lamindb 1.7.1__tar.gz → 1.9.0__tar.gz

{lamindb-1.7.1 → lamindb-1.9.0}/.github/workflows/build.yml

@@ -22,6 +22,7 @@ jobs:
           filters: |
             curator:
               - 'lamindb/curators/**'
+              - 'lamindb/examples/cellxgene/**'
               - 'tests/curators/**'
 
       - id: set-matrix
@@ -162,6 +163,7 @@ jobs:
       - 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 clidocs
       - run: nox -s docs
       - run: rm -r ./_build/html/.doctrees # do not want to deploy with cloudflare
       - uses: cloudflare/wrangler-action@v3

{lamindb-1.7.1 → lamindb-1.9.0}/.gitignore

@@ -1,6 +1,8 @@
 __MACOSX/
 
 # LaminDB
+profile_output*
+docs/cli.md
 .coveragerc
 *.db
 *.lndb
@@ -219,4 +221,4 @@ _build
 .vscode
 
 # cxg
-!lamindb/curators/_cellxgene_schemas/schema_versions.csv
+!lamindb/examples/cellxgene/cxg_schema_versions.csv

lamindb-1.9.0/PKG-INFO

@@ -0,0 +1,144 @@
+Metadata-Version: 2.3
+Name: lamindb
+Version: 1.9.0
+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==1.6.0
+Requires-Dist: lamindb_setup[aws]==1.8.2
+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,<=0.12.0
+Requires-Dist: fsspec
+Requires-Dist: graphviz
+Requires-Dist: psycopg2-binary
+Requires-Dist: bionty>=1.6.1rc1 ; extra == "bionty"
+Requires-Dist: clinicore>=1.2.1 ; extra == "clinicore"
+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 ; 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: nbproject==0.11.1 ; extra == "jupyter"
+Requires-Dist: jupytext ; extra == "jupyter"
+Requires-Dist: nbconvert>=7.2.1 ; extra == "jupyter"
+Requires-Dist: mistune!=3.1.0 ; extra == "jupyter"
+Requires-Dist: wetlab>=1.3.1 ; extra == "wetlab"
+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: bionty
+Provides-Extra: clinicore
+Provides-Extra: dev
+Provides-Extra: fcs
+Provides-Extra: gcp
+Provides-Extra: jupyter
+Provides-Extra: wetlab
+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 framework for biology
+
+<!-- first two sentences sync from preface.md -->
+
+LaminDB is an open-source data framework to enable learning at scale in computational biology.
+It lets you track data transformations, validate & annotate datasets, and query a built-in database for biological metadata & data structures.
+
+## Setup
+
+<!-- copied from quick-setup-lamindb.md -->
+
+Install the `lamindb` Python package:
+
+```shell
+pip install 'lamindb[jupyter,bionty]'  # support notebooks & biological ontologies
+```
+
+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 -->
+
+Running this code inside a script via `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/EkQATsQL5wqC95Wj0003.png" width="220">
+
+You'll know how that artifact was created.
+
+```python
+artifact.describe()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BOTCBgHDAvwglN3U0001.png" width="850">
+
+Conversely, you can query artifacts by the script that created them.
+
+```python
+ln.Artifact.get(transform__key="create-fasta.py")  # query artifact by transform key
+```
+
+Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/fgKBV8qdSnbIga0i).
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480001.png" width="850">
+
+## 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).
+

lamindb-1.9.0/README.md

@@ -0,0 +1,85 @@
+[![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 framework for biology
+
+<!-- first two sentences sync from preface.md -->
+
+LaminDB is an open-source data framework to enable learning at scale in computational biology.
+It lets you track data transformations, validate & annotate datasets, and query a built-in database for biological metadata & data structures.
+
+## Setup
+
+<!-- copied from quick-setup-lamindb.md -->
+
+Install the `lamindb` Python package:
+
+```shell
+pip install 'lamindb[jupyter,bionty]'  # support notebooks & biological ontologies
+```
+
+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 -->
+
+Running this code inside a script via `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/EkQATsQL5wqC95Wj0003.png" width="220">
+
+You'll know how that artifact was created.
+
+```python
+artifact.describe()
+```
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/BOTCBgHDAvwglN3U0001.png" width="850">
+
+Conversely, you can query artifacts by the script that created them.
+
+```python
+ln.Artifact.get(transform__key="create-fasta.py")  # query artifact by transform key
+```
+
+Data lineage is just one type of metadata to help analysis and model training through queries, validation, and annotation. Here is a more [comprehensive example](https://lamin.ai/laminlabs/lamindata/artifact/fgKBV8qdSnbIga0i).
+
+<img src="https://lamin-site-assets.s3.amazonaws.com/.lamindb/6sofuDVvTANB0f480001.png" width="850">
+
+## 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).

{lamindb-1.7.1 → lamindb-1.9.0}/docs/arrays.ipynb

@@ -551,7 +551,7 @@
    "execution_count": null,
    "metadata": {
     "tags": [
-     "hide-cell"
+     "hide-output"
     ]
    },
    "outputs": [],
@@ -563,7 +563,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py312",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -577,7 +577,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.10.16"
   },
   "nbproject": {
    "id": "YVUCtH4GfQOy",