lamindb 0.68.1__tar.gz → 0.68.2__tar.gz

{lamindb-0.68.1 → lamindb-0.68.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.68.1
+Version: 0.68.2
 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==0.62.1
+Requires-Dist: lnschema_core==0.63.0
 Requires-Dist: lamindb_setup==0.66.1
 Requires-Dist: lamin_utils==0.13.0
-Requires-Dist: lamin_cli==0.9.1
+Requires-Dist: lamin_cli==0.9.3
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0

{lamindb-0.68.1 → lamindb-0.68.2}/docs/changelog.md

@@ -1,12 +1,17 @@
 # Changelog
 
-- 🚸 Restore `auto_connect=True` on `lamin init` [PR](https://github.com/laminlabs/lamindb/pull/1483) [@falexwolf](https://github.com/falexwolf)
 ```{eval-rst}
 .. role:: small
 ```
 
 ## 0.68
 
+### 0.68.2 {small}`2024-03-11`
+
+- 🚸 Move transform & run artifacts into cache before uploading [PR](https://github.com/laminlabs/lamindb/pull/1488) [@falexwolf](https://github.com/falexwolf)
+- 🚸 More sensible transform types [PR](https://github.com/laminlabs/lamindb/pull/1486) [@falexwolf](https://github.com/falexwolf)
+- 🚚 Rename `lnschema_lamin1` to `wetlab` [PR](https://github.com/laminlabs/lamindb/pull/1487) [@falexwolf](https://github.com/falexwolf)
+
 ### 0.68.1 {small}`2024-03-08`
 
 - 🚸 You can now use `ln.connect()` to connect to a LaminDB instance [PR](https://github.com/laminlabs/lamindb/pull/1480) [@falexwolf](https://github.com/falexwolf)

{lamindb-0.68.1 → lamindb-0.68.2}/docs/introduction.ipynb

@@ -983,18 +983,18 @@
     "\n",
     "If you run `lamin save <notebook_path>`, you will save the notebook to your default storage location.\n",
     "\n",
-    "You can explore the notebook report corresponding to the quickstart [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?id=FPnfDtJz8qbEz8) in LaminHub.\n",
+    "You can explore the notebook report corresponding to the quickstart [here](https://lamin.ai/laminlabs/lamindata/Transform?id=FPnfDtJz8qbEz8) in LaminHub.\n",
     "\n",
     "## Custom schemas\n",
     "\n",
     "LaminDB can be customized & extended with schema & app plug-ins building on the [Django](https://github.com/django/django) ecosystem. Examples are\n",
     "\n",
     "- [bionty](./bionty): Registries for basic biological entities, coupled to public ontologies.\n",
-    "- [lnschema_lamin1](https://github.com/laminlabs/lnschema-lamin1): Exemplary custom schema to manage samples, treatments, etc. \n",
+    "- [wetlab](https://github.com/laminlabs/wetlab): Exemplary custom schema to manage samples, treatments, etc. \n",
     "\n",
     "If you'd like to create your own schema or app:\n",
     "\n",
-    "1. Create a git repository with registries similar to [lnschema_lamin1](https://github.com/laminlabs/lnschema-lamin1)\n",
+    "1. Create a git repository with registries similar to [wetlab](https://github.com/laminlabs/wetlab)\n",
     "2. Create & deploy migrations via `lamin migrate create` and `lamin migrate deploy`\n",
     "\n",
     "It's fastest if we do this for you based on our templates within an enterprise plan.\n",
@@ -1044,7 +1044,7 @@
     "\n",
     "- [lamindb](https://github.com/laminlabs/lamindb): Core API, which builds on the [core schema](https://github.com/laminlabs/lnschema-core).\n",
     "- [bionty](https://github.com/laminlabs/bionty): Registries for basic biological entities, coupled to public ontologies.\n",
-    "- [lnschema-lamin1](https://github.com/laminlabs/lnschema-lamin1): Exemplary custom schema to manage samples, treatments, etc.\n",
+    "- [wetlab](https://github.com/laminlabs/wetlab): Exemplary custom schema to manage samples, treatments, etc.\n",
     "- [lamindb-setup](https://github.com/laminlabs/lamindb-setup): Setup & configure LaminDB, client for LaminHub.\n",
     "- [lamin-cli](https://github.com/laminlabs/lamin-cli): CLI for `lamindb` and `lamindb-setup`.\n",
     "- [nbproject](https://github.com/laminlabs/nbproject): Metadata parser for Jupyter notebooks.\n",

{lamindb-0.68.1 → lamindb-0.68.2}/docs/schemas.ipynb

@@ -115,7 +115,7 @@
     "\n",
     "The only convention required by LaminDB for plugging in a valid (minimal) Django app.\n",
     "\n",
-    "You'll see how simple it is if you look at this example: [github.com/laminlabs/lnschema-lamin1](https://github.com/laminlabs/lnschema-lamin1).\n",
+    "You'll see how simple it is if you look at this example: [github.com/laminlabs/wetlab](https://github.com/laminlabs/wetlab).\n",
     "\n",
     "Schema management needs two CLI calls (see {doc}`/setup`):\n",
     "\n",

{lamindb-0.68.1 → lamindb-0.68.2}/docs/storage/prepare-transfer-local-to-cloud.ipynb

@@ -24,7 +24,7 @@
    "source": [
     "import lamindb as ln\n",
     "import bionty as bt\n",
-    "import lnschema_lamin1 as ln1\n",
+    "import wetlab as ln1\n",
     "import pandas as pd"
    ]
   },
@@ -34,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.setup.init(storage=\"./test-transfer-to-cloud\", schema=\"bionty,lamin1\")\n",
+    "ln.setup.init(storage=\"./test-transfer-to-cloud\", schema=\"bionty,wetlab\")\n",
     "ln.setup.settings.auto_connect = False"
    ]
   },

{lamindb-0.68.1 → lamindb-0.68.2}/docs/tutorial.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "![](https://img.shields.io/badge/tutorial1/2-lightgrey)\n",
     "[![](https://img.shields.io/badge/Source%20on%20GitHub-orange)](https://github.com/laminlabs/lamindb/blob/main/docs/tutorial.ipynb)\n",
-    "[![](https://img.shields.io/badge/Source%20%26%20report%20on%20LaminHub-mediumseagreen)](https://lamin.ai/laminlabs/lamindata/record/core/Transform?uid=NJvdsWWbJlZSz8)"
+    "[![](https://img.shields.io/badge/Source%20%26%20report%20on%20LaminHub-mediumseagreen)](https://lamin.ai/laminlabs/lamindata/Transform?uid=NJvdsWWbJlZSz8)"
    ]
   },
   {
@@ -875,7 +875,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This enables you to query source code and report via `transform.source_code` and `transform.latest_report` and see it in the hub, e.g., [here](https://lamin.ai/laminlabs/lamindata/record/core/Transform?uid=NJvdsWWbJlZSz8).\n",
+    "This enables you to query source code and report via `transform.source_code` and `transform.latest_report` and see it in the hub, e.g., [here](https://lamin.ai/laminlabs/lamindata/Transform?uid=NJvdsWWbJlZSz8).\n",
     "\n",
     "<img src=\"https://lamin-site-assets.s3.amazonaws.com/.lamindb/RGXj5wcAf7EAc6J8aBoM.png\" width=\"700px\">"
    ]

{lamindb-0.68.1 → lamindb-0.68.2}/docs/tutorial2.ipynb

@@ -64,7 +64,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.connect(\"lamin-tutorial\")\n",
     "ln.settings.verbosity = \"hint\""
    ]
   },

{lamindb-0.68.1 → lamindb-0.68.2}/lamindb/__init__.py

@@ -55,7 +55,7 @@ Modules & settings:
 
 """
 
-__version__ = "0.68.1"  # denote a release candidate for 0.1.0 with 0.1rc1
+__version__ = "0.68.2"  # denote a release candidate for 0.1.0 with 0.1rc1
 
 import os as _os
 

{lamindb-0.68.1 → lamindb-0.68.2}/lamindb/_transform.py

@@ -1,13 +1,11 @@
-from typing import TYPE_CHECKING, Optional
+from typing import Optional
 
-from lnschema_core.models import TRANSFORM_TYPE_DEFAULT, Artifact, Run, Transform
+from lnschema_core.models import Artifact, Run, Transform
+from lnschema_core.types import TransformType
 
 from ._run import delete_run_artifacts
 from .core.versioning import get_uid_from_old_version, init_uid
 
-if TYPE_CHECKING:
-    from lnschema_core.types import TransformType
-
 
 def __init__(transform: Transform, *args, **kwargs):
     if len(args) == len(transform._meta.concrete_fields):
@@ -23,7 +21,7 @@ def __init__(transform: Transform, *args, **kwargs):
     (kwargs.pop("initial_version_id") if "initial_version_id" in kwargs else None)
     version: Optional[str] = kwargs.pop("version") if "version" in kwargs else None
     type: Optional[TransformType] = (
-        kwargs.pop("type") if "type" in kwargs else TRANSFORM_TYPE_DEFAULT
+        kwargs.pop("type") if "type" in kwargs else TransformType.pipeline
     )
     reference: Optional[str] = (
         kwargs.pop("reference") if "reference" in kwargs else None

{lamindb-0.68.1 → lamindb-0.68.2}/lamindb/core/_run_context.py

@@ -25,12 +25,6 @@ msg_path_failed = (
 )
 
 
-# we don't want a real error here, as this is so frequent
-# in VSCode
-class UpdateNbWithNonInteractiveEditor(SystemExit):
-    pass
-
-
 class NotebookNotSavedError(Exception):
     pass
 
@@ -290,7 +284,7 @@ class run_context:
                 transform_type = (
                     TransformType.notebook
                     if is_run_from_ipython
-                    else TransformType.pipeline
+                    else TransformType.script
                 )
                 cls._create_or_load_transform(
                     stem_uid=stem_uid,

{lamindb-0.68.1 → lamindb-0.68.2}/noxfile.py

@@ -71,7 +71,7 @@ def install(session, group):
     elif group == "storage":
         extras += "aws,zarr,bionty,jupyter,postgres"
         session.run(
-            *"pip install --no-deps lnschema_lamin1@git+https://github.com/laminlabs/lnschema-lamin1".split()
+            *"pip install --no-deps wetlab@git+https://github.com/laminlabs/wetlab".split()
         )
     elif group == "docs":
         extras += "bionty"

{lamindb-0.68.1 → lamindb-0.68.2}/pyproject.toml

@@ -16,10 +16,10 @@ classifiers = [
 ]
 dependencies = [
     # Lamin PINNED packages
-    "lnschema_core==0.62.1",
+    "lnschema_core==0.63.0",
     "lamindb_setup==0.66.1",
     "lamin_utils==0.13.0",
-    "lamin_cli==0.9.1",
+    "lamin_cli==0.9.3",
     # others
     "rapidfuzz",
     "pyarrow",

lamindb-0.68.2/sub/lamin-cli/lamin_cli/__init__.py

@@ -0,0 +1,3 @@
+"""Lamin CLI."""
+
+__version__ = "0.9.3"

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lamin-cli/lamin_cli/__main__.py

@@ -160,7 +160,7 @@ def schema(action: str):
 )
 def save(filepath: str):
     """Save notebook or script."""
-    from lamin_cli._transform import save
+    from lamin_cli._save import save
 
     if save(filepath) is not None:
         sys.exit(1)

lamindb-0.68.1/sub/lamin-cli/lamin_cli/_transform.py → lamindb-0.68.2/sub/lamin-cli/lamin_cli/_save.py

@@ -7,7 +7,7 @@ import lamindb_setup as ln_setup
 from lamin_utils import logger
 
 
-def save(filepath: str) -> Optional[str]:
+def save(filepath_str: str) -> Optional[str]:
     # this will be gone once we get rid of lamin load or enable loading multiple
     # instances sequentially
     auto_connect_state = ln_setup.settings.auto_connect
@@ -18,9 +18,10 @@ def save(filepath: str) -> Optional[str]:
     from lamindb.core._run_context import get_stem_uid_and_version_from_file
 
     is_notebook = False
-    stem_uid, transform_version = get_stem_uid_and_version_from_file(filepath)
+    stem_uid, transform_version = get_stem_uid_and_version_from_file(filepath_str)
+    filepath = Path(filepath_str)
 
-    if filepath.endswith(".ipynb"):
+    if filepath.suffix == ".ipynb":
         is_notebook = True
         try:
             import nbstripout  # noqa
@@ -69,16 +70,27 @@ def save(filepath: str) -> Optional[str]:
             return "aborted-save-notebook-created-by-different-user"
     if is_notebook:
         # convert the notebook file to html
-        filepath_html = filepath.replace(".ipynb", ".html")
         # log_level is set to 40 to silence the nbconvert logging
         result = subprocess.run(
-            f"jupyter nbconvert --to html {filepath} --Application.log_level=40",
+            "jupyter nbconvert --to html"
+            f" {filepath.as_posix()} --Application.log_level=40",
             shell=True,
         )
+        # move the temporary file into the cache dir in case it's accidentally
+        # in an existing storage location -> we want to move associated
+        # artifacts into default storage and not register them in an existing
+        # location
+        filepath_html = filepath.with_suffix(".html")  # current location
+        filepath_html.rename(
+            ln_setup.settings.storage.cache_dir / filepath_html.name
+        )  # move
+        filepath_html = (
+            ln_setup.settings.storage.cache_dir / filepath_html.name
+        )  # adjust location
         assert result.returncode == 0
         # copy the notebook file to a temporary file
-        source_code_path = filepath.replace(".ipynb", "_stripped.ipynb")
-        shutil.copy2(filepath, source_code_path)
+        source_code_path = ln_setup.settings.storage.cache_dir / filepath.name
+        shutil.copy2(filepath, source_code_path)  # copy
         result = subprocess.run(f"nbstripout {source_code_path}", shell=True)
         assert result.returncode == 0
     else:
@@ -162,10 +174,6 @@ def save(filepath: str) -> Optional[str]:
         run.save()
         transform.latest_report = run.report
     transform.save()
-    if is_notebook:
-        # clean up
-        Path(source_code_path).unlink()
-        Path(filepath_html).unlink()
     logger.success(f"saved transform.source_code: {transform.source_code}")
     if is_notebook:
         logger.success(f"saved transform.latest_report: {transform.latest_report}")

lamindb-0.68.1/sub/lamin-cli/tests/test_notebooks.py → lamindb-0.68.2/sub/lamin-cli/tests/test_save_notebooks.py

@@ -85,9 +85,11 @@ def test_save_consecutive():
     # now, we have the associated artifacts
     transform = ln.Transform.filter(uid="hlsFXswrJjtt5zKv").one_or_none()
     assert transform is not None
-    assert transform.latest_report is not None
+    assert transform.latest_report.path.exists()
+    assert transform.latest_run.report.path == transform.latest_report.path
     assert transform.source_code.hash == "6-8KV-p3YkRaeMRSLKdlIg"
-    assert transform.latest_run.environment is not None
+    assert transform.latest_run.environment.path.exists()
+    assert transform.source_code.path.exists()
 
     # now, assume the user modifies the notebook and saves
     # it without changing stem uid or version
@@ -113,9 +115,11 @@ def test_save_consecutive():
     # now, the source code should be overwritten
     transform = ln.Transform.filter(uid="hlsFXswrJjtt5zKv").one_or_none()
     assert transform is not None
-    assert transform.latest_report is not None
+    assert transform.latest_report.path.exists()
+    assert transform.latest_run.report.path == transform.latest_report.path
     assert transform.source_code.hash == "x5sT09ofzAocBmchbh6Aog"
-    assert transform.latest_run.environment is not None
+    assert transform.latest_run.environment.path.exists()
+    assert transform.source_code.path.exists()
 
     # now, assume the user renames the notebook
     new_path = notebook_path.with_name("new_name.ipynb")

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lamindb-setup/docs/changelog.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚚 Rename `lnschema_lamin1` to `wetlab` | [676](https://github.com/laminlabs/lamindb-setup/pull/676) | [falexwolf](https://github.com/falexwolf) | 2024-03-09 |
 🚸 Restore `auto_connect=True` after `lamin init` | [674](https://github.com/laminlabs/lamindb-setup/pull/674) | [falexwolf](https://github.com/falexwolf) | 2024-03-08 | 0.66.1
 🐛 Fix hosted regions list | [673](https://github.com/laminlabs/lamindb-setup/pull/673) | [Koncopd](https://github.com/Koncopd) | 2024-03-07 | 0.66.0
 🚑️ Fix bionty reload | [672](https://github.com/laminlabs/lamindb-setup/pull/672) | [sunnyosun](https://github.com/sunnyosun) | 2024-03-07 |

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lamindb-setup/docs/hub-prod/test-import-schema.ipynb

@@ -28,7 +28,7 @@
    },
    "outputs": [],
    "source": [
-    "!lamin init --storage test-implicit-load --schema bionty"
+    "!lamin init --storage test-implicit-load --schema wetlab,bionty"
    ]
   },
   {
@@ -50,7 +50,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import lnschema_bionty as lb"
+    "import wetlab as lb"
    ]
   },
   {
@@ -70,7 +70,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lb.Gene"
+    "lb.Experiment"
    ]
   },
   {
@@ -110,7 +110,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "2lhqA4uTKSFP",

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lamindb-setup/lamindb_setup/_exportdb.py

@@ -30,7 +30,7 @@ MODELS = {
         "Ethnicity": False,
         "PublicSource": False,
     },
-    # "lamin1": {
+    # "wetlab": {
     #     "ExperimentType": False,
     #     "Experiment": False,
     #     "Well": False,

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lamindb-setup/noxfile.py

@@ -46,9 +46,7 @@ def install(session: nox.Session, group: str) -> None:
         session.run(
             *"pip install git+https://github.com/laminlabs/lnschema-bionty".split()
         )
-        session.run(
-            *"pip install git+https://github.com/laminlabs/lnschema-lamin1".split()
-        )
+        session.run(*"pip install git+https://github.com/laminlabs/wetlab".split())
         session.run(*"pip install -e .[aws,dev]".split())
         # need for CLI, but this is bad because it's downstream
         session.run(*"git clone https://github.com/laminlabs/lamin-cli".split())

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lnschema-core/CHANGELOG.md

@@ -3,6 +3,7 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚸 More sensible transform types | [352](https://github.com/laminlabs/lnschema-core/pull/352) | [falexwolf](https://github.com/falexwolf) | 2024-03-09 | 0.63.0
 🏷️ Replace PathLike with UPathStr | [351](https://github.com/laminlabs/lnschema-core/pull/351) | [falexwolf](https://github.com/falexwolf) | 2024-03-05 | 0.62.1
 🚚 Rename dev to core | [349](https://github.com/laminlabs/lnschema-core/pull/349) | [falexwolf](https://github.com/falexwolf) | 2024-02-29 |
 ✨ Add unknown_label to Collection.mapped signature | [345](https://github.com/laminlabs/lnschema-core/pull/345) | [Koncopd](https://github.com/Koncopd) | 2024-02-27 |

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lnschema-core/lnschema_core/__init__.py

@@ -1,6 +1,6 @@
 """LaminDB's core registries."""
 
-__version__ = "0.62.1"
+__version__ = "0.63.0"
 
 
 from lamindb_setup import _check_instance_setup

lamindb-0.68.2/sub/lnschema-core/lnschema_core/migrations/0040_alter_transform_type.py

@@ -0,0 +1,24 @@
+# Generated by Django 5.1 on 2024-03-09 05:20
+
+from django.db import migrations, models
+
+import lnschema_core.types
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lnschema_core", "0039_remove_collection_artifacts_collectionartifact_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="transform",
+            name="type",
+            field=models.CharField(
+                choices=[("pipeline", "pipeline"), ("notebook", "notebook"), ("upload", "upload"), ("script", "script")],
+                db_index=True,
+                default=lnschema_core.types.TransformType["pipeline"],
+                max_length=20,
+            ),
+        ),
+    ]

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lnschema-core/lnschema_core/models.py

@@ -1,4 +1,3 @@
-import builtins
 import sys
 from datetime import datetime
 from pathlib import Path
@@ -57,10 +56,6 @@ if TYPE_CHECKING or _INSTANCE_SETUP:
     from lamindb.core import FeatureManager, LabelManager
 
 
-IPYTHON = getattr(builtins, "__IPYTHON__", False)
-TRANSFORM_TYPE_DEFAULT = TransformType.notebook if IPYTHON else TransformType.pipeline
-
-
 class IsVersioned:
     """Base class for versioned models."""
 
@@ -842,14 +837,9 @@ class Transform(Registry, HasParents, IsVersioned):
         max_length=20,
         choices=TransformType.choices(),
         db_index=True,
-        default=TRANSFORM_TYPE_DEFAULT,
+        default=TransformType.pipeline,
     )
-    """Transform type.
-
-    Defaults to `"notebook"` if run from ipython and to `"pipeline"` if run from python.
-
-    If run from the UI, it defaults to `app`.
-    """
+    """Transform type (default `"pipeline"`)."""
     latest_report = models.ForeignKey("Artifact", PROTECT, default=None, null=True, related_name="latest_report_of")
     """Latest run report."""
     source_code = models.ForeignKey("Artifact", PROTECT, default=None, null=True, related_name="source_code_of")
@@ -1675,8 +1665,8 @@ class Artifact(Registry, Data, IsTree, IsVersioned):
         .. note::
 
             If you have a high number of files (several 100k) and don't want to
-            track them individually, consider creating a :class:`~lamindb.Collection` via
-            ``Collection(path, meta=metadata)`` for them. See, e.g., :doc:`docs:rxrx`.
+            track them individually, create a single :class:`~lamindb.Artifact` via
+            ``Artifact(path)`` for them. See, e.g., :doc:`docs:rxrx`.
 
         Args:
             path: Source path of folder.

{lamindb-0.68.1 → lamindb-0.68.2}/sub/lnschema-core/lnschema_core/types.py

@@ -34,8 +34,8 @@ class ChoicesMixin:
 class TransformType(ChoicesMixin, Enum):
     pipeline = "pipeline"
     notebook = "notebook"
-    app = "app"
-    api = "api"
+    upload = "upload"
+    script = "script"
 
 
 class VisibilityChoice(IntegerChoices):

lamindb-0.68.1/sub/lamin-cli/lamin_cli/__init__.py

@@ -1,3 +0,0 @@
-"""Lamin CLI."""
-
-__version__ = "0.9.1"