lamindb 0.76.4__py3-none-any.whl → 0.76.5__py3-none-any.whl

lamindb/__init__.py

@@ -41,7 +41,7 @@ Modules and settings.
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.76.4"
+__version__ = "0.76.5"
 
 import os as _os
 
@@ -108,6 +108,6 @@ if _check_instance_setup(from_lamindb=True):
     track = context.track  # backward compat
     finish = context.finish  # backward compat
     Curate = Curator  # backward compat
-    settings.__doc__ = """Global :class:`~lamindb.core.Settings`."""
-    context.__doc__ = """Global :class:`~lamindb.core.Context`."""
+    settings.__doc__ = """Global settings (:class:`~lamindb.core.Settings`)."""
+    context.__doc__ = """Global run context (:class:`~lamindb.core.Context`)."""
     from django.db.models import Q

lamindb/_finish.py

@@ -94,6 +94,7 @@ def save_context_core(
     transform: Transform,
     filepath: Path,
     finished_at: bool = False,
+    ignore_non_consecutive: bool | None = None,
     from_cli: bool = False,
 ) -> str | None:
     import lamindb as ln
@@ -118,17 +119,18 @@ def save_context_core(
             logger.error("install nbproject & jupytext: pip install nbproject jupytext")
             return None
         notebook_content = read_notebook(filepath)  # type: ignore
-        is_consecutive = check_consecutiveness(
-            notebook_content, calling_statement=".finish()"
-        )
-        if not is_consecutive:
-            msg = "   Do you still want to proceed with finishing? (y/n) "
-            if os.getenv("LAMIN_TESTING") is None:
-                response = input(msg)
-            else:
-                response = "n"
-            if response != "y":
-                return "aborted-non-consecutive"
+        if not ignore_non_consecutive:  # ignore_non_consecutive is None or False
+            is_consecutive = check_consecutiveness(
+                notebook_content, calling_statement=".finish()"
+            )
+            if not is_consecutive:
+                response = "n"  # ignore_non_consecutive == False
+                if ignore_non_consecutive is None:
+                    response = input(
+                        "   Do you still want to proceed with finishing? (y/n) "
+                    )
+                if response != "y":
+                    return "aborted-non-consecutive"
         # write the report
         report_path = ln_setup.settings.storage.cache_dir / filepath.name.replace(
             ".ipynb", ".html"
@@ -144,23 +146,20 @@ def save_context_core(
     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
+        or transform.source_code is not None  # equivalent to transform.hash 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)
-        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(
-                    f"You are about to replace (overwrite) existing source code (hash '{transform._source_code_artifact.hash}') for transform version"
-                    f" '{transform.version}'. Proceed? (y/n)"
-                )
-            else:
-                response = "y"
+        ref_hash = (
+            transform.hash
+            if transform.hash is not None
+            else transform._source_code_artifact.hash
+        )
+        if hash != ref_hash:
+            response = input(
+                f"You are about to overwrite existing source code (hash '{ref_hash}') for Transform('{transform.uid}')."
+                f"Proceed? (y/n)"
+            )
             if response == "y":
                 transform.source_code = source_code_path.read_text()
                 transform.hash = hash
@@ -210,13 +209,9 @@ def save_context_core(
         if run.report_id is not None:
             hash, _ = hash_file(report_path)  # ignore hash_type for now
             if hash != run.report.hash:
-                if os.getenv("LAMIN_TESTING") is None:
-                    # in test, auto-confirm overwrite
-                    response = input(
-                        f"You are about to replace (overwrite) an existing run report (hash '{run.report.hash}'). Proceed? (y/n)"
-                    )
-                else:
-                    response = "y"
+                response = input(
+                    f"You are about to overwrite an existing report (hash '{run.report.hash}') for Run('{run.uid}'). Proceed? (y/n)"
+                )
                 if response == "y":
                     run.report.replace(report_path)
                     run.report.save(upload=True)

lamindb/_transform.py

@@ -37,8 +37,11 @@ def __init__(transform: Transform, *args, **kwargs):
             "Only name, key, version, type, revises, reference, "
             f"reference_type can be passed, but you passed: {kwargs}"
         )
-    if revises is None and key is not None:
-        revises = Transform.filter(key=key).order_by("-created_at").first()
+    if revises is None:
+        if key is not None:
+            revises = Transform.filter(key=key).order_by("-created_at").first()
+        elif uid is not None and not uid.endswith("0000"):
+            revises = Transform.filter(uid__startswith=uid[:-4]).one_or_none()
     if revises is not None and key is not None and revises.key != key:
         note = message_update_key_in_version_family(
             suid=revises.stem_uid,

lamindb/core/_context.py

@@ -7,6 +7,7 @@ from datetime import datetime, timezone
 from pathlib import Path, PurePath
 from typing import TYPE_CHECKING
 
+import lamindb_setup as ln_setup
 from lamin_utils import logger
 from lamindb_setup.core.hashing import hash_file
 from lnschema_core import Run, Transform, ids
@@ -111,7 +112,18 @@ def pretty_pypackages(dependencies: dict) -> str:
 class Context:
     """Run context.
 
-    Bundles all metadata to track run contexts.
+    Enables convenient data lineage tracking by managing a transform & run
+    upon :meth:`~lamindb.core.Context.track` & :meth:`~lamindb.core.Context.finish`.
+
+    Examples:
+
+        Is typically used via :class:`~lamindb.context`:
+
+        >>> import lamindb as ln
+        >>> ln.context.track()
+        >>> # do things while tracking data lineage
+        >>> ln.context.finish()
+
     """
 
     def __init__(self):
@@ -165,42 +177,35 @@ class Context:
         self,
         *,
         params: dict | None = None,
-        transform: Transform | None = None,
         new_run: bool | None = None,
         path: str | None = None,
+        transform: Transform | None = None,
     ) -> None:
-        """Track notebook or script run.
+        """Starts data lineage tracking for a run.
 
-        Creates or loads a global :class:`~lamindb.Run` that enables data
-        lineage tracking.
+        - sets :attr:`~lamindb.core.Context.transform` &
+          :attr:`~lamindb.core.Context.run` by creating or loading `Transform` &
+          `Run` records
+        - saves compute environment as a `requirements.txt` file: `run.environment`
 
-        Saves source code and compute environment.
-
-        If :attr:`~lamindb.core.Settings.sync_git_repo` is set, will first check
-        whether the script exists in the git repository and add a link.
+        If :attr:`~lamindb.core.Settings.sync_git_repo` is set, checks whether a
+        script-like transform exists in a git repository and links it.
 
         Args:
             params: A dictionary of parameters to track for the run.
-            transform: Can be of type `"pipeline"` or `"notebook"`
-                (:class:`~lamindb.core.types.TransformType`).
             new_run: If `False`, loads latest run of transform
                 (default notebook), if `True`, creates new run (default pipeline).
             path: Filepath of notebook or script. Only needed if it can't be
                 automatically detected.
+            transform: Useful to track an abstract pipeline.
 
         Examples:
 
-            To track a notebook or script, call:
+            To track the run of a notebook or script, call:
 
             >>> import lamindb as ln
             >>> ln.context.track()
 
-            If you'd like to track an abstract pipeline run, pass a
-            :class:`~lamindb.Transform` object of ``type`` ``"pipeline"``:
-
-            >>> ln.Transform(name="Cell Ranger", version="2", type="pipeline").save()
-            >>> transform = ln.Transform.get(name="Cell Ranger", version="2")
-            >>> ln.context.track(transform=transform)
         """
         self._path = None
         if transform is None:
@@ -488,10 +493,31 @@ class Context:
                 self._logging_message += f"loaded Transform('{transform.uid}')"
         self._transform = transform
 
-    def finish(self) -> None:
-        """Mark a tracked run as finished.
+    def finish(self, ignore_non_consecutive: None | bool = None) -> None:
+        """Mark the run context as finished.
+
+        - writes a timestamp: `run.finished_at`
+        - saves the source code: `transform.source_code`
+
+        When called in the last cell of a notebook:
+
+        - prompts for user input if not consecutively executed
+        - requires to save the notebook in your editor
+        - saves a run report: `run.report`
+
+        Args:
+            ignore_non_consecutive: Whether to ignore if a notebook was non-consecutively executed.
+
+        Examples:
+
+            >>> import lamindb as ln
+            >>> ln.context.track()
+            >>> # do things while tracking data lineage
+            >>> ln.context.finish()
+
+        See Also:
+            `lamin save script.py` or `lamin save notebook.ipynb` → `docs </cli#lamin-save>`__
 
-        Saves source code and, for notebooks, a run report to your default storage location.
         """
         from lamindb._finish import save_context_core
 
@@ -510,18 +536,16 @@ class Context:
             # nothing else to do
             return None
         if is_run_from_ipython:  # notebooks
-            if (
-                get_seconds_since_modified(context._path) > 3
-                and os.getenv("LAMIN_TESTING") is None
-            ):
+            if get_seconds_since_modified(context._path) > 2 and not ln_setup._TESTING:
                 raise NotebookFileNotSavedToDisk(
-                    "Please save the notebook manually in your editor right before running `ln.finish()`"
+                    "Please save the notebook manually in your editor right before running `ln.context.finish()`"
                 )
         save_context_core(
             run=context.run,
             transform=context.run.transform,
             filepath=context._path,
             finished_at=True,
+            ignore_non_consecutive=ignore_non_consecutive,
         )
 
 

lamindb/integrations/_vitessce.py

@@ -73,12 +73,16 @@ def save_vitessce_config(
                 )
             else:
                 dataset_artifacts.append(artifact)
-    # link inputs
+    # the below will be replaced with a `ln.tracked()` decorator soon
     with logger.mute():
-        transform = Transform(name="save_vitessce_config", type="function", version="2")
+        transform = Transform(
+            uid="kup03MJBsIVa0001",
+            name="save_vitessce_config",
+            type="function",
+            version="2",
+        )
         transform.save()
-    run = Run(transform=transform)
-    run.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

{lamindb-0.76.4.dist-info → lamindb-0.76.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.4
+Version: 0.76.5
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -10,9 +10,9 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Requires-Dist: lnschema_core==0.73.5
-Requires-Dist: lamindb_setup==0.76.8
+Requires-Dist: lamindb_setup==0.77.1
 Requires-Dist: lamin_utils==0.13.4
-Requires-Dist: lamin_cli==0.17.0
+Requires-Dist: lamin_cli==0.17.1
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0

{lamindb-0.76.4.dist-info → lamindb-0.76.5.dist-info}/RECORD

@@ -1,4 +1,4 @@
-lamindb/__init__.py,sha256=faIPIM0ynMz0AU9pziDSQJT-rQhUXqpJ3PWRlmijqbs,2319
+lamindb/__init__.py,sha256=jllkTTXtX6UHCCnv7BvPAywnywCNWlWm0l5UbCnK9nM,2344
 lamindb/_artifact.py,sha256=QjCge5kaAcfhGv84s299OT99LmHTSYDxgzw5kN-x3-8,44416
 lamindb/_can_validate.py,sha256=9di9FLmC2m3dpT42sceF34UEFzQITi2e_hjVMa8DIc4,18261
 lamindb/_collection.py,sha256=F_VgpLBprrzUQ-tPngWvO9vFd7jX66MVwIi031JOris,14871
@@ -6,7 +6,7 @@ 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=NEZmTW7sWzwi-QYTwVgoOeeD-pZxWBrZOITK_YoJreU,9434
+lamindb/_finish.py,sha256=riwm7mA-RXej_L0iz_svt6j5Z6faQb3NmQGKjAwhx8g,9282
 lamindb/_from_values.py,sha256=8kYpR8Q85EOaTcsPGjVHeZh29fGVgum5OEQf4Hsz_80,13533
 lamindb/_is_versioned.py,sha256=5lAnhTboltFkZCKVRV1uxkm0OCjJz_HKi3yQq_vEuMs,1306
 lamindb/_parents.py,sha256=eMavdd6IO6STOVJSlR2TzdRtx6sKYDKsMOtlR3DZlgQ,15599
@@ -16,12 +16,12 @@ 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=Rgj8uq6t4NpyP7DtQ-0IRJs7vSEKHyWftY5dvwKNFgs,4063
+lamindb/_transform.py,sha256=ekwHQc4fv8PV1cffCYtTPfxL1RJtENd9_Y3v9CwxqYc,4213
 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=hxPWM_Jnrllx0G_6itEGU2meXwptkkgiL9zsBvlhHM4,1495
-lamindb/core/_context.py,sha256=U-vmMH4s0ZfvS6KBRj5mOsOFuvcioJ7FgUdn0OOkLvA,19972
+lamindb/core/_context.py,sha256=zt4aJz_IxPu3ujENyPjwJCebh_3w5Vu6QkDh0dspZFA,20719
 lamindb/core/_data.py,sha256=eocOXsZGu62LPtz6yIlvHhPSJTf3yF2ITZTffyflWYI,16269
 lamindb/core/_feature_manager.py,sha256=94tX6gq_Rx7fkDARQBxB2z92qUDpHocFSAdKv5izMT4,32490
 lamindb/core/_label_manager.py,sha256=zCE-PS1Y5ALpzoSOx1P6ZTFVPgFNRAmmyTQF0e8QBXA,9131
@@ -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
-lamindb/integrations/_vitessce.py,sha256=4DM_EXe-o7BVmX7QGTiwREWMHDzAtOqpqDvL70xQKfE,4451
+lamindb/integrations/_vitessce.py,sha256=671jHIF8LgUjcOgRvJNhP0aK1Xty9pHkQ8ukx1U2gLY,4578
 lamindb/setup/__init__.py,sha256=OwZpZzPDv5lPPGXZP7-zK6UdO4FHvvuBh439yZvIp3A,410
 lamindb/setup/core/__init__.py,sha256=SevlVrc2AZWL3uALbE5sopxBnIZPWZ1IB0NBDudiAL8,167
-lamindb-0.76.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-lamindb-0.76.4.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-lamindb-0.76.4.dist-info/METADATA,sha256=X_O43XFARj0Vg5pAgez5uCI4IQG5jUp6cqd_pMAc0YQ,2372
-lamindb-0.76.4.dist-info/RECORD,,
+lamindb-0.76.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+lamindb-0.76.5.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
+lamindb-0.76.5.dist-info/METADATA,sha256=lmB6jhR6ZnklsigeYZFeCiNWMyGHqStcg_teeo1JmNk,2372
+lamindb-0.76.5.dist-info/RECORD,,