lamindb 0.76.10__tar.gz → 0.76.12__tar.gz

{lamindb-0.76.10 → lamindb-0.76.12}/.github/workflows/build.yml

@@ -107,7 +107,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: "3.10" # use 3.10, 3.8 and 3.11 give issues
-      - run: pip install -U laminci
+      - run: pip install "laminci@git+https://x-access-token:${{ secrets.LAMIN_BUILD_DOCS }}@github.com/laminlabs/laminci"
       - run: nox -s "install_ci(group='docs')"
       - uses: actions/download-artifact@v4
       - run: nox -s docs

{lamindb-0.76.10 → lamindb-0.76.12}/.gitmodules

@@ -16,3 +16,6 @@
 [submodule "sub/clinicore"]
 	path = sub/clinicore
 	url = https://github.com/laminlabs/clinicore
+[submodule "sub/findrefs"]
+	path = sub/findrefs
+	url = https://github.com/laminlabs/findrefs

{lamindb-0.76.10 → lamindb-0.76.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.10
+Version: 0.76.12
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9
@@ -8,10 +8,10 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: lnschema_core==0.74.6
-Requires-Dist: lamindb_setup==0.77.6
+Requires-Dist: lnschema_core==0.75.0
 Requires-Dist: lamin_utils==0.13.6
-Requires-Dist: lamin_cli==0.17.7
+Requires-Dist: lamin_cli==0.18.0
+Requires-Dist: lamindb_setup
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
@@ -23,7 +23,7 @@ Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.51.0 ; extra == "bionty"
+Requires-Dist: bionty==0.51.2 ; extra == "bionty"
 Requires-Dist: line_profiler ; extra == "dev"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"

{lamindb-0.76.10 → lamindb-0.76.12}/docs/api.md

@@ -18,6 +18,8 @@ cli
 lamindb
 bionty
 wetlab
+clinicore
+findrefs
 ```
 
 ```{toctree}

lamindb-0.76.12/docs/clinicore.md

@@ -0,0 +1,5 @@
+# `clinicore`
+
+```{eval-rst}
+.. automodule:: clinicore
+```

{lamindb-0.76.10 → lamindb-0.76.12}/docs/curate-any.ipynb

@@ -24,7 +24,7 @@
     "\n",
     "{class}`~lamindb.core.CanValidate` methods validate against the registries in your LaminDB instance.\n",
     "In {doc}`./bio-registries`, you'll see how to extend standard validation to validation against _public references_ using a `ReferenceTable` ontology object: `public = Record.public()`.\n",
-    "By default, {meth}`~lamindb.core.Record.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
+    "By default, {meth}`~lamindb.core.CanValidate.from_values` considers a match in a public reference a validated value for any {mod}`bionty` entity.\n",
     "\n",
     ":::"
    ]
@@ -131,7 +131,7 @@
    "source": [
     "Following the suggestions to register new labels:\n",
     "\n",
-    "Bulk creating records using {meth}`~lamindb.core.Record.from_values` only returns validated records:\n",
+    "Bulk creating records using {meth}`~lamindb.core.CanValidate.from_values` only returns validated records:\n",
     "\n",
     "Note: Terms validated with public reference are also created with `.from_values`, see {doc}`/bio-registries` for details."
    ]

lamindb-0.76.12/docs/findrefs.md

@@ -0,0 +1,5 @@
+# `findrefs`
+
+```{eval-rst}
+.. automodule:: findrefs
+```

{lamindb-0.76.10 → lamindb-0.76.12}/docs/scripts/run-track-with-params.py

@@ -10,8 +10,11 @@ if __name__ == "__main__":
     params = {
         "input_dir": args.input_dir,
         "learning_rate": args.learning_rate,
-        "downsample": args.downsample,
+        "preprocess_params": {
+            "downsample": args.downsample,
+            "normalization": "the_good_one",
+        },
     }
-    ln.track("JjRF4mACd9m00000", params=params)
+    ln.track("JjRF4mACd9m00001", params=params)
     # your code
     ln.finish()

{lamindb-0.76.10 → lamindb-0.76.12}/docs/setup.ipynb

@@ -254,25 +254,39 @@
    "source": [
     "`lamindb` mantains cache for cloud instances, i.e. instances having storage set to an AWS S3 bucket.\n",
     "\n",
-    "Cache directory can be accessed via {class}`lamindb.settings`.\n",
-    "\n",
-    "```\n",
-    "ln.settings.storage.cache_dir\n",
-    "```\n",
-    "\n",
-    "or print the cache directory path with CLI\n",
-    "\n",
-    "```\n",
-    "lamin cache get\n",
-    "```\n",
-    "\n",
-    "It can be configured using the settings\n",
-    "\n",
-    "```\n",
-    "ln.settings.storage.cache_dir = \"some/path/to/cache\"\n",
-    "```\n",
-    "\n",
-    "or using CLI\n",
+    "Cache directory can be accessed via {class}`lamindb.settings`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ln.settings.cache_dir"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "or print the cache directory path with CLI"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!lamin cache get"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "It can be also configured via \n",
     "\n",
     "```\n",
     "lamin cache set some/path/to/cache\n",

{lamindb-0.76.10 → lamindb-0.76.12}/docs/storage/prepare-transfer-local-to-cloud.ipynb

@@ -34,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.setup.init(storage=\"./test-transfer-to-cloud\", schema=\"bionty,wetlab\")\n",
+    "ln.setup.init(storage=\"./test-transfer-to-cloud\", schema=\"bionty,wetlab,findrefs\")\n",
     "ln.setup.settings.auto_connect = False"
    ]
   },

{lamindb-0.76.10 → lamindb-0.76.12}/docs/storage/vitessce.ipynb

@@ -82,7 +82,7 @@
     "vc = VitessceConfig(schema_version=\"1.0.15\")\n",
     "vc.add_dataset(name=\"test1\").add_object(\n",
     "    AnnDataWrapper(\n",
-    "        adata_url=dataset_artifact.path.to_url(),\n",
+    "        adata_artifact=dataset_artifact,\n",
     "        obs_embedding_paths=[\"obsm/X_umap\"],\n",
     "    ),\n",
     ")\n",
@@ -134,39 +134,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# use a corrupted suffix\n",
+    "# pass an artifact URL instead of the artifact object itself\n",
     "vc = VitessceConfig(schema_version=\"1.0.15\")\n",
-    "vc.add_dataset(name=\"test1\").add_object(\n",
-    "    AnnDataWrapper(\n",
-    "        adata_url=dataset_artifact.path.to_url() + \".random\",\n",
-    "        obs_embedding_paths=[\"obsm/X_umap\"],\n",
-    "    ),\n",
-    ")\n",
-    "with pytest.raises(ValueError) as error:\n",
-    "    ln.integrations.save_vitessce_config(vc)\n",
-    "print(error.exconly())\n",
-    "assert error.exconly().startswith(\"ValueError: Suffix should be '.zarr' or one of\")\n",
-    "assert error.exconly().endswith(\".random\")\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# use a corrupted stem_uid\n",
-    "vc = VitessceConfig(schema_version=\"1.0.15\")\n",
-    "vc.add_dataset(name=\"test1\").add_object(\n",
-    "    AnnDataWrapper(\n",
-    "        adata_url=dataset_artifact.path.to_url().replace(dataset_artifact.stem_uid, \"not-a-valid-uid\"),\n",
-    "        obs_embedding_paths=[\"obsm/X_umap\"],\n",
-    "    ),\n",
-    ")\n",
-    "with pytest.raises(ValueError) as error:\n",
-    "    ln.integrations.save_vitessce_config(vc)\n",
+    "with pytest.raises(AttributeError) as error:\n",
+    "    vc.add_dataset(name=\"test1\").add_object(\n",
+    "        AnnDataWrapper(\n",
+    "            adata_artifact=dataset_artifact.path.to_url(),\n",
+    "            obs_embedding_paths=[\"obsm/X_umap\"],\n",
+    "        ),\n",
+    "    )\n",
     "print(error.exconly())\n",
-    "assert error.exconly().startswith(\"ValueError: Could not find dataset with stem uid 'not-a-valid-uid' in lamindb\")"
+    "assert error.exconly().startswith(\"AttributeError: 'str' object has no attribute 'path'\")\n"
    ]
   },
   {

{lamindb-0.76.10 → lamindb-0.76.12}/docs/track.ipynb

@@ -29,7 +29,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Initiate tracking"
+    "## Track data lineage"
    ]
   },
   {
@@ -39,47 +39,20 @@
     "Call {meth}`~lamindb.track` to register a data transformation and start tracking inputs & outputs of a run. You will find your notebook or script in the {class}`~lamindb.Transform` registry along with pipelines & functions. {class}`~lamindb.Run` stores executions."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "import lamindb as ln\n",
-    "\n",
-    "# call `ln.track()` to generate a uid that identifies your code\n",
-    "\n",
-    "ln.track(\"9priar0hoE5u0000\")  # call `ln.track(uid)` to track a run with inputs & outputs"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "LaminDB now automatically tracks all input and output data of the current run.\n",
+    "```python\n",
+    "import lamindb as ln\n",
     "\n",
-    "Note: You can access a `requirments.txt` via `ln.context.run.environment`."
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Track run report & source code"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "If you want to save the run report & source code for a notebook or script, call:\n",
+    "# --> `ln.track()` generates a uid for your code\n",
+    "# --> `ln.track(uid)` initiates a tracked run\n",
+    "ln.track(\"9priar0hoE5u0000\")\n",
     "\n",
-    "```python\n",
-    "ln.finish()\n",
+    "# your code\n",
+    "\n",
+    "ln.finish()  # mark run as finished, save execution report, source code & environment\n",
     "```"
    ]
   },
@@ -87,7 +60,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Below is how a notebook with run report looks on the hub.\n",
+    "Below is how [a notebook](https://lamin.ai/laminlabs/lamindata/transform/PtTXoc0RbOIq65cN) with run report looks on the hub.\n",
     "\n",
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/RGXj5wcAf7EAc6J8dJfH.png\" width=\"900px\">"
    ]
@@ -168,6 +141,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "(track-run-parameters)=\n",
+    "\n",
     "## Track run parameters"
    ]
   },
@@ -188,9 +163,11 @@
    },
    "outputs": [],
    "source": [
+    "import lamindb as ln\n",
+    "\n",
     "ln.Param(name=\"input_dir\", dtype=\"str\").save()\n",
     "ln.Param(name=\"learning_rate\", dtype=\"float\").save()\n",
-    "ln.Param(name=\"downsample\", dtype=\"bool\").save()"
+    "ln.Param(name=\"preprocess_params\", dtype=\"dict\").save()"
    ]
   },
   {
@@ -248,14 +225,24 @@
    },
    "outputs": [],
    "source": [
-    "ln.Run.params.filter(learning_rate=0.01, input_dir=\"./mydataset\").df()"
+    "ln.Run.params.filter(learning_rate=0.01, input_dir=\"./mydataset\", preprocess_params__downsample=True).df()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Look at the parameter values that were used for a given run."
+    "Note that:\n",
+    "\n",
+    "* `preprocess_params__downsample=True` traverses the dictionary `preprocess_params` to find the key `\"downsample\"` and match it to `True`\n",
+    "* nested keys like `\"downsample\"` in a dictionary do not appear in `Param` and hence, do not get validated"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Below is how you get the parameter values that were used for a given run."
    ]
   },
   {
@@ -272,6 +259,35 @@
     "run.params.get_values()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Or [on the hub](https://lamin.ai/laminlabs/lamindata/transform/JjRF4mACd9m00001).\n",
+    "\n",
+    "<img width=\"500\" alt=\"image\" src=\"https://github.com/user-attachments/assets/d8a5df37-d585-4940-b6f0-91f99b6c436c\">"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you want to query all parameter values across all runs, use {class}`~lamindb.core.ParamValue`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "ln.core.ParamValue.df(include=[\"param__name\", \"created_by__handle\"])"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -322,7 +338,7 @@
    },
    "outputs": [],
    "source": [
-    "assert run.params.get_values() == {'downsample': True, 'input_dir': './mydataset', 'learning_rate': 0.01}\n",
+    "assert run.params.get_values() == {'input_dir': './mydataset', 'learning_rate': 0.01, 'preprocess_params': {'downsample': True, 'normalization': 'the_good_one'}}\n",
     "\n",
     "# clean up test instance\n",
     "!rm -r ./test-track\n",

{lamindb-0.76.10 → lamindb-0.76.12}/docs/tutorial.ipynb

@@ -116,9 +116,9 @@
    "source": [
     "import lamindb as ln\n",
     "\n",
-    "# call `ln.track()` to generate a uid that identifies your code\n",
-    "\n",
-    "ln.track(\"NJvdsWWbJlZS0000\")  # call `ln.track(uid)` to track a run with inputs & outputs\n"
+    "# --> `ln.track()` generates a uid for your code\n",
+    "# --> `ln.track(uid)` initiates a tracked run\n",
+    "ln.track(\"NJvdsWWbJlZS0000\")\n"
    ]
   },
   {
@@ -197,7 +197,8 @@
    },
    "outputs": [],
    "source": [
-    "ln.UPath(\"s3://lamindata/iris_studies\").view_tree()"
+    "# we use anon=True here in case no aws credentials are configured\n",
+    "ln.UPath(\"s3://lamindata/iris_studies\", anon=True).view_tree()"
    ]
   },
   {

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/__init__.py

@@ -43,7 +43,7 @@ Modules and settings.
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "0.76.10"
+__version__ = "0.76.12"
 
 import os as _os
 

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/_artifact.py

@@ -10,7 +10,7 @@ import fsspec
 import lamindb_setup as ln_setup
 import pandas as pd
 from anndata import AnnData
-from django.db.models import Q, QuerySet
+from django.db.models import Q
 from lamin_utils import colors, logger
 from lamindb_setup import settings as setup_settings
 from lamindb_setup._init_instance import register_storage_in_instance
@@ -180,7 +180,7 @@ def process_data(
                 f" be '{suffix}'."
             )
         cache_name = f"{provisional_uid}{suffix}"
-        path = settings.storage.cache_dir / cache_name
+        path = settings.cache_dir / cache_name
         # Alex: I don't understand the line below
         if path.suffixes == []:
             path = path.with_suffix(suffix)
@@ -344,7 +344,7 @@ def get_artifact_kwargs_from_data(
 
     if revises is not None:  # update provisional_uid
         provisional_uid, revises = create_uid(revises=revises, version=version)
-        if settings.storage.cache_dir in path.parents:
+        if settings.cache_dir in path.parents:
             path = path.rename(path.with_name(f"{provisional_uid}{suffix}"))
 
     check_path_in_storage = False
@@ -749,10 +749,6 @@ def from_dir(
     run: Run | None = None,
 ) -> list[Artifact]:
     """{}"""  # noqa: D415
-    logger.warning(
-        "this creates one artifact per file in the directory - consider"
-        " ln.Artifact(dir_path) to get one artifact for the entire directory"
-    )
     folderpath: UPath = create_path(path)  # returns Path for local
     default_storage = settings.storage.record
     using_key = settings._using_key
@@ -1125,7 +1121,7 @@ def save(self, upload: bool | None = None, **kwargs) -> Artifact:
         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
+        local_path_cache = ln_setup.settings.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(

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/_filter.py

@@ -2,8 +2,6 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
-from lnschema_core import Artifact, Collection
-
 from ._query_set import QuerySet, process_expressions
 
 if TYPE_CHECKING:

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/_finish.py

@@ -35,6 +35,13 @@ def prepare_notebook(
                     if strip_title:
                         lines.pop(i)
                         cell["source"] = "\n".join(lines)
+        # strip resaved finish error if present
+        # this is normally the last cell
+        if cell["cell_type"] == "code" and ".finish(" in cell["source"]:
+            for output in cell["outputs"]:
+                if output.get("ename", None) == "NotebookNotSaved":
+                    cell["outputs"] = []
+                    break
     return None
 
 
@@ -112,7 +119,7 @@ def save_context_core(
         notebook_content = read_notebook(filepath)  # type: ignore
         if not ignore_non_consecutive:  # ignore_non_consecutive is None or False
             is_consecutive = check_consecutiveness(
-                notebook_content, calling_statement=".finish()"
+                notebook_content, calling_statement=".finish("
             )
             if not is_consecutive:
                 response = "n"  # ignore_non_consecutive == False
@@ -123,12 +130,12 @@ def save_context_core(
                 if response != "y":
                     return "aborted-non-consecutive"
         # write the report
-        report_path = ln_setup.settings.storage.cache_dir / filepath.name.replace(
+        report_path = ln_setup.settings.cache_dir / filepath.name.replace(
             ".ipynb", ".html"
         )
         notebook_to_report(filepath, report_path)
         # write the source code
-        source_code_path = ln_setup.settings.storage.cache_dir / filepath.name.replace(
+        source_code_path = ln_setup.settings.cache_dir / filepath.name.replace(
             ".ipynb", ".py"
         )
         notebook_to_script(transform, filepath, source_code_path)
@@ -164,7 +171,7 @@ def save_context_core(
         transform.hash = hash
 
     # track environment
-    env_path = ln_setup.settings.storage.cache_dir / f"run_env_pip_{run.uid}.txt"
+    env_path = ln_setup.settings.cache_dir / f"run_env_pip_{run.uid}.txt"
     if env_path.exists():
         overwrite_env = True
         if run.environment_id is not None and from_cli:

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/_query_set.py

@@ -139,7 +139,7 @@ class QuerySet(models.QuerySet):
 
     See Also:
 
-        `django QuerySet <https://docs.djangoproject.com/en/4.2/ref/models/querysets/>`__ # noqa
+        `django QuerySet <https://docs.djangoproject.com/en/4.2/ref/models/querysets/>`__
 
     Examples:
 
@@ -154,7 +154,7 @@ class QuerySet(models.QuerySet):
     ) -> pd.DataFrame:
         """{}"""  # noqa: D415
         # re-order the columns
-        exclude_field_names = ["created_at"]
+        exclude_field_names = ["updated_at"]
         field_names = [
             field.name
             for field in self.model._meta.fields

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/_record.py

@@ -15,7 +15,7 @@ from lamindb_setup._connect_instance import (
     update_db_using_local,
 )
 from lamindb_setup.core._docs import doc_args
-from lamindb_setup.core._hub_core import connect_instance
+from lamindb_setup.core._hub_core import connect_instance_hub
 from lamindb_setup.core._settings_store import instance_settings_file
 from lnschema_core.models import IsVersioned, Record, Run, Transform
 
@@ -380,11 +380,9 @@ def using(
         return QuerySet(model=cls, using=None)
     owner, name = get_owner_name_from_identifier(instance)
     settings_file = instance_settings_file(name, owner)
-    cache_filepath = (
-        ln_setup.settings.storage.cache_dir / f"instance--{owner}--{name}--uid.txt"
-    )
+    cache_filepath = ln_setup.settings.cache_dir / f"instance--{owner}--{name}--uid.txt"
     if not settings_file.exists():
-        result = connect_instance(owner=owner, name=name)
+        result = connect_instance_hub(owner=owner, name=name)
         if isinstance(result, str):
             raise RuntimeError(
                 f"Failed to load instance {instance}, please check your permissions!"
@@ -469,9 +467,7 @@ def get_transfer_run(record) -> Run:
 
     slug = record._state.db
     owner, name = get_owner_name_from_identifier(slug)
-    cache_filepath = (
-        ln_setup.settings.storage.cache_dir / f"instance--{owner}--{name}--uid.txt"
-    )
+    cache_filepath = ln_setup.settings.cache_dir / f"instance--{owner}--{name}--uid.txt"
     if not cache_filepath.exists():
         raise SystemExit("Need to call .using() before")
     instance_uid = cache_filepath.read_text()

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/_save.py

@@ -168,7 +168,7 @@ def copy_or_move_to_cache(
 
     local_path = local_path.resolve()
     is_dir = local_path.is_dir()
-    cache_dir = settings._storage_settings.cache_dir
+    cache_dir = settings.cache_dir
 
     # just delete from the cache dir if storage_path is local
     if cache_path is None:

{lamindb-0.76.10 → lamindb-0.76.12}/lamindb/core/_context.py

@@ -562,26 +562,32 @@ class Context:
 
             return "CMD + s" if platform.system() == "Darwin" else "CTRL + s"
 
-        if context.run is None:
+        if self.run is None:
             raise TrackNotCalled("Please run `ln.track()` before `ln.finish()`")
-        if context._path is None:
-            if context.run.transform.type in {"script", "notebook"}:
+        if self._path is None:
+            if self.run.transform.type in {"script", "notebook"}:
                 raise ValueError(
-                    f"Transform type is not allowed to be 'script' or 'notebook' but is {context.run.transform.type}."
+                    "Transform type is not allowed to be 'script' or 'notebook' because `context._path` is `None`."
                 )
-            context.run.finished_at = datetime.now(timezone.utc)
-            context.run.save()
+            self.run.finished_at = datetime.now(timezone.utc)
+            self.run.save()
             # nothing else to do
             return None
         if is_run_from_ipython:  # notebooks
-            if get_seconds_since_modified(context._path) > 2 and not ln_setup._TESTING:
+            import nbproject
+
+            # it might be that the user modifies the title just before ln.finish()
+            if (nbproject_title := nbproject.meta.live.title) != self.transform.name:
+                self.transform.name = nbproject_title
+                self.transform.save()
+            if get_seconds_since_modified(self._path) > 2 and not ln_setup._TESTING:
                 raise NotebookNotSaved(
                     f"Please save the notebook in your editor (shortcut `{get_shortcut()}`) right before calling `ln.finish()`"
                 )
         save_context_core(
-            run=context.run,
-            transform=context.run.transform,
-            filepath=context._path,
+            run=self.run,
+            transform=self.run.transform,
+            filepath=self._path,
             finished_at=True,
             ignore_non_consecutive=ignore_non_consecutive,
         )