📝 Adapt intro to the new ln.track()

.gitignore

@@ -133,3 +133,4 @@ lamin_sphinx
 docs/conf.py
 _docs_tmp*
 docs/modules.md
+docs/paradisi05_laminopathic_nuclei.jpg

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
@@ -24,7 +24,7 @@ repos:
               docs/notes/
           )
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
@@ -44,7 +44,7 @@ repos:
       - id: trailing-whitespace
       - id: check-case-conflict
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.14.1
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]

docs/changelog/soon/lamindb.md

@@ -1,7 +1,7 @@
 - 🩹 migrate without setting auto-connect to False [PR](https://github.com/laminlabs/lamindb-setup/pull/942) [@Koncopd](https://github.com/Koncopd)
 - 🚸 Error on auto-connect [PR](https://github.com/laminlabs/lamindb-setup/pull/941) [@falexwolf](https://github.com/falexwolf)
 - ♻️ Add contenttypes Django plugin [PR](https://github.com/laminlabs/lamindb-setup/pull/940) [@falexwolf](https://github.com/falexwolf)
-- 🚚  Rename `FeatureSet` to `Schema` and migrate to lamindb 1.0a5 [PR](https://github.com/laminlabs/lamindb/pull/2348) [@falexwolf](https://github.com/falexwolf)
+- 🚚 Rename `FeatureSet` to `Schema` and migrate to lamindb 1.0a5 [PR](https://github.com/laminlabs/lamindb/pull/2348) [@falexwolf](https://github.com/falexwolf)
 - 🐛 Skip deleting storage when deleting outdated versions of folder-like artifacts [PR](https://github.com/laminlabs/lamindb/pull/2349) [@Koncopd](https://github.com/Koncopd)
 - ♻️ Refactor key and name change checks [PR](https://github.com/laminlabs/lamindb/pull/2345) [@Koncopd](https://github.com/Koncopd)
 - 🚚 Migrate to lamindb 1.0a4 [PR](https://github.com/laminlabs/lamindb/pull/2343) [@falexwolf](https://github.com/falexwolf)

docs/changelog/soon/usecases.md

@@ -6,7 +6,7 @@
 - 🚚 Migrate to lamindb 1.0 [PR](https://github.com/laminlabs/wetlab/pull/90) [@falexwolf](https://github.com/falexwolf)
 - 🚚 Migrate to lamindb 1.0 [PR](https://github.com/laminlabs/ourprojects/pull/8) [@falexwolf](https://github.com/falexwolf)
 - 🐛 Fix default values [PR](https://github.com/laminlabs/cellxgene-lamin/pull/119) [@Zethson](https://github.com/Zethson)
-- ✅  Fail CI if `cellxgene-schema` CLI validation fails [PR](https://github.com/laminlabs/cellxgene-lamin/pull/111) [@Zethson](https://github.com/Zethson)
+- ✅ Fail CI if `cellxgene-schema` CLI validation fails [PR](https://github.com/laminlabs/cellxgene-lamin/pull/111) [@Zethson](https://github.com/Zethson)
 - 🎨 Set up sources dynamically [PR](https://github.com/laminlabs/wetlab/pull/91) [@sunnyosun](https://github.com/sunnyosun)
 - 🎨 Do not check embedding in .validate [PR](https://github.com/laminlabs/cellxgene-lamin/pull/114) [@sunnyosun](https://github.com/sunnyosun)
 - 🏗️ Integrate `lnschema-core` into `lamindb` [PR](https://github.com/laminlabs/ourprojects/pull/7) [@falexwolf](https://github.com/falexwolf)

docs/includes/features-lamindb.md

@@ -10,7 +10,7 @@ The following detailed specs are for the Python package `lamindb`. For the analo
 - Slice large array stores: {class}`~lamindb.Artifact.open` → [guide](cellxgene)
 - Cache & load artifacts: {class}`~lamindb.Artifact.cache`, {class}`~lamindb.Artifact.load`
 - Manage features & labels: {class}`~lamindb.Feature`, {class}`~lamindb.FeatureSet`, {class}`~lamindb.ULabel`
-- Plug-in custom [schemas](/schemas) & manage schema migrations
+- Plug-in custom [modules](/modules) & manage schema migrations
 - Use array formats in memory & storage: [DataFrame](/tutorial), [AnnData](/arrays), [MuData](multimodal), [SOMA](cellxgene), ... backed by [parquet](/tutorial), [zarr](/arrays), [TileDB](cellxgene), [HDF5](/arrays), [h5ad](/arrays), [DuckDB](rxrx), ...
 - Create iterable collections of artifacts with data loaders: {class}`~lamindb.Collection`
 - Version artifacts, collections & transforms: {class}`~lamindb.core.IsVersioned`

docs/integrations.md

@@ -8,14 +8,13 @@ Additional registries can be found here:
 - [wetlab](/wetlab): Basic wetlab entities
 - [clinicore](/clinicore): Basic clinical entities
 - [cellregistry](/cellregistry): A registry for single cells
-- [ourprojects](/ourprojects): Manage projects, teams & references
 - [omop](/omop): OMOP Common Data Model
 
 Please [reach out](https://lamin.ai/contact) to have your schema module featured.
 
 ## Git
 
-Sync tracked scripts in lamindb with git commits: [guide](track.ipynb#sync-scripts-with-github)
+Sync tracked scripts in lamindb with git commits: [guide](track.ipynb#sync-scripts-with-git)
 
 ## MLOps
 

docs/introduction.ipynb

@@ -194,9 +194,8 @@
    "source": [
     "import lamindb as ln\n",
     "\n",
-    "# --> `ln.track()` generates a uid for your code\n",
-    "# --> `ln.track(uid)` initiates a tracked run\n",
-    "ln.track(\"FPnfDtJz8qbE0000\")"
+    "# track the current notebook\n",
+    "ln.track()"
    ]
   },
   {
@@ -519,10 +518,10 @@
    "outputs": [],
    "source": [
     "# get a single record by uid (here, the latest version of the current notebook)\n",
-    "transform = ln.Transform.get(\"FPnfDtJz8qbE\")\n",
+    "transform = ln.Transform.get(ln.context.transform.uid)\n",
     "\n",
     "# get a single record by matching a field\n",
-    "transform = ln.Transform.get(name=\"Introduction\")\n",
+    "transform = ln.Transform.get(type=\"notebook\")\n",
     "\n",
     "# get a set of records by filtering on description\n",
     "ln.Artifact.filter(description=\"my RNA-seq\").df()\n",
@@ -532,7 +531,7 @@
     "\n",
     "# query all artifacts ingested from a notebook with \"intro\" in the name and labeled \"Candidate marker study\"\n",
     "artifacts = ln.Artifact.filter(\n",
-    "    transform__name__icontains=\"intro\", ulabels=candidate_marker_study\n",
+    "    transform__description__icontains=\"intro\", ulabels=candidate_marker_study\n",
     ").all()"
    ]
   },
@@ -1281,7 +1280,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

docs/tutorial.ipynb

@@ -526,7 +526,7 @@
     "   ```\n",
     ":::\n",
     "\n",
-    "Filter the {class}`~lamindb.Transform` registry for a name:"
+    "Filter the {class}`~lamindb.Transform` registry for a description:"
    ]
   },
   {
@@ -539,7 +539,9 @@
    },
    "outputs": [],
    "source": [
-    "transform = ln.Transform.get(name__icontains=\"Artifacts\")  # get exactly one result\n",
+    "transform = ln.Transform.get(\n",
+    "    description__icontains=\"Artifacts\"\n",
+    ")  # get exactly one result\n",
     "transform"
    ]
   },
@@ -933,7 +935,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "lamindb",
    "language": "python",
    "name": "python3"
   },
@@ -947,12 +949,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.17"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "ae1fefc8646a06dd2e75004cd934adda7c5727b046986a772e3b44b0ffba9754"
-   }
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

noxfile.py

@@ -226,16 +226,27 @@ def pull_artifacts(session):
 
 @nox.session
 def install(session):
+    from pathlib import Path
+
+    tmp_lamindb_path = Path("tmp_lamindb")
+    tmp_lamindb_path.mkdir(parents=True, exist_ok=True)
+
     run(
         session,
-        "pip install --no-deps git+https://github.com/laminlabs/lnschema-core git+https://github.com/laminlabs/bionty git+https://github.com/laminlabs/lamindb-setup git+https://github.com/laminlabs/wetlab git+https://github.com/laminlabs/clinicore git+https://github.com/laminlabs/cellregistry git+https://github.com/laminlabs/ourprojects",
+        f"git clone -b main --depth 1 --recursive --shallow-submodules https://github.com/laminlabs/lamindb {str(tmp_lamindb_path)}",
     )
+
     run(
         session,
-        "pip install"
-        " lamindb[bionty,jupyter,aws]@git+https://github.com/laminlabs/lamindb@main",
+        f"uv pip install --system --no-deps {str(tmp_lamindb_path / 'sub/lamindb-setup')} {str(tmp_lamindb_path / 'sub/lamin-cli')} {str(tmp_lamindb_path / 'sub/bionty')} {str(tmp_lamindb_path / 'sub/wetlab')} {str(tmp_lamindb_path / 'sub/clinicore')}",
     )
-    run(session, "pip install spatialdata")  # temporarily
+    run(
+        session,
+        f"uv pip install --system {str(tmp_lamindb_path.resolve())}[bionty,jupyter]",
+    )
+    run(session, "pip install --no-deps git+https://github.com/laminlabs/cellregistry")
+
+    run(session, "uv pip install --system spatialdata")  # temporarily
     run(session, "lamin settings set private-django-api true")
 
 
@@ -250,7 +261,7 @@ def run_nbs(session):
 def init(session):
     run(
         session,
-        "lamin init --storage ./docsbuild --schema bionty,wetlab,clinicore,cellregistry,ourprojects",
+        "lamin init --storage ./docsbuild --schema bionty,wetlab,clinicore,cellregistry",
     )