lamindb 0.32.0__tar.gz → 0.33.0__tar.gz

{lamindb-0.32.0 → lamindb-0.33.0}/.github/workflows/build.yml

@@ -21,6 +21,7 @@ jobs:
       - name: Checkout main
         uses: actions/checkout@v3
         with:
+          submodules: recursive
           fetch-depth: 0
       - name: Checkout lndocs
         uses: actions/checkout@v3
@@ -46,7 +47,7 @@ jobs:
         run: |
           python -m pip install -U pip
           pip install -U laminci
-          pip install lamindb
+          pip install -U lamindb
           sudo apt-get -y install graphviz
           sudo apt-get install libpq-dev
       - name: Lint

lamindb-0.33.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "lnschema-core"]
+	path = lnschema-core
+	url = https://github.com/laminlabs/lnschema-core.git

lamindb-0.33.0/PKG-INFO

@@ -0,0 +1,236 @@
+Metadata-Version: 2.1
+Name: lamindb
+Version: 0.33.0
+Summary: LaminDB: Manage R&D data & analyses.
+Author-email: Lamin Labs <laminlabs@gmail.com>
+Description-Content-Type: text/markdown
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Requires-Dist: lndb>=0.37.4
+Requires-Dist: lnschema_core==0.29.5
+Requires-Dist: lnschema_wetlab==0.13.4
+Requires-Dist: lnschema_bionty==0.8.0
+Requires-Dist: nbproject>=0.8.3
+Requires-Dist: readfcs>=1.1.0
+Requires-Dist: anndata>=0.8.0
+Requires-Dist: hjson
+Requires-Dist: sqlmodel>=0.0.8
+Requires-Dist: typeguard
+Requires-Dist: tabulate
+Requires-Dist: erdiagram
+Requires-Dist: zarr
+Requires-Dist: pre-commit ; extra == "dev"
+Requires-Dist: nox ; extra == "dev"
+Requires-Dist: laminci>=0.2.5 ; extra == "dev"
+Requires-Dist: pytest>=6.0 ; extra == "test"
+Requires-Dist: coverage ; extra == "test"
+Requires-Dist: pytest-cov ; extra == "test"
+Requires-Dist: scanpy ; extra == "test"
+Requires-Dist: scikit-learn>=1.1.1 ; extra == "test"
+Requires-Dist: nbproject_test>=0.3.0 ; extra == "test"
+Requires-Dist: psycopg2-binary ; extra == "test"
+Requires-Dist: matplotlib<3.7 ; extra == "test"
+Project-URL: Home, https://github.com/laminlabs/lamindb
+Provides-Extra: dev
+Provides-Extra: test
+
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](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)
+[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
+
+# LaminDB: Manage R&D data & analyses
+
+_Curate, store, track, query, integrate, and learn from biological data._
+
+LaminDB is an open-source data lake for R&D in biology. It manages indexed **object storage** (local directories, S3, GCP) with a mapped **SQL database** (SQLite, Postgres, and soon, BigQuery).
+
+One cool thing is that you can readily create distributed _LaminDB instances_ at any scale. Get started on your laptop, deploy in the cloud, or work with a mesh of instances for different teams and purposes.
+
+```{warning}
+
+Public beta: Currently only recommended for collaborators as we still make breaking changes.
+
+```
+
+## Installation
+
+LaminDB is a python package available for Python versions 3.8+.
+
+```shell
+pip install lamindb
+```
+
+## Import
+
+In your python script, import LaminDB as:
+
+```python
+import lamindb as ln
+```
+
+## Quick setup
+
+Quick setup on the command line:
+
+- Sign up via `lamin signup <email>`
+- Log in via `lamin login <handle>`
+- Set up an instance via `lamin init --storage <storage> --schema <schema_modules>`
+
+:::{dropdown} Example code
+
+```shell
+lamin signup testuser1@lamin.ai
+lamin login testuser1
+lamin init --storage ./mydata --schema bionty,wetlab
+```
+
+:::
+
+See {doc}`/guide/setup` for more.
+
+## Track & query data
+
+### Track data sources, data, and metadata
+
+::::{tab-set}
+:::{tab-item} Within an interactive notebook
+
+```{code-block} python
+import lamindb as ln
+
+ln.Run() # data source (a run record) is created
+#> ℹ️ Instance: testuser2/mydata
+#> ℹ️ User: testuser2
+#> ℹ️ Loaded run:
+#> Run(id='L1oBMKW60ndt5YtjRqav', notebook_id='sePTpDsGJRq3', notebook_v='0', created_by='bKeW4T6E', created_at=datetime.datetime(2023, 3, 14, 21, 49, 36))
+
+df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
+
+# create a data object with SQL metadata record including hash
+# link run record
+dobject = ln.DObject(df, name="My dataframe")
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c')
+
+# upload serialized version to the configured storage
+# commit a DObject record to the SQL database
+ln.add(dobject)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))
+```
+
+:::
+:::{tab-item} Within a regular pipeline
+
+```{code-block} python
+# create (or query) a pipeline record
+pipeline = lns.Pipeline(name="My pipeline")
+#> Pipeline(id='fhn5Zydf', v='1', name='My pipeline', created_by='bKeW4T6E')
+
+# create a run from the above pipeline as the data source
+run = ln.Run(pipeline=pipeline)
+#> Run(id='2aaKWH8dwBE6hnj3n9K9', pipeline_id='fhn5Zydf', pipeline_v='1', created_by='bKeW4T6E')
+
+# access pipeline from run via
+print(run.pipeline)
+#> Pipeline(id='fhn5Zydf', v='1', name='My pipeline', created_by='bKeW4T6E')
+
+df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
+
+# create a data object with SQL metadata record including hash and link run record
+dobject = ln.DObject(df, name="My dataframe", source=run)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c')
+
+# Tip: If you work with a single thread, you can pass `global_context=True` to ln.Run(), allowing you to omit source=run
+
+# upload serialized version to the configured storage
+# commit a DObject record to the SQL database
+ln.add(dobject)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))
+```
+
+:::
+::::
+
+### Query & load data
+
+```python
+dobject = ln.select(ln.DObject, name="My dataframe").one()
+#> [DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))]
+df = dobject.load()
+#>      a	b
+#>  0	1	3
+#>  1	2	4
+```
+
+Get the data ingested by the latest run:
+
+```python
+run = ln.select(ln.Run).order_by(ln.Run.created_at.desc()).first()
+#> Run(id='L1oBMKW60ndt5YtjRqav', notebook_id='sePTpDsGJRq3', notebook_v='0', created_by='bKeW4T6E', created_at=datetime.datetime(2023, 3, 14, 21, 49, 36))
+dobject = ln.select(ln.DObject).where(ln.DObject.source == run).all()
+#> [DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))]
+```
+
+<br>
+
+See {doc}`/guide/track` for more.
+
+## Track biological metadata
+
+### Track biological features
+
+```python
+import bionty as bt  # Lamin's manager for biological knowledge
+import lamindb as ln
+
+ln.Run()  # assume we're in a notebook and don't need to pass pipeline_name
+
+# a sample single cell RNA-seq dataset
+adata = ln.dev.datasets.anndata_mouse_sc_lymph_node()
+
+# Create a reference
+# - ensembl id as the standardized id
+# - mouse as the species
+reference = bt.Gene(species="mouse")
+
+# parse gene identifiers from data and map on reference
+features = ln.Features(adata, reference)
+#> 🔶 id column not found, using index as features.
+#> ✅ 0 terms (0.0%) are mapped.
+#> 🔶 10000 terms (100.0%) are not mapped.
+# The result is a hashed feature set record:
+print(features)
+#> Features(id='2Mv3JtH-ScBVYHilbLaQ', type='gene', created_by='bKeW4T6E')
+# genes records can be accessed via:
+print(features.genes[:3])
+#> [Gene(id='ENSMUSG00000020592', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000034931', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000071005', species_id='NCBI_10090')]
+
+# track data with features
+dobject = ln.DObject(adata, name="Mouse Lymph Node scRNA-seq", features=features)
+
+# access linked gene references
+print(dobject.features.genes[:3])
+#> [Gene(id='ENSMUSG00000020592', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000034931', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000071005', species_id='NCBI_10090')]
+
+# upload serialized data to configured storage
+# commit a DObject record to the SQL database
+# commit all linked features to the SQL database
+ln.add(dobject)
+```
+
+<br>
+
+See {doc}`/guide/features` for more.
+
+```{tip}
+- Each page in this guide is a Jupyter Notebook, which you can download [here](https://github.com/laminlabs/lamindb/tree/main/docs/guide).
+- You can run these notebooks in hosted versions of JupyterLab, e.g., [Saturn Cloud](https://github.com/laminlabs/run-lamin-on-saturn), Google Vertex AI, and others.
+- We recommend using [JupyterLab](https://jupyterlab.readthedocs.io/) for best notebook tracking experience.
+```
+
+📬 [Reach out](https://lamin.ai/contact) to report issues, learn about data modules that connect your assays, pipelines & workflows within our data platform enterprise plan.
+

lamindb-0.33.0/README.md

@@ -0,0 +1,198 @@
+[![Stars](https://img.shields.io/github/stars/laminlabs/lamindb?logo=GitHub&color=yellow)](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)
+[![pypi](https://img.shields.io/pypi/v/lamindb?color=blue&label=pypi%20package)](https://pypi.org/project/lamindb)
+
+# LaminDB: Manage R&D data & analyses
+
+_Curate, store, track, query, integrate, and learn from biological data._
+
+LaminDB is an open-source data lake for R&D in biology. It manages indexed **object storage** (local directories, S3, GCP) with a mapped **SQL database** (SQLite, Postgres, and soon, BigQuery).
+
+One cool thing is that you can readily create distributed _LaminDB instances_ at any scale. Get started on your laptop, deploy in the cloud, or work with a mesh of instances for different teams and purposes.
+
+```{warning}
+
+Public beta: Currently only recommended for collaborators as we still make breaking changes.
+
+```
+
+## Installation
+
+LaminDB is a python package available for Python versions 3.8+.
+
+```shell
+pip install lamindb
+```
+
+## Import
+
+In your python script, import LaminDB as:
+
+```python
+import lamindb as ln
+```
+
+## Quick setup
+
+Quick setup on the command line:
+
+- Sign up via `lamin signup <email>`
+- Log in via `lamin login <handle>`
+- Set up an instance via `lamin init --storage <storage> --schema <schema_modules>`
+
+:::{dropdown} Example code
+
+```shell
+lamin signup testuser1@lamin.ai
+lamin login testuser1
+lamin init --storage ./mydata --schema bionty,wetlab
+```
+
+:::
+
+See {doc}`/guide/setup` for more.
+
+## Track & query data
+
+### Track data sources, data, and metadata
+
+::::{tab-set}
+:::{tab-item} Within an interactive notebook
+
+```{code-block} python
+import lamindb as ln
+
+ln.Run() # data source (a run record) is created
+#> ℹ️ Instance: testuser2/mydata
+#> ℹ️ User: testuser2
+#> ℹ️ Loaded run:
+#> Run(id='L1oBMKW60ndt5YtjRqav', notebook_id='sePTpDsGJRq3', notebook_v='0', created_by='bKeW4T6E', created_at=datetime.datetime(2023, 3, 14, 21, 49, 36))
+
+df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
+
+# create a data object with SQL metadata record including hash
+# link run record
+dobject = ln.DObject(df, name="My dataframe")
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c')
+
+# upload serialized version to the configured storage
+# commit a DObject record to the SQL database
+ln.add(dobject)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))
+```
+
+:::
+:::{tab-item} Within a regular pipeline
+
+```{code-block} python
+# create (or query) a pipeline record
+pipeline = lns.Pipeline(name="My pipeline")
+#> Pipeline(id='fhn5Zydf', v='1', name='My pipeline', created_by='bKeW4T6E')
+
+# create a run from the above pipeline as the data source
+run = ln.Run(pipeline=pipeline)
+#> Run(id='2aaKWH8dwBE6hnj3n9K9', pipeline_id='fhn5Zydf', pipeline_v='1', created_by='bKeW4T6E')
+
+# access pipeline from run via
+print(run.pipeline)
+#> Pipeline(id='fhn5Zydf', v='1', name='My pipeline', created_by='bKeW4T6E')
+
+df = pd.DataFrame({"a": [1, 2], "b": [3, 4]})
+
+# create a data object with SQL metadata record including hash and link run record
+dobject = ln.DObject(df, name="My dataframe", source=run)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c')
+
+# Tip: If you work with a single thread, you can pass `global_context=True` to ln.Run(), allowing you to omit source=run
+
+# upload serialized version to the configured storage
+# commit a DObject record to the SQL database
+ln.add(dobject)
+#> DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))
+```
+
+:::
+::::
+
+### Query & load data
+
+```python
+dobject = ln.select(ln.DObject, name="My dataframe").one()
+#> [DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))]
+df = dobject.load()
+#>      a	b
+#>  0	1	3
+#>  1	2	4
+```
+
+Get the data ingested by the latest run:
+
+```python
+run = ln.select(ln.Run).order_by(ln.Run.created_at.desc()).first()
+#> Run(id='L1oBMKW60ndt5YtjRqav', notebook_id='sePTpDsGJRq3', notebook_v='0', created_by='bKeW4T6E', created_at=datetime.datetime(2023, 3, 14, 21, 49, 36))
+dobject = ln.select(ln.DObject).where(ln.DObject.source == run).all()
+#> [DObject(id='dZvGD7YUKCKG4X4aLd5K', name='My dataframe', suffix='.parquet', size=2240, hash='R2_kKlH1nBGesMdyulMYkA', source_id='L1oBMKW60ndt5YtjRqav', storage_id='wor0ul6c', created_at=datetime.datetime(2023, 3, 14, 21, 49, 46))]
+```
+
+<br>
+
+See {doc}`/guide/track` for more.
+
+## Track biological metadata
+
+### Track biological features
+
+```python
+import bionty as bt  # Lamin's manager for biological knowledge
+import lamindb as ln
+
+ln.Run()  # assume we're in a notebook and don't need to pass pipeline_name
+
+# a sample single cell RNA-seq dataset
+adata = ln.dev.datasets.anndata_mouse_sc_lymph_node()
+
+# Create a reference
+# - ensembl id as the standardized id
+# - mouse as the species
+reference = bt.Gene(species="mouse")
+
+# parse gene identifiers from data and map on reference
+features = ln.Features(adata, reference)
+#> 🔶 id column not found, using index as features.
+#> ✅ 0 terms (0.0%) are mapped.
+#> 🔶 10000 terms (100.0%) are not mapped.
+# The result is a hashed feature set record:
+print(features)
+#> Features(id='2Mv3JtH-ScBVYHilbLaQ', type='gene', created_by='bKeW4T6E')
+# genes records can be accessed via:
+print(features.genes[:3])
+#> [Gene(id='ENSMUSG00000020592', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000034931', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000071005', species_id='NCBI_10090')]
+
+# track data with features
+dobject = ln.DObject(adata, name="Mouse Lymph Node scRNA-seq", features=features)
+
+# access linked gene references
+print(dobject.features.genes[:3])
+#> [Gene(id='ENSMUSG00000020592', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000034931', species_id='NCBI_10090'),
+#>  Gene(id='ENSMUSG00000071005', species_id='NCBI_10090')]
+
+# upload serialized data to configured storage
+# commit a DObject record to the SQL database
+# commit all linked features to the SQL database
+ln.add(dobject)
+```
+
+<br>
+
+See {doc}`/guide/features` for more.
+
+```{tip}
+- Each page in this guide is a Jupyter Notebook, which you can download [here](https://github.com/laminlabs/lamindb/tree/main/docs/guide).
+- You can run these notebooks in hosted versions of JupyterLab, e.g., [Saturn Cloud](https://github.com/laminlabs/run-lamin-on-saturn), Google Vertex AI, and others.
+- We recommend using [JupyterLab](https://jupyterlab.readthedocs.io/) for best notebook tracking experience.
+```
+
+📬 [Reach out](https://lamin.ai/contact) to report issues, learn about data modules that connect your assays, pipelines & workflows within our data platform enterprise plan.

{lamindb-0.32.0 → lamindb-0.33.0}/docs/changelog.md

@@ -3,10 +3,17 @@
 <!-- prettier-ignore -->
 Name | PR | Developer | Date | Version
 --- | --- | --- | --- | ---
+🚚 Replace `ln.nb.header()` with `ln.Run()` except in `faq/nb` | [564](https://github.com/laminlabs/lamindb/pull/564) | [falexwolf](https://github.com/falexwolf) | 2023-03-14 | 0.33.0
+🚸 Smart about `global_context` and `load_latest` when run from notebook | [563](https://github.com/laminlabs/lamindb/pull/563) | [falexwolf](https://github.com/falexwolf) | 2023-03-14 |
+✨ `ln.Features` | [562](https://github.com/laminlabs/lamindb/pull/562) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-14 |
+🏗️ Introduce `lamindb.context` and enable `ln.Run` to create contexts | [561](https://github.com/laminlabs/lamindb/pull/561) | [falexwolf](https://github.com/falexwolf) | 2023-03-13 |
+📝 Improve the docstrings of `ln.add` and `ln.delete` | [559](https://github.com/laminlabs/lamindb/pull/559) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-10 |
+📝 Hide CI related cells in notebooks | [558](https://github.com/laminlabs/lamindb/pull/558) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-10 |
+📝 Update docs to clarify sign up and log in | [557](https://github.com/laminlabs/lamindb/pull/557) | [lawrlee](https://github.com/lawrlee) | 2023-03-10 |
 📝 Prettier species query | [555](https://github.com/laminlabs/lamindb/pull/555) | [falexwolf](https://github.com/falexwolf) | 2023-03-09 | 0.32.0
 📝 Refactor docs sidebar | [553](https://github.com/laminlabs/lamindb/pull/553) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-09 |
-⬆️ Upgrade setup | [554](https://github.com/laminlabs/lamindb/pull/554) | [falexwolf](https://github.com/falexwolf) | 2023-03-09 |
-⬆️  Stable release of lnschema-bionty, remove knowledge | [552](https://github.com/laminlabs/lamindb/pull/552) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-09 |
+⬆️ Upgrade `ln.setup` | [554](https://github.com/laminlabs/lamindb/pull/554) | [falexwolf](https://github.com/falexwolf) | 2023-03-09 |
+🔥 Remove `ln.knowledge` <span class="badge badge-warning">Breaking</span> | [552](https://github.com/laminlabs/lamindb/pull/552) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-09 |
 ➖ Remove bionty as a dependency | [551](https://github.com/laminlabs/lamindb/pull/551) | [sunnyosun](https://github.com/sunnyosun) | 2023-03-09 | 0.32.0rc1
 📝 Replace `ln.knowledge` with `bionty` in docs | [547](https://github.com/laminlabs/lamindb/pull/547) | [falexwolf](https://github.com/falexwolf) | 2023-03-07 | 0.31.1
 📝 Link FAQ and guide to session and notebook API | [550](https://github.com/laminlabs/lamindb/pull/550) | [falexwolf](https://github.com/falexwolf) | 2023-03-07 |

{lamindb-0.32.0 → lamindb-0.33.0}/docs/faq/data-validation.ipynb

@@ -309,7 +309,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.12 ('base1')",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -323,7 +323,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.9.15"
   }
  },
  "nbformat": 4,

{lamindb-0.32.0 → lamindb-0.33.0}/docs/faq/ingest-acid.ipynb

@@ -40,7 +40,7 @@
     "import lamindb as ln\n",
     "import lamindb.schema as lns\n",
     "\n",
-    "ln.nb.header()"
+    "ln.Run()"
    ]
   },
   {

{lamindb-0.32.0 → lamindb-0.33.0}/docs/faq/ingest-same-file-twice.ipynb

@@ -30,7 +30,7 @@
     "import lamindb as ln\n",
     "import pytest\n",
     "\n",
-    "ln.nb.header()"
+    "ln.Run()"
    ]
   },
   {

{lamindb-0.32.0 → lamindb-0.33.0}/docs/faq/ingest.ipynb

@@ -50,20 +50,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "NO_SOURCE_ERROR = \"\"\"\n",
-    "Error: Please link a data source using the `source` argument.\n",
-    "Fix: Link a data source by passing a run, e.g., via\n",
-    "\n",
-    "pipeline = ln.select(\"My ingestion pipeline\").one()\n",
-    "run = lns.Run(pipeline=pipeline)\n",
-    "dobject = ln.DObject(..., source=run)\n",
-    "\n",
-    "Or, if you're in a notebook, call `ln.nb.header()` at the top, which creates\n",
-    "a global run context for the notebook.\n",
-    "\n",
-    "More details: https://lamin.ai/docs/faq/ingest\n",
-    "\"\"\"\n",
-    "with pytest.raises(ValueError, match=re.escape(NO_SOURCE_ERROR)):\n",
+    "with pytest.raises(ValueError):\n",
     "    dobject = ln.DObject(df)"
    ]
   },
@@ -152,7 +139,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Alternatively, we can call `ln.nb.header()`, which auto-assigns the notebook run as the data source:"
+    "Alternatively, we can call `ln.Run()`, which auto-assigns the notebook run as the data source:"
    ]
   },
   {
@@ -161,7 +148,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.nb.header()"
+    "ln.Run()"
    ]
   },
   {
@@ -195,7 +182,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.nb.run"
+    "ln.context.run"
    ]
   },
   {
@@ -211,10 +198,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "NO_NAME_ERROR = \"\"\"\n",
-    "Pass a name in `ln.DObject(..., name=name)` when ingesting in-memory data.\n",
-    "\"\"\"\n",
-    "with pytest.raises(ValueError, match=re.escape(NO_NAME_ERROR)):\n",
+    "with pytest.raises(ValueError):\n",
     "    dobject = ln.DObject(df)"
    ]
   }

{lamindb-0.32.0 → lamindb-0.33.0}/docs/faq/lazy-loading.ipynb

@@ -29,7 +29,7 @@
     "import lamindb.schema as lns\n",
     "\n",
     "ln.setup.load(\"testuser1/mydata\")\n",
-    "ln.nb.header()"
+    "ln.Run()"
    ]
   },
   {
@@ -68,7 +68,7 @@
    "outputs": [],
    "source": [
     "with ln.Session() as ss:\n",
-    "    features_session = ss.select(lns.Features, id=featureset_id).one()\n",
+    "    features_session = ss.select(ln.Features, id=featureset_id).one()\n",
     "    gene_subset = features_session.genes[:3]"
    ]
   },

{lamindb-0.32.0 → lamindb-0.33.0}/docs/faq/nb.ipynb

@@ -12,17 +12,18 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We've seen the default behavior in the guide (passing `run=None` to `nb.header(`)`).\n",
+    "```{warning}\n",
     "\n",
-    "Here, we look at the two other ways for calling it:\n",
+    "This API is subject to change! It's remaining for some time for backward compat.\n",
     "\n",
-    "- Passing `run=\"new\"`\n",
-    "- Passing an instance of `lns.Run`\n",
+    "```\n",
     "\n",
-    "```{seealso}\n",
+    "We've seen the default behavior in the guide (passing `run=None` to `nb.header()`).\n",
+    "\n",
+    "Here, we look at the two other ways for calling it:\n",
     "\n",
-    "For all other parameters, see the doc of [nbproject](https://lamin.ai/docs/nbproject).\n",
-    "```"
+    "- Passing `run=\"new\"`\n",
+    "- Passing an instance of `lns.Run`"
    ]
   },
   {
@@ -68,6 +69,29 @@
     "    ln.nb.header(run=\"foo\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Passing nothing will load the latest run:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ln.nb.header()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This publishes the notebook."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,