498,7 @@ def transfer_to_default_db(
 
 
 # docstring handled through attach_func_to_class_method
-def save(self, *args, **kwargs) -> None:
+def save(self, *args, **kwargs) -> Registry:
     using_key = None
     if "using" in kwargs:
         using_key = kwargs["using"]
@@ -540,6 +540,7 @@ def save(self, *args, **kwargs) -> None:
             self.features._add_from(self_on_db, **add_from_kwargs)
             logger.info("transfer labels")
             self.labels.add_from(self_on_db, **add_from_kwargs)
+    return self
 
 
 METHOD_NAMES = [

lamindb/_save.py

@@ -291,7 +291,9 @@ def upload_artifact(
         and artifact._memory_rep is not None
     ):
         logger.save(msg)
-        print_progress = partial(print_hook, filepath=storage_path, action="uploading")
+        print_progress = partial(
+            print_hook, objectname=storage_path.name, action="uploading"
+        )
         write_adata_zarr(artifact._memory_rep, storage_path, callback=print_progress)
     elif hasattr(artifact, "_to_store") and artifact._to_store:
         logger.save(msg)

lamindb/core/_run_context.py

@@ -3,16 +3,11 @@ from __future__ import annotations
 import builtins
 import hashlib
 import os
-import re
-import subprocess
-import sys
 from datetime import datetime, timezone
 from pathlib import Path, PurePath
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 from lamin_utils import logger
-from lamindb_setup import settings as setup_settings
-from lamindb_setup.core import InstanceSettings
 from lnschema_core import Run, Transform, ids
 from lnschema_core.types import TransformType
 from lnschema_core.users import current_user_id
@@ -59,42 +54,6 @@ def get_uid_ext(version: str) -> str:
     return encodebytes(hashlib.md5(version.encode()).digest())[:4]
 
 
-def get_stem_uid_and_version_from_file(file_path: Path) -> tuple[str, str]:
-    # line-by-line matching might be faster, but let's go with this for now
-    with open(file_path) as file:
-        content = file.read()
-
-    if file_path.suffix == ".py":
-        stem_uid_pattern = re.compile(
-            r'\.transform\.stem_uid\s*=\s*["\']([^"\']+)["\']'
-        )
-        version_pattern = re.compile(r'\.transform\.version\s*=\s*["\']([^"\']+)["\']')
-    elif file_path.suffix == ".ipynb":
-        stem_uid_pattern = re.compile(
-            r'\.transform\.stem_uid\s*=\s*\\["\']([^"\']+)\\["\']'
-        )
-        version_pattern = re.compile(
-            r'\.transform\.version\s*=\s*\\["\']([^"\']+)\\["\']'
-        )
-    else:
-        raise ValueError("Only .py and .ipynb files are supported.")
-
-    # Search for matches in the entire file content
-    stem_uid_match = stem_uid_pattern.search(content)
-    version_match = version_pattern.search(content)
-
-    # Extract values if matches are found
-    stem_uid = stem_uid_match.group(1) if stem_uid_match else None
-    version = version_match.group(1) if version_match else None
-
-    if stem_uid is None or version is None:
-        raise SystemExit(
-            f"ln.settings.transform.stem_uid and ln.settings.transform.version aren't set in {file_path}\n"
-            "Call ln.track() and copy/paste the output into the notebook"
-        )
-    return stem_uid, version
-
-
 def update_stem_uid_or_version(
     stem_uid: str,
     version: str,

lamindb/core/_settings.py

@@ -5,7 +5,7 @@ from typing import TYPE_CHECKING, Literal, Mapping
 
 import lamindb_setup as ln_setup
 from lamin_utils import logger
-from lamindb_setup._add_remote_storage import switch_default_storage
+from lamindb_setup._add_remote_storage import add_managed_storage
 from lamindb_setup.core._settings import settings as setup_settings
 from lamindb_setup.core._settings_instance import sanitize_git_repo_url
 
@@ -92,11 +92,11 @@ class Settings:
         self.__using_key = value
 
     @property
-    def _storage_settings(self) -> ln_setup.dev.StorageSettings:
+    def _storage_settings(self) -> ln_setup.core.StorageSettings:
         if self._using_storage is None:
             storage_settings = ln_setup.settings.storage
         else:
-            storage_settings = ln_setup.dev.StorageSettings(root=self._using_storage)
+            storage_settings = ln_setup.core.StorageSettings(root=self._using_storage)
         return storage_settings
 
     @property
@@ -127,7 +127,7 @@ class Settings:
 
         Examples:
 
-        You can set the root via:
+        You can switch to another managed storage location via:
 
         >>> ln.settings.storage = "s3://some-bucket"
 
@@ -143,14 +143,27 @@ class Settings:
 
     @storage.setter
     def storage(self, path_kwargs: str | Path | UPath | tuple[str | UPath, Mapping]):
-        logger.warning(
-            "you'll no longer be able to set arbitrary storage locations soon"
-        )
         if isinstance(path_kwargs, tuple):
             path, kwargs = path_kwargs
         else:
             path, kwargs = path_kwargs, {}
-        switch_default_storage(path, **kwargs)
+        add_managed_storage(path, **kwargs)
+
+    @property
+    def storage_local(self) -> Path:
+        """An additional local default storage (a path to its root).
+
+        Is only available if :attr:`~lamindb.setup.core.InstanceSettings.keep_artifacts_local` is enabled.
+
+        Guide: :doc:`faq/keep-artifacts-local`
+
+        Shortcut for: `ln.setup.settings.instance.storage_local.root`
+        """
+        return ln_setup.settings.instance.storage_local.root
+
+    @storage_local.setter
+    def storage_local(self, local_root: Path):
+        ln_setup.settings.instance.storage_local = local_root
 
     @property
     def verbosity(self) -> str:
@@ -162,8 +175,6 @@ class Settings:
         - 'info': 💡 also show info messages
         - 'hint': 💡 also show hint messages
         - 'debug': 🐛 also show detailed debug messages
-
-        This is based on Scanpy's and Django's verbosity setting.
         """
         return VERBOSITY_TO_STR[self._verbosity_int]
 

lamindb/core/storage/paths.py

@@ -75,9 +75,6 @@ def attempt_accessing_path(
                 settings.storage, access_token=access_token
             )
     else:
-        logger.debug(
-            "artifact.path is slightly slower for files outside default storage"
-        )
         if artifact._state.db not in ("default", None) and using_key is None:
             storage = (
                 Storage.using(artifact._state.db).filter(id=artifact.storage_id).one()
@@ -141,8 +138,14 @@ def delete_storage(storagepath: Path):
     # replace with check_path_is_child_of_root but this needs to first be debugged
     # if not check_path_is_child_of_root(storagepath, settings.storage):
     if not storagepath.is_relative_to(settings.storage):  # type: ignore
-        logger.warning("couldn't delete files outside of default storage")
-        return "did-not-delete"
+        allow_delete = False
+        if setup_settings.instance.keep_artifacts_local:
+            allow_delete = storagepath.is_relative_to(
+                setup_settings.instance.storage_local.root
+            )
+        if not allow_delete:
+            logger.warning("couldn't delete files outside of default storage")
+            return "did-not-delete"
     # only delete files in the default storage
     if storagepath.is_file():
         storagepath.unlink()

{lamindb-0.70.4.dist-info → lamindb-0.71.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.70.4
+Version: 0.71.0
 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==0.65.2
-Requires-Dist: lamindb_setup==0.70.0
+Requires-Dist: lnschema_core==0.66.0
+Requires-Dist: lamindb_setup==0.71.0
 Requires-Dist: lamin_utils==0.13.2
-Requires-Dist: lamin_cli==0.12.3
+Requires-Dist: lamin_cli==0.13.0
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -23,10 +23,7 @@ Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
-Requires-Dist: urllib3<2 ; extra == "aws"
-Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"
-Requires-Dist: s3fs==2023.12.2 ; extra == "aws"
-Requires-Dist: fsspec[s3]==2023.12.2 ; extra == "aws"
+Requires-Dist: lamindb_setup[aws] ; extra == "aws"
 Requires-Dist: bionty==0.42.9 ; extra == "bionty"
 Requires-Dist: pandas<2 ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
@@ -39,7 +36,7 @@ Requires-Dist: nbproject_test>=0.5.1 ; extra == "dev"
 Requires-Dist: faker-biology ; extra == "dev"
 Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
-Requires-Dist: fsspec[gs]==2023.12.2 ; extra == "gcp"
+Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
 Requires-Dist: nbproject==0.10.0 ; extra == "jupyter"
 Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"

{lamindb-0.70.4.dist-info → lamindb-0.71.0.dist-info}/RECORD

@@ -1,20 +1,20 @@
-lamindb/__init__.py,sha256=n_WJSqcrctVzdr83pL8gZ--FI9vu1ZoqTL5AXEdq8LA,2163
+lamindb/__init__.py,sha256=T_mLeXTbOSi7s2DSoGxF-FrVBCSQLvBj5t02ueRNWSI,2182
 lamindb/_annotate.py,sha256=kgbilILfgzoS-GEpjxzVwRMs7CoSa9BNEcIWXFBW69I,43915
-lamindb/_artifact.py,sha256=E104JM5_Brw7BxJLBTE0acl7Oz7j5R7pPgVgrbHz79I,39279
+lamindb/_artifact.py,sha256=875jV8J-GgvhoscWPmg73ogTa9rAVHQdAqc3V8S46Sc,40157
 lamindb/_can_validate.py,sha256=nvoZG-35n3HofkY4Xc6hBv9AV54_RDan7Hzp5TuqY9I,14709
 lamindb/_collection.py,sha256=SDM35R_5WHrgLKjVb14Q8-Rz_gn5hdZLJobPcanm4PM,14627
 lamindb/_feature.py,sha256=srAKchY7gqD-h-cWlEiAWuHlpFKFwv0PWIA-JX0Go8c,6758
 lamindb/_feature_set.py,sha256=AzjOcHzQajpeikPOAic-aj0z_C5b7VpHVegg3ThRSLw,9045
 lamindb/_filter.py,sha256=xnjJzjF3Zj4dK_Kfymvhgczk27MhhXz5ZYc7XINbgHY,1331
-lamindb/_finish.py,sha256=oR7oe6By3vEhF0twDBqSdT1EF28MPhyiS_cfZP0CcCw,8040
+lamindb/_finish.py,sha256=iUo6j89_hTP-OuRfUAj_i1YB1B5FU9QTtwxXKdX_J_4,8279
 lamindb/_from_values.py,sha256=DVXjnQ2wwNw-2bFzy0uXLdVlqoprrn95hTnrXwn-KqM,12638
 lamindb/_is_versioned.py,sha256=0PgRCmxEmYDcAjllLSOYZm132B1lW6QgmBBERhRyFt0,1341
 lamindb/_parents.py,sha256=N9T8jbd3eaoHDLE9TD1y1QgGcO81E6Brapy8LILzRCQ,14790
 lamindb/_query_manager.py,sha256=3zokXqxgj9vTJBnN2sbYKS-q69fyDDPF_aGq_rFHzXU,4066
 lamindb/_query_set.py,sha256=K_0rJ6Keltl3Pvglvd7kkzkJEy2u6Kp0TKiHLzwqH18,11359
-lamindb/_registry.py,sha256=-Bv10zSr6IY7QM5pu_35NiVjQDJnBcXRECVe9h7GEuY,19336
+lamindb/_registry.py,sha256=fmX-BUnan3Y0WrEAx3qNwRYCIJwJgjoKnRnpgcXujEI,19358
 lamindb/_run.py,sha256=b7A52M1On3QzFgIYyfQoz5Kk7V3wcu9p_Prq5bzd8v8,1838
-lamindb/_save.py,sha256=C4sPr0slgMmxDdiOcaLhIiHOqW9c3DnIz1uj9NlsnXQ,11431
+lamindb/_save.py,sha256=r-pUKi2xBW25brIMzDbf8iI-4xggX-X2C9cIYHzK1uI,11460
 lamindb/_storage.py,sha256=VW8xq3VRv58-ciholvOdlcgvp_OIlLxx5GxLt-e2Irs,614
 lamindb/_transform.py,sha256=rxojJ91qQSkeYDHYbwqjFAYxBMgJd3cq_K7Z0n5g8Aw,3482
 lamindb/_ulabel.py,sha256=e5dw9h1tR0_u-DMn7Gzx0WhUhV5w7j4v3QbnLWQV7eI,1941
@@ -25,8 +25,8 @@ lamindb/core/_data.py,sha256=xULvge-txEO4r4amNQZRZTH3n3BqOLWauyNfxbB6WOA,17674
 lamindb/core/_feature_manager.py,sha256=LlYgU71AoTnrseWFCq-oZkUAYWITtRR7BNFm0AhHe-c,15773
 lamindb/core/_label_manager.py,sha256=0RtegYnK3zIisOnd970EobOrHMpp7OCH-mEoPrPXw2c,9075
 lamindb/core/_mapped_collection.py,sha256=_OwFZh5SePDUD70XIK5kngv3we_Z5-YdGHNfpUSatSQ,19469
-lamindb/core/_run_context.py,sha256=tqKPNkryy4yc7vtYSIfGjUu_pJSBQt1Kx8Cbq9vwXK8,17726
-lamindb/core/_settings.py,sha256=r9si7wJb31tI4vfz9dUN4iXe6QQU7FjnqAEsHy2UDzM,5727
+lamindb/core/_run_context.py,sha256=zwsaq1iW3yb8Y6IjpWzqUL3e0i4l1bnmPF6V2USMqpI,16155
+lamindb/core/_settings.py,sha256=lhfn6gRjZw0atrA5Hr34m1nkPFXd8DAUMEesCGat1tA,6130
 lamindb/core/_sync_git.py,sha256=IlTqw55inPp_RZbN_YScaCeKza7LeF9mClQw55W3_d4,3921
 lamindb/core/_track_environment.py,sha256=xLZ6kgzxWS6MWZ5LQ_wkbJX99vmYOT8iQ-Fz4OHCgWw,754
 lamindb/core/_transform_settings.py,sha256=eV96QKX9jOojjzF-a0oo0wXQsMXN2F6QV7orE06oFC8,161
@@ -44,12 +44,12 @@ lamindb/core/storage/_backed_access.py,sha256=eManrLsu3pSSQAyAKy47FDBm-iHgjaNfHA
 lamindb/core/storage/_valid_suffixes.py,sha256=sewRRU3I6fJ-Jd5ACNcco_o3hic9zmqTs8BuZui-450,133
 lamindb/core/storage/_zarr.py,sha256=5ceEz6YIvgvUnVVNWhK5Z4W0WfrvyvY82Yna5jSX1_E,3661
 lamindb/core/storage/objects.py,sha256=5LbBeZVKuOOB8DceSE-PN8elKY0N9OhFXZPQJE4lK48,1538
-lamindb/core/storage/paths.py,sha256=kvu4Xi4dvreXpg4iuskN_nd2yyGmEdCmoIfi3nCrTyo,7728
+lamindb/core/storage/paths.py,sha256=ib50kmRGhjRTHak20i94ruXVqLL9xQnQuqJSHEW50Q8,7866
 lamindb/integrations/__init__.py,sha256=aH2PmO2m4-vwIifMYTB0Fyyr_gZWtVnV71jT0tVWSw0,123
 lamindb/integrations/_vitessce.py,sha256=b0FqTBsP-M6Q7xCYXVwFwM8DOIeeOBZEhYbryhtq4gk,2535
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.70.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.70.4.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.70.4.dist-info/METADATA,sha256=tpsQ0FARcje5BTONwg1mer7gucqwICMw1RmApXGME0I,2835
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