lamindb 1.11.1__tar.gz → 1.11.3__tar.gz

lamindb-1.11.3/PKG-INFO

@@ -0,0 +1,180 @@
+Metadata-Version: 2.3
+Name: lamindb
+Version: 1.11.3
+Summary: A data framework for biology.
+Author-email: Lamin Labs <open-source@lamin.ai>
+Requires-Python: >=3.10,<3.14
+Description-Content-Type: text/markdown
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: lamin_utils==0.15.0
+Requires-Dist: lamin_cli==1.7.2
+Requires-Dist: lamindb_setup[aws]==1.10.2
+Requires-Dist: bionty>=1.7a1
+Requires-Dist: wetlab>=1.5a1
+Requires-Dist: nbproject==0.11.1
+Requires-Dist: jupytext
+Requires-Dist: nbconvert>=7.2.1
+Requires-Dist: mistune!=3.1.0
+Requires-Dist: pyyaml
+Requires-Dist: pyarrow
+Requires-Dist: pandera>=0.24.0
+Requires-Dist: typing_extensions!=4.6.0
+Requires-Dist: python-dateutil
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: scipy<1.15.0
+Requires-Dist: anndata>=0.8.0,<=0.12.1
+Requires-Dist: fsspec
+Requires-Dist: graphviz
+Requires-Dist: psycopg2-binary
+Requires-Dist: tomlkit ; extra == "dev"
+Requires-Dist: line_profiler ; extra == "dev"
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: nox ; extra == "dev"
+Requires-Dist: laminci>=0.3 ; extra == "dev"
+Requires-Dist: pytest>=6.0 ; extra == "dev"
+Requires-Dist: coverage ; extra == "dev"
+Requires-Dist: pytest-cov<7.0.0 ; extra == "dev"
+Requires-Dist: mudata ; extra == "dev"
+Requires-Dist: nbproject_test>=0.6.0 ; extra == "dev"
+Requires-Dist: faker-biology ; extra == "dev"
+Requires-Dist: pronto ; extra == "dev"
+Requires-Dist: readfcs>=2.0.1 ; extra == "fcs"
+Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
+Requires-Dist: numcodecs<0.16.0 ; extra == "zarr"
+Requires-Dist: zarr>=2.16.0,<3.0.0a0 ; extra == "zarr"
+Project-URL: Home, https://github.com/laminlabs/lamindb
+Provides-Extra: dev
+Provides-Extra: fcs
+Provides-Extra: gcp
+Provides-Extra: zarr
+
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub)](https://github.com/laminlabs/lamindb)
+[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
+[![Docs](https://img.shields.io/badge/docs-humans-yellow)](https://docs.lamin.ai)
+[![DocsLLMs](https://img.shields.io/badge/docs-LLMs-yellow)](https://docs.lamin.ai/summary.md)
+[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
+[![PyPI Downloads](https://img.shields.io/pepy/dt/lamindb?logo=pypi)](https://pepy.tech/project/lamindb)
+
+# LaminDB - A data lakehouse for biology
+
+LaminDB is an open-source data lakehouse to enable learning at scale in biology.
+It organizes datasets through validation & annotation and provides data lineage, queryability, and reproducibility on top of [FAIR](https://en.wikipedia.org/wiki/FAIR_data) data.
+
+<details>
+<summary>Why?</summary>
+
+Reproducing analytical results or understanding how a dataset or model was created can be a pain.
+Let alone training models on historical data, LIMS & ELN systems, orthogonal assays, or datasets generated by other teams.
+Even maintaining a mere overview of a project's or team's datasets & analyses is harder than it sounds.
+
+Biological datasets are typically managed with versioned storage systems, GUI-focused community or SaaS platforms, structureless data lakes, rigid data warehouses (SQL, monolithic arrays), and data lakehouses for tabular data.
+
+LaminDB extends the lakehouse architecture to biological registries & datasets beyond tables (`DataFrame`, `AnnData`, `.zarr`, `.tiledbsoma`, ...) with enough structure to enable queries and enough freedom to keep the pace of R&D high.
+Moreover, it provides context through data lineage -- tracing data and code, scientists and models -- and abstractions for biological domain knowledge and experimental metadata.
+
+</details>
+
+**Highlights.**
+
+- **data lineage:** track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
+- **unified infrastructure:** access diverse storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
+- **lakehouse capabilities**: manage, monitor & validate features, labels & dataset schemas; perform distributed queries and batch loading
+- **biological data formats:** validate & annotate formats like `DataFrame`, `AnnData`, `MuData`, ... backed by `parquet`, `zarr`, HDF5, LanceDB, DuckDB, ...
+- **biological entities**: organize experimental metadata & extensible ontologies in registries based on the Django ORM
+- **reproducible & auditable:** auto-version & timestamp execution reports, source code & compute environments, attribute records to users
+- **zero lock-in & scalable:** runs in your infrastructure; is _not_ a client for a rate-limited REST API
+- **extendable:** create custom plug-ins for your own applications based on the Django ecosystem
+- **integrations:** visualization tools like [vitessce](https://docs.lamin.ai/vitessce), workflow managers like [nextflow](https://docs.lamin.ai/nextflow) & [redun](https://docs.lamin.ai/redun), and [other tools](https://docs.lamin.ai/integrations)
+- **production-ready:** used in BigPharma, BioTech, hospitals & top labs
+
+LaminDB can be connected to LaminHub to serve as a [LIMS](https://en.wikipedia.org/wiki/Laboratory_information_management_system) for wetlab scientists, closing the drylab-wetlab feedback loop: [lamin.ai](https://lamin.ai)
+
+## Docs
+
+Copy [summary.md](https://docs.lamin.ai/summary.md) into an LLM chat and let AI explain or read the [docs](https://docs.lamin.ai).
+
+## Setup
+
+<!-- copied from quick-setup-lamindb.md -->
+
+Install the `lamindb` Python package:
+
+```shell
+pip install lamindb
+```
+
+Create a LaminDB instance:
+
+```shell
+lamin init --storage ./quickstart-data  # or s3://my-bucket, gs://my-bucket
+```
+
+Or if you have write access to an instance, connect to it:
+
+```shell
+lamin connect account/name
+```
+
+## Quickstart
+
+<!-- copied from preface.md -->
+
+Track a script or notebook run with source code, inputs, outputs, logs, and environment.
+
+<!-- copied from py-quickstart.py -->
+
+```python
+import lamindb as ln
+
+ln.track()  # track a run
+open("sample.fasta", "w").write(">seq1\nACGT\n")
+ln.Artifact("sample.fasta", key="sample.fasta").save()  # create an artifact
+ln.finish()  # finish the run
+```
+
+<!-- from here on, slight deviation from preface.md, where all this is treated in the walk through in more depth -->
+
+This code snippet creates an artifact, which can store a dataset or model as a file or folder in various formats.
+Running the snippet as a script (`python create-fasta.py`) produces the following data lineage.
+
+```python
+artifact = ln.Artifact.get(key="sample.fasta")  # query artifact by key
+artifact.view_lineage()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/EkQATsQL5wqC95Wj0005.png" width="250">
+
+You'll know how that artifact was created and what it's used for ([interactive visualization](https://lamin.ai/laminlabs/lamindata/artifact/8incOOgjn6F0K1TS)) in addition to capturing basic metadata:
+
+```python
+artifact.describe()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BOTCBgHDAvwglN3U0002.png" width="550">
+
+You can organize datasets with validation & annotation of any kind of metadata to then access them via queries & search. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480002.png" width="850">
+
+To annotate an artifact with a label, use:
+
+```python
+my_experiment = ln.ULabel(name="My experiment").save()  # create a label in the universal label ontology
+artifact.ulabels.add(my_experiment)  # annotate the artifact with the label
+```
+
+To query for a set of artifacts, use the `filter()` statement.
+
+```python
+ln.Artifact.filter(ulabels=my_experiment, suffix=".fasta").to_dataframe()  # query by suffix and the ulabel we just created
+ln.Artifact.filter(transform__key="create-fasta.py").to_dataframe()  # query by the name of the script we just ran
+```
+
+If you have a structured dataset like a `DataFrame`, an `AnnData`, or another array, you can validate the content of the dataset (and parse annotations).
+Here is an example for a dataframe: [docs.lamin.ai/introduction#validate-an-artifact](https://docs.lamin.ai/introduction#validate-an-artifact).
+
+With a large body of validated datasets, you can then access data through distributed queries & batch streaming, see here: [docs.lamin.ai/arrays](https://docs.lamin.ai/arrays).
+

lamindb-1.11.3/README.md

@@ -0,0 +1,126 @@
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub)](https://github.com/laminlabs/lamindb)
+[![codecov](https://codecov.io/gh/laminlabs/lamindb/branch/main/graph/badge.svg?token=VKMRJ7OWR3)](https://codecov.io/gh/laminlabs/lamindb)
+[![Docs](https://img.shields.io/badge/docs-humans-yellow)](https://docs.lamin.ai)
+[![DocsLLMs](https://img.shields.io/badge/docs-LLMs-yellow)](https://docs.lamin.ai/summary.md)
+[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
+[![PyPI Downloads](https://img.shields.io/pepy/dt/lamindb?logo=pypi)](https://pepy.tech/project/lamindb)
+
+# LaminDB - A data lakehouse for biology
+
+LaminDB is an open-source data lakehouse to enable learning at scale in biology.
+It organizes datasets through validation & annotation and provides data lineage, queryability, and reproducibility on top of [FAIR](https://en.wikipedia.org/wiki/FAIR_data) data.
+
+<details>
+<summary>Why?</summary>
+
+Reproducing analytical results or understanding how a dataset or model was created can be a pain.
+Let alone training models on historical data, LIMS & ELN systems, orthogonal assays, or datasets generated by other teams.
+Even maintaining a mere overview of a project's or team's datasets & analyses is harder than it sounds.
+
+Biological datasets are typically managed with versioned storage systems, GUI-focused community or SaaS platforms, structureless data lakes, rigid data warehouses (SQL, monolithic arrays), and data lakehouses for tabular data.
+
+LaminDB extends the lakehouse architecture to biological registries & datasets beyond tables (`DataFrame`, `AnnData`, `.zarr`, `.tiledbsoma`, ...) with enough structure to enable queries and enough freedom to keep the pace of R&D high.
+Moreover, it provides context through data lineage -- tracing data and code, scientists and models -- and abstractions for biological domain knowledge and experimental metadata.
+
+</details>
+
+**Highlights.**
+
+- **data lineage:** track inputs & outputs of notebooks, scripts, functions & pipelines with a single line of code
+- **unified infrastructure:** access diverse storage locations (local, S3, GCP, ...), SQL databases (Postgres, SQLite) & ontologies
+- **lakehouse capabilities**: manage, monitor & validate features, labels & dataset schemas; perform distributed queries and batch loading
+- **biological data formats:** validate & annotate formats like `DataFrame`, `AnnData`, `MuData`, ... backed by `parquet`, `zarr`, HDF5, LanceDB, DuckDB, ...
+- **biological entities**: organize experimental metadata & extensible ontologies in registries based on the Django ORM
+- **reproducible & auditable:** auto-version & timestamp execution reports, source code & compute environments, attribute records to users
+- **zero lock-in & scalable:** runs in your infrastructure; is _not_ a client for a rate-limited REST API
+- **extendable:** create custom plug-ins for your own applications based on the Django ecosystem
+- **integrations:** visualization tools like [vitessce](https://docs.lamin.ai/vitessce), workflow managers like [nextflow](https://docs.lamin.ai/nextflow) & [redun](https://docs.lamin.ai/redun), and [other tools](https://docs.lamin.ai/integrations)
+- **production-ready:** used in BigPharma, BioTech, hospitals & top labs
+
+LaminDB can be connected to LaminHub to serve as a [LIMS](https://en.wikipedia.org/wiki/Laboratory_information_management_system) for wetlab scientists, closing the drylab-wetlab feedback loop: [lamin.ai](https://lamin.ai)
+
+## Docs
+
+Copy [summary.md](https://docs.lamin.ai/summary.md) into an LLM chat and let AI explain or read the [docs](https://docs.lamin.ai).
+
+## Setup
+
+<!-- copied from quick-setup-lamindb.md -->
+
+Install the `lamindb` Python package:
+
+```shell
+pip install lamindb
+```
+
+Create a LaminDB instance:
+
+```shell
+lamin init --storage ./quickstart-data  # or s3://my-bucket, gs://my-bucket
+```
+
+Or if you have write access to an instance, connect to it:
+
+```shell
+lamin connect account/name
+```
+
+## Quickstart
+
+<!-- copied from preface.md -->
+
+Track a script or notebook run with source code, inputs, outputs, logs, and environment.
+
+<!-- copied from py-quickstart.py -->
+
+```python
+import lamindb as ln
+
+ln.track()  # track a run
+open("sample.fasta", "w").write(">seq1\nACGT\n")
+ln.Artifact("sample.fasta", key="sample.fasta").save()  # create an artifact
+ln.finish()  # finish the run
+```
+
+<!-- from here on, slight deviation from preface.md, where all this is treated in the walk through in more depth -->
+
+This code snippet creates an artifact, which can store a dataset or model as a file or folder in various formats.
+Running the snippet as a script (`python create-fasta.py`) produces the following data lineage.
+
+```python
+artifact = ln.Artifact.get(key="sample.fasta")  # query artifact by key
+artifact.view_lineage()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/EkQATsQL5wqC95Wj0005.png" width="250">
+
+You'll know how that artifact was created and what it's used for ([interactive visualization](https://lamin.ai/laminlabs/lamindata/artifact/8incOOgjn6F0K1TS)) in addition to capturing basic metadata:
+
+```python
+artifact.describe()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BOTCBgHDAvwglN3U0002.png" width="550">
+
+You can organize datasets with validation & annotation of any kind of metadata to then access them via queries & search. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/9K1dteZ6Qx0EXK8g).
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480002.png" width="850">
+
+To annotate an artifact with a label, use:
+
+```python
+my_experiment = ln.ULabel(name="My experiment").save()  # create a label in the universal label ontology
+artifact.ulabels.add(my_experiment)  # annotate the artifact with the label
+```
+
+To query for a set of artifacts, use the `filter()` statement.
+
+```python
+ln.Artifact.filter(ulabels=my_experiment, suffix=".fasta").to_dataframe()  # query by suffix and the ulabel we just created
+ln.Artifact.filter(transform__key="create-fasta.py").to_dataframe()  # query by the name of the script we just ran
+```
+
+If you have a structured dataset like a `DataFrame`, an `AnnData`, or another array, you can validate the content of the dataset (and parse annotations).
+Here is an example for a dataframe: [docs.lamin.ai/introduction#validate-an-artifact](https://docs.lamin.ai/introduction#validate-an-artifact).
+
+With a large body of validated datasets, you can then access data through distributed queries & batch streaming, see here: [docs.lamin.ai/arrays](https://docs.lamin.ai/arrays).

{lamindb-1.11.1 → lamindb-1.11.3}/docs/query-search.md

@@ -1,4 +1,4 @@
-# Query & search
+# Query, search & stream
 
 ```{toctree}
 :maxdepth: 1

{lamindb-1.11.1 → lamindb-1.11.3}/docs/registries.ipynb

@@ -9,7 +9,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "1",
    "metadata": {},
@@ -175,7 +174,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "15",
    "metadata": {},
@@ -184,7 +182,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "16",
    "metadata": {},
@@ -223,7 +220,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "19",
    "metadata": {},
@@ -259,7 +255,7 @@
    "id": "22",
    "metadata": {},
    "source": [
-    "{class}`~lamindb.models.SQLRecord.get` errors if more than one matching records are found."
+    "{meth}`~lamindb.models.SQLRecord.get` errors if more than one matching records are found."
    ]
   },
   {
@@ -283,7 +279,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "24",
    "metadata": {},
@@ -292,7 +287,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "25",
    "metadata": {},
@@ -315,14 +309,13 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "27",
    "metadata": {},
    "source": [
     "To access the results encoded in a filter statement, execute its return value with one of:\n",
     "\n",
-    "- {meth}`~lamindb.models.QuerySet.df`: A pandas `DataFrame` with each record in a row.\n",
+    "- {meth}`~lamindb.models.QuerySet.to_dataframe`: A pandas `DataFrame` with each record in a row.\n",
     "- {meth}`~lamindb.models.QuerySet.all`: A {class}`~lamindb.models.QuerySet`.\n",
     "- {meth}`~lamindb.models.QuerySet.one`: Exactly one record. Will raise an error if there is none. Is equivalent to the `.get()` method shown above.\n",
     "- {meth}`~lamindb.models.QuerySet.one_or_none`: Either one record or `None` if there is no query result."
@@ -453,7 +446,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "40",
    "metadata": {},
@@ -492,7 +484,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "44",
    "metadata": {},
@@ -501,7 +492,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "45",
    "metadata": {},
@@ -526,7 +516,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "47",
    "metadata": {},
@@ -585,7 +574,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "52",
    "metadata": {},
@@ -596,7 +584,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "53",
    "metadata": {},
@@ -619,7 +606,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "55",
    "metadata": {},
@@ -628,7 +614,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "56",
    "metadata": {},
@@ -651,7 +636,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "58",
    "metadata": {},
@@ -674,7 +658,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "60",
    "metadata": {},
@@ -737,7 +720,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "65",
    "metadata": {},
@@ -782,7 +764,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "69",
    "metadata": {},
@@ -851,7 +832,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "lamindb",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -865,7 +846,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.10.16"
   }
  },
  "nbformat": 4,

{lamindb-1.11.1 → lamindb-1.11.3}/lamindb/__init__.py

@@ -114,7 +114,7 @@ Backwards compatibility.
 
 # ruff: noqa: I001
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.11.1"
+__version__ = "1.11.3"
 
 import warnings as _warnings
 

{lamindb-1.11.1 → lamindb-1.11.3}/lamindb/models/query_set.py

@@ -155,19 +155,29 @@ def process_expressions(queryset: QuerySet, expressions: dict) -> dict:
         expressions,
     )
     if issubclass(queryset.model, SQLRecord):
-        # branch_id is set to 1 unless expressions contains id or uid
-        if not (
-            "id" in expressions
-            or "uid" in expressions
-            or "uid__startswith" in expressions
-        ):
-            if not any(e.startswith("branch_id") for e in expressions):
-                expressions["branch_id"] = 1  # default branch_id
-            # if branch_id is None, do not apply a filter
-            # otherwise, it would mean filtering for NULL values, which doesn't make
-            # sense for a non-NULLABLE column
-            elif "branch_id" in expressions and expressions["branch_id"] is None:
-                expressions.pop("branch_id")
+        # branch_id is set to 1 unless expressions contains id, uid or hash
+        id_uid_hash = {"id", "uid", "hash", "id__in", "uid__in", "hash__in"}
+        if not any(expression in id_uid_hash for expression in expressions):
+            expressions_have_branch = False
+            branch_branch_id = {"branch", "branch_id"}
+            branch_branch_id__ = ("branch__", "branch_id__")
+            for expression in expressions:
+                if expression in branch_branch_id or expression.startswith(
+                    branch_branch_id__
+                ):
+                    expressions_have_branch = True
+                    break
+            if not expressions_have_branch:
+                # TODO: should be set to the current default branch
+                expressions["branch_id"] = 1
+            else:
+                # if branch_id is None, do not apply a filter
+                # otherwise, it would mean filtering for NULL values, which doesn't make
+                # sense for a non-NULLABLE column
+                if "branch_id" in expressions and expressions["branch_id"] is None:
+                    expressions.pop("branch_id")
+                if "branch" in expressions and expressions["branch"] is None:
+                    expressions.pop("branch")
     if queryset._db is not None:
         # only check for database mismatch if there is a defined database on the
         # queryset
@@ -226,8 +236,6 @@ def get(
     else:
         assert idlike is None  # noqa: S101
         expressions = process_expressions(qs, expressions)
-        # don't want branch_id here in .get(), only in .filter()
-        expressions.pop("branch_id", None)
         # inject is_latest for consistency with idlike
         is_latest_was_not_in_expressions = "is_latest" not in expressions
         if issubclass(registry, IsVersioned) and is_latest_was_not_in_expressions:
@@ -241,7 +249,7 @@ def get(
                 result = qs.filter(**expressions).order_by("-created_at").first()
                 if result is not None:
                     return result
-            raise registry.DoesNotExist from e
+            raise e
 
 
 class SQLRecordList(UserList, Generic[T]):

{lamindb-1.11.1 → lamindb-1.11.3}/lamindb/models/save.py

@@ -234,7 +234,15 @@ def check_and_attempt_upload(
             try:
                 copy_or_move_to_cache(artifact, storage_path, cache_path)
             except Exception as e:
-                logger.warning(f"A problem with cache on saving: {e}")
+                if not str(e).startswith(
+                    "[WinError 32] The process cannot access the file "
+                    "because it is being used by another process"
+                ):
+                    # ignore WinError 32 error, this just means that the file is still open on save
+                    # it is saved at this point, so not a big deal if copy or move to cache fails
+                    # this mostly happens for run logs
+                    # just ignore without a warning
+                    logger.warning(f"A problem with cache on saving: {e}")
         # after successful upload, we should remove the attribute so that another call
         # call to save won't upload again, the user should call replace() then
         del artifact._local_filepath
@@ -269,7 +277,9 @@ def copy_or_move_to_cache(
     # non-local storage_path further
     if local_path != cache_path:
         if cache_path.exists():
-            logger.warning(f"replacing the existing cache path {cache_path.as_posix()}")
+            logger.important_hint(
+                f"replacing the existing cache path {cache_path.as_posix()}"
+            )
             if cache_path.is_dir():
                 shutil.rmtree(cache_path)
             else:

{lamindb-1.11.1 → lamindb-1.11.3}/lamindb/models/schema.py

@@ -258,6 +258,12 @@ class Schema(SQLRecord, CanCurate, TracksRun):
 
     Composite schemas can have multiple slots, e.g., for an `AnnData`, one schema for slot `obs` and another one for `var`.
 
+    To create a schema, one of the following must be passed:
+    - `features`: A list of :class:`~lamindb.Feature` records, e.g., `[Feature(...), Feature(...)]`.
+    - `itype`: A registry field, e.g., `Feature` or `bionty.Gene.ensembl_gene_id`, to constrain feature identifiers to be valid identifiers of the registry.
+    - `slots`: A dictionary mapping slot names to :class:`~lamindb.Schema` objects, e.g., `{"obs": Schema(...), "var": Schema(...), "obsm": Schema(...)}`.
+    - `is_type=True`: To create a schema type, e.g., `ln.Schema(name="ProteinPanel", is_type=True)`.
+
     Args:
         features: `list[SQLRecord] | list[tuple[Feature, dict]] | None = None` Feature
             records, e.g., `[Feature(...), Feature(...)]` or Features with their config, e.g., `[Feature(...).with_config(optional=True)]`.
@@ -565,6 +571,10 @@ class Schema(SQLRecord, CanCurate, TracksRun):
             coerce_dtype=coerce_dtype,
             n_features=n_features,
         )
+        if not features and not slots and not is_type and not itype:
+            raise InvalidArgument(
+                "Please pass features or slots or itype or set is_type=True"
+            )
         if not is_type:
             schema = (
                 Schema.objects.using(using)
@@ -1211,12 +1221,14 @@ def get_type_str(dtype: str | None) -> str | None:
     return type_str
 
 
-def _get_related_name(self: Schema) -> str:
+def _get_related_name(self: Schema) -> str | None:
     related_models = dict_related_model_to_related_name(self, instance=self._state.db)
-    related_name = related_models.get(
-        parse_cat_dtype(self.itype, is_itype=True)["registry_str"]
-    )
-    return related_name
+    if self.itype:
+        related_name = related_models.get(
+            parse_cat_dtype(self.itype, is_itype=True)["registry_str"]
+        )
+        return related_name
+    return None
 
 
 class SchemaFeature(BaseSQLRecord, IsLink):

{lamindb-1.11.1 → lamindb-1.11.3}/lamindb/models/sqlrecord.py

@@ -350,7 +350,7 @@ def delete_record(record: BaseSQLRecord, is_soft: bool = True):
             with transaction.atomic():
                 new_latest.save()
                 delete()
-            logger.warning(f"new latest version is: {new_latest}")
+            logger.important_hint(f"new latest version is: {new_latest}")
             return None
     # deal with all other cases of the nested if condition now
     delete()

{lamindb-1.11.1 → lamindb-1.11.3}/pyproject.toml

@@ -17,8 +17,8 @@ classifiers = [
 dependencies = [
     # Lamin PINNED packages
     "lamin_utils==0.15.0",
-    "lamin_cli==1.7.1",
-    "lamindb_setup[aws]==1.10.1",
+    "lamin_cli==1.7.2",
+    "lamindb_setup[aws]==1.10.2",
     # Lamin OPTIONAL packages, included to avoid users forgetting about passing extras,
     # which has happened very often these past years
     # these are small packages with few dependencies