lamindb 0.76.4__tar.gz → 0.76.5__tar.gz

{lamindb-0.76.4 → lamindb-0.76.5}/.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
-blank_issues_enabled: false
+blank_issues_enabled: true
 contact_links:
     - name: LaminHub issues
       url: https://github.com/laminlabs/laminhub-public

{lamindb-0.76.4 → lamindb-0.76.5}/PKG-INFO

@@ -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 → lamindb-0.76.5}/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-0.76.4 → lamindb-0.76.5}/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-0.76.4 → lamindb-0.76.5}/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-0.76.4 → lamindb-0.76.5}/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-0.76.4 → lamindb-0.76.5}/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 → lamindb-0.76.5}/noxfile.py

@@ -57,7 +57,7 @@ def install(session):
         "./sub/bionty",
     ]
     top_deps = [
-        "./sub/lamindb[aws,bionty,jupyter]",
+        ".[aws,bionty,jupyter]",
     ]
     cmds = [
         f"uv pip install {'--system' if CI else ''} --no-cache-dir {' '.join(base_deps)}",

{lamindb-0.76.4 → lamindb-0.76.5}/pyproject.toml

@@ -17,9 +17,9 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lnschema_core==0.73.5",
-    "lamindb_setup==0.76.8",
+    "lamindb_setup==0.77.1",
     "lamin_utils==0.13.4",
-    "lamin_cli==0.17.0",
+    "lamin_cli==0.17.1",
     # others
     "rapidfuzz",
     "pyarrow",

lamindb-0.76.5/sub/lamin-cli/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
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lamindb-0.76.5/sub/lamin-cli/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "0.17.1"

{lamindb-0.76.4 → lamindb-0.76.5}/sub/lamin-cli/lamin_cli/__main__.py

@@ -96,35 +96,51 @@ def main():
 
 
 @main.command()
-@click.argument("user", type=str)
-@click.option("--key", type=str, default=None, help="API key")
+@click.argument("user", type=str, default=None, required=False)
+@click.option("--key", type=str, default=None, help="The API key.")
 def login(user: str, key: Optional[str]):
     """Log into LaminHub.
 
-    Upon logging in the first time, you need to pass your API key via
+    Upon logging in the first time, you need to pass your API key via:
 
     ```
     lamin login myemail@acme.com --key YOUR_API_KEY
     ```
 
-    You'll find your API key in the top right corner under "Settings".
+    You'll find your API key on LaminHub in the top right corner under "Settings".
 
     After this, you can either use `lamin login myhandle` or `lamin login myemail@acme.com`
+
+    You can also call this without arguments:
+
+    ```
+    lamin login
+    ```
+
+    You will be prompted for your Beta API key unless you set an environment variable `LAMIN_API_KEY`.
     """
     from lamindb_setup._setup_user import login
 
-    return login(user, key=key)
+    if user is None:
+        if "LAMIN_API_KEY" in os.environ:
+            api_key = os.environ["LAMIN_API_KEY"]
+        else:
+            api_key = input("Your API key: ")
+    else:
+        api_key = None
+
+    return login(user, key=key, api_key=api_key)
 
 
 # fmt: off
 @main.command()
-@click.option("--storage", type=str, help="local dir, s3://bucket_name, gs://bucket_name")  # noqa: E501
-@click.option("--db", type=str, default=None, help="postgres database connection URL, do not pass for SQLite")  # noqa: E501
-@click.option("--schema", type=str, default=None, help="comma-separated string of schema modules")  # noqa: E501
-@click.option("--name", type=str, default=None, help="instance name")
+@click.option("--storage", type=str, help="Local directory, s3://bucket_name, gs://bucket_name.")  # noqa: E501
+@click.option("--db", type=str, default=None, help="Postgres database connection URL, do not pass for SQLite.")  # noqa: E501
+@click.option("--schema", type=str, default=None, help="Comma-separated string of schema modules.")  # noqa: E501
+@click.option("--name", type=str, default=None, help="The instance name.")
 # fmt: on
 def init(storage: str, db: Optional[str], schema: Optional[str], name: Optional[str]):
-    """Init a lamindb instance."""
+    """Init a LaminDB instance."""
     from lamindb_setup._init_instance import init as init_
 
     return init_(storage=storage, db=db, schema=schema, name=name)
@@ -188,12 +204,25 @@ def logout():
 
 
 @main.command()
-@click.argument("url", type=str)
-def get(url: str):
-    """Get an object from a lamin.ai URL."""
+@click.argument("entity", type=str)
+@click.option("--uid", help="Filter by creator")
+@click.option("--key", help="The key for the entity")
+def get(entity: str, uid: str = None, key: str = None):
+    """Query an entity.
+
+    Pass a lamin.ai URL, 'artifact', or 'transform', for example:
+
+    ```
+    lamin get https://lamin.ai/account/instance/artifact/e2G7k9EVul4JbfsEYAy5
+    lamin get artifact --key mydatasets/mytable.parquet
+    lamin get artifact --uid e2G7k9EVul4JbfsEYAy5
+    lamin get transform --key analysis.ipynb
+    lamin get transform --uid Vul4JbfsEYAy5
+    ```
+    """
     from lamin_cli._get import get
 
-    return get(url)
+    return get(entity, uid, key)
 
 
 @main.command()