lamindb 0.76.3__tar.gz → 0.76.6__tar.gz

{lamindb-0.76.3 → lamindb-0.76.6}/.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
-blank_issues_enabled: false
+blank_issues_enabled: true
 contact_links:
     - name: LaminHub issues
       url: https://github.com/laminlabs/laminhub-public

{lamindb-0.76.3 → lamindb-0.76.6}/.github/workflows/build.yml

@@ -72,13 +72,14 @@ jobs:
           aws-region: us-east-1
       - run: nox -s "build(group='${{ matrix.group }}')"
       - name: upload coverage
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: coverage--${{ matrix.group }}
           path: .coverage
+          include-hidden-files: true
       - name: upload docs
         if: ${{ matrix.group == 'tutorial' || matrix.group == 'guide' || matrix.group == 'biology' || matrix.group == 'faq' || matrix.group == 'storage' }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: docs-${{ matrix.group }}
           path: ./docs/${{ matrix.group }}
@@ -108,7 +109,7 @@ jobs:
           python-version: "3.10" # use 3.10, 3.8 and 3.11 give issues
       - run: pip install -U laminci
       - run: nox -s "install_ci(group='docs')"
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
       - run: nox -s docs
       - uses: nwtgck/actions-netlify@v1.2
         with:
@@ -138,7 +139,7 @@ jobs:
           python -m pip install -U uv
           uv pip install --system coverage[toml]
           uv pip install --system --no-deps .
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
       - name: run coverage
         run: |
           coverage combine coverage--*/.coverage*

{lamindb-0.76.3 → lamindb-0.76.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: lamindb
-Version: 0.76.3
+Version: 0.76.6
 Summary: A data framework for biology.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.8
@@ -9,22 +9,22 @@ 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==0.73.3
-Requires-Dist: lamindb_setup==0.76.7
+Requires-Dist: lnschema_core==0.74.1
+Requires-Dist: lamindb_setup==0.77.1
 Requires-Dist: lamin_utils==0.13.4
-Requires-Dist: lamin_cli==0.16.2
+Requires-Dist: lamin_cli==0.17.2
 Requires-Dist: rapidfuzz
 Requires-Dist: pyarrow
 Requires-Dist: typing_extensions!=4.6.0
 Requires-Dist: python-dateutil
-Requires-Dist: anndata>=0.8.0,<=0.10.8
+Requires-Dist: anndata>=0.8.0,<=0.10.9
 Requires-Dist: scipy<1.13.0rc1
 Requires-Dist: fsspec
 Requires-Dist: pandas
 Requires-Dist: graphviz
 Requires-Dist: psycopg2-binary
 Requires-Dist: lamindb_setup[aws] ; extra == "aws"
-Requires-Dist: bionty==0.49.0 ; extra == "bionty"
+Requires-Dist: bionty==0.50.1 ; extra == "bionty"
 Requires-Dist: pre-commit ; extra == "dev"
 Requires-Dist: nox ; extra == "dev"
 Requires-Dist: laminci>=0.3 ; extra == "dev"
@@ -38,7 +38,7 @@ Requires-Dist: django-schema-graph ; extra == "erdiagram"
 Requires-Dist: readfcs>=1.1.8 ; extra == "fcs"
 Requires-Dist: lamindb_setup[gcp] ; extra == "gcp"
 Requires-Dist: nbproject==0.10.4 ; extra == "jupyter"
-Requires-Dist: nbstripout==0.6.1 ; extra == "jupyter"
+Requires-Dist: jupytext ; extra == "jupyter"
 Requires-Dist: nbconvert ; extra == "jupyter"
 Requires-Dist: zarr>=2.16.0 ; extra == "zarr"
 Project-URL: Home, https://github.com/laminlabs/lamindb

{lamindb-0.76.3 → lamindb-0.76.6}/docs/api.md

@@ -12,33 +12,19 @@ cli
 
 ```{toctree}
 :maxdepth: 1
-:caption: Core API
+:caption: Python
 :hidden:
 
 lamindb
-```
-
-```{toctree}
-:maxdepth: 1
-:caption: Plugins
-:hidden:
-
 bionty
 wetlab
 ```
 
 ```{toctree}
 :maxdepth: 1
-:caption: SDK
+:caption: R & REST
 :hidden:
 
+laminr
 rest
 ```
-
-```{toctree}
-:maxdepth: 1
-:caption: Utilities
-:hidden:
-
-readfcs
-```

{lamindb-0.76.3 → lamindb-0.76.6}/docs/arrays.ipynb

@@ -20,7 +20,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We saw how LaminDB allows to query & search across artifacts & collections using registries: {doc}`records`.\n",
+    "We saw how LaminDB allows to query & search across artifacts & collections using registries: {doc}`registries`.\n",
     "\n",
     "Let us now look at the following case:\n",
     "\n",

lamindb-0.76.6/docs/introduction.ipynb

@@ -0,0 +1,34 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Introduction\n",
+    "\n",
+    "See https://github.com/laminlabs/lamin-docs/blob/main/docs/introduction.ipynb"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "py39",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

lamindb-0.76.6/docs/laminr.md

@@ -0,0 +1,3 @@
+# `laminr`
+
+[github.com/laminlabs/laminr](https://github.com/laminlabs/laminr)

{lamindb-0.76.3 → lamindb-0.76.6}/docs/query-search.md

@@ -3,6 +3,6 @@
 ```{toctree}
 :maxdepth: 1
 
-records
+registries
 arrays
 ```

lamindb-0.76.3/docs/records.ipynb → lamindb-0.76.6/docs/registries.ipynb

@@ -9,6 +9,14 @@
     "# Query & search registries"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "2079f103",
+   "metadata": {},
+   "source": [
+    "This guide walks through all the ways of finding metadata records in LaminDB registries."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -20,7 +28,16 @@
    },
    "outputs": [],
    "source": [
-    "!lamin init --storage ./mydata"
+    "# !pip install lamindb\n",
+    "!lamin init --storage ./test-registries"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "86abfd19",
+   "metadata": {},
+   "source": [
+    "We'll need some toy data."
    ]
   },
   {
@@ -39,7 +56,10 @@
     "# create toy data\n",
     "ln.Artifact(ln.core.datasets.file_jpg_paradisi05(), description=\"My image\").save()\n",
     "ln.Artifact.from_df(ln.core.datasets.df_iris(), description=\"The iris collection\").save()\n",
-    "ln.Artifact(ln.core.datasets.file_fastq(), description=\"My fastq\").save()"
+    "ln.Artifact(ln.core.datasets.file_fastq(), description=\"My fastq\").save()\n",
+    "\n",
+    "# see the content of the artifact registry\n",
+    "ln.Artifact.df()"
    ]
   },
   {
@@ -57,19 +77,27 @@
    "id": "5cb551b4",
    "metadata": {},
    "source": [
-    "For entities where we don't store more than 100k records, a look up object can be a convenient way of selecting a record.\n",
+    "For registries with less than 100k records, auto-completing a `Lookup` object is the most convenient way of finding a record.\n",
     "\n",
-    "Consider the `User` registry:"
+    "For example, take the `User` registry:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "01e2465f",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "users = ln.User.lookup(field=\"handle\")"
+    "# query the database for all users, optionally pass the field that creates the key\n",
+    "users = ln.User.lookup(field=\"handle\")\n",
+    "\n",
+    "# the lookup object is a NamedTuple\n",
+    "users"
    ]
   },
   {
@@ -78,14 +106,18 @@
    "id": "82a31938",
    "metadata": {},
    "source": [
-    "With auto-complete, we find a user:"
+    "With auto-complete, we find a specific user record:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "31853b49",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "user = users.testuser1\n",
@@ -97,17 +129,22 @@
    "id": "bf7e1415",
    "metadata": {},
    "source": [
-    "You can also get a dictionary, if you prefer:"
+    "You can also get a dictionary:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "04130d47",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "users_dict = ln.User.lookup().dict()"
+    "users_dict = ln.User.lookup().dict()\n",
+    "users_dict"
    ]
   },
   {
@@ -118,15 +155,28 @@
     "## Query exactly one record"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ba40b102",
+   "metadata": {},
+   "source": [
+    "{class}`~lamindb.core.Record.get` errors if more than one matching records are found."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "463ff17c",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
-    "# by uid\n",
+    "# by the universal base62 uid\n",
     "ln.User.get(\"DzTjkKse\")\n",
+    "\n",
     "# by any expression involving fields\n",
     "ln.User.get(handle=\"testuser1\")"
    ]
@@ -153,7 +203,11 @@
    "cell_type": "code",
    "execution_count": null,
    "id": "33c8e061",
-   "metadata": {},
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "ln.Artifact.filter(created_by=user).df()"
@@ -197,7 +251,15 @@
    "id": "8edf4a74",
    "metadata": {},
    "source": [
-    "## Search for metadata"
+    "## Search for records"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a925a678",
+   "metadata": {},
+   "source": [
+    "Search the toy data:"
    ]
   },
   {
@@ -220,41 +282,37 @@
    "id": "b8ba2bfe",
    "metadata": {},
    "source": [
-    "Let us create 500 notebook objects with fake titles and save them:"
+    "Let us create 500 notebook objects with fake titles, save, and search them:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "272962fc",
-   "metadata": {},
+   "id": "4b0b0c0c",
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
    "outputs": [],
    "source": [
     "transforms = [ln.Transform(name=title, type=\"notebook\") for title in ln.core.datasets.fake_bio_notebook_titles(n=500)]\n",
-    "ln.save(transforms)"
+    "ln.save(transforms)\n",
+    "\n",
+    "# search\n",
+    "ln.Transform.search(\"intestine\").df().head(5)"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
-   "id": "48422cb6",
+   "id": "4ba825ab",
    "metadata": {},
    "source": [
-    "We can now search for any combination of terms:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "4b0b0c0c",
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "ln.Transform.search(\"intestine\").df().head()"
+    "```{note}\n",
+    "\n",
+    "Currently, the LaminHub UI search is more powerful than the search of the `lamindb` open-source package.\n",
+    "\n",
+    "```"
    ]
   },
   {
@@ -274,7 +332,7 @@
    "source": [
     "Django has a double-under-score syntax to filter based on related tables.\n",
     "\n",
-    "This syntax enables you to traverse several layers of relations:"
+    "This syntax enables you to traverse several layers of relations and leverage different comparators."
    ]
   },
   {
@@ -288,7 +346,7 @@
    },
    "outputs": [],
    "source": [
-    "ln.Artifact.filter(run__created_by__handle__startswith=\"testuse\").df()  "
+    "ln.Artifact.filter(created_by__handle__startswith=\"testuse\").df()  "
    ]
   },
   {
@@ -303,13 +361,23 @@
     "\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "dc54f4f6",
+   "metadata": {},
+   "source": [
+    "## Comparators"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
    "id": "28710b83",
    "metadata": {},
    "source": [
-    "Beyond `__startswith`, Django supports about [two dozen field comparators](https://docs.djangoproject.com/en/stable/ref/models/querysets/#field-lookups) `field__comparator=value`. Below follow some of them."
+    "You can qualify the type of comparison in a query by using a comparator.\n",
+    "\n",
+    "Below follows a list of the most import, but Django supports about [two dozen field comparators](https://docs.djangoproject.com/en/stable/ref/models/querysets/#field-lookups) `field__comparator=value`."
    ]
   },
   {
@@ -367,29 +435,6 @@
     "ln.Artifact.filter(created_by=user, size__lt=1e4).df()"
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "id": "5b6efb3d",
-   "metadata": {},
-   "source": [
-    "### or"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0d1b9a73",
-   "metadata": {
-    "tags": [
-     "hide-output"
-    ]
-   },
-   "outputs": [],
-   "source": [
-    "ln.Artifact.filter().filter(ln.Q(suffix=\".jpg\") | ln.Q(suffix=\".fastq.gz\")).df()"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -456,7 +501,7 @@
    },
    "outputs": [],
    "source": [
-    "ln.Transform.filter(name__contains=\"search\").df().head(10)"
+    "ln.Transform.filter(name__contains=\"search\").df().head(5)"
    ]
   },
   {
@@ -478,7 +523,7 @@
    },
    "outputs": [],
    "source": [
-    "ln.Transform.filter(name__icontains=\"Search\").df().head(10)"
+    "ln.Transform.filter(name__icontains=\"Search\").df().head(5)"
    ]
   },
   {
@@ -504,20 +549,71 @@
     "ln.Transform.filter(name__startswith=\"Research\").df()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "c621ad18",
+   "metadata": {},
+   "source": [
+    "### or"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cf35d05f",
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "ln.Artifact.filter(ln.Q(suffix=\".jpg\") | ln.Q(suffix=\".fastq.gz\")).df()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6bf07110",
+   "metadata": {},
+   "source": [
+    "### negate/ unequal"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7b8724e1",
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "ln.Artifact.filter(~ln.Q(suffix=\".jpg\")).df()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ffb9c7a9",
+   "metadata": {},
+   "source": [
+    "Clean up the test instance."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "72b03f8b",
    "metadata": {
     "tags": [
-     "hide-cell"
+     "hide-output"
     ]
    },
    "outputs": [],
    "source": [
-    "# clean up test instance\n",
-    "!lamin delete --force mydata\n",
-    "!rm -r mydata"
+    "!rm -r ./test-registries\n",
+    "!lamin delete --force test-registries"
    ]
   }
  ],