🔖 Relase db 1.2.0 (#216)

falexwolf · web-flow · commit e2e2255e2f11 · 2025-03-09T17:11:49.000+01:00
* 🔖 Relase db 1.2.0

* 💚 Fix build

* ♻️ Fix references
diff --git a/docs/arc-virtual-cell-atlas.ipynb b/docs/arc-virtual-cell-atlas.ipynb
@@ -244,7 +244,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cell_lines = bt.CellLine.lookup()\n",
     "drugs = wl.Compound.lookup()\n",
     "\n",
     "artifacts_a549_piroxicam = collection.artifacts.filter(\n",
@@ -324,7 +323,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "filter_expr = (pc.field(\"cell_name\") == cell_lines.a549.name) & (\n",
+    "filter_expr = (pc.field(\"cell_name\") == \"A549\") & (\n",
     "    pc.field(\"drug\") == drugs.piroxicam.name\n",
     ")\n",
     "df = dataset.scanner(filter=filter_expr).to_table().to_pandas()\n",
diff --git a/docs/changelog/2025.md b/docs/changelog/2025.md
@@ -14,6 +14,21 @@
 .. role:: small
 ```
 
+## 2025-03-09 {small}`db 1.2.0`
+
+- ✨ Introduce `Artifact.from_spatialdata()` and re-factor validation of `spatialdata` stores [PR](https://github.com/laminlabs/lamindb/pull/2461) [@Zethson](https://github.com/Zethson)
+- ✨ Enable `ln.track(project="My project")` to auto-link entities to projects [PR](https://github.com/laminlabs/lamindb/pull/2529) [@falexwolf](https://github.com/falexwolf)
+- ✨ Add `.load()` for artifacts holding `SpatialData` objects [PR](https://github.com/laminlabs/lamindb/pull/2532) [@Zethson](https://github.com/Zethson)
+- 🎨 When re-creating an `Artifact`, link subsequent runs instead of updating `.run` and linking previous runs [PR](https://github.com/laminlabs/lamindb/pull/2515) [@falexwolf](https://github.com/falexwolf)
+- 🚸 Introduce `.slots` in `Schema`, `Curator`, and `FeatureManager` to access schemas and curators by dataset slot [PR](https://github.com/laminlabs/lamindb/pull/2530) [@sunnyosun](https://github.com/sunnyosun)
+- 🏗️ Re-structure internal API away from monkey-patching Django models [PR](https://github.com/laminlabs/lamindb/pull/2516) [@falexwolf](https://github.com/falexwolf)
+- 🐛 Fix passing a path manually when no path found by `nbproject` [PR](https://github.com/laminlabs/lamindb/pull/2537) [@Koncopd](https://github.com/Koncopd)
+- 🩹 Do not overwrite `._state_db` of models when the current instance is passed to `.using` [PR](https://github.com/laminlabs/lamindb/pull/2534) [@Koncopd](https://github.com/Koncopd)
+- 🔊 Do not show track warning for read-only connections [PR](https://github.com/laminlabs/lamindb/pull/2527) [@Koncopd](https://github.com/Koncopd)
+- 🚸 Raise `NotImplementedError` in `Artifact.load()` if there is no loader [PR](https://github.com/laminlabs/lamindb/pull/2514) [@Koncopd](https://github.com/Koncopd)
+- ✨ Support R2 [PR](https://github.com/laminlabs/lamindb-setup/pull/979) [@Koncopd](https://github.com/Koncopd)
+- ✨ Allow to use `Artifact.open()` and `Artifact.load()` for `.gz` files [PR](https://github.com/laminlabs/lamindb/pull/2506) [@Koncopd](https://github.com/Koncopd)
+
 ## 2025-02-27 {small}`db 1.1.1`
 
 - 🚸 Make the `obs` and `var` `DataFrameCurator` objects accessible via `AnnDataCurator.slots` [PR](https://github.com/laminlabs/lamindb/pull/2505) [@sunnyosun](https://github.com/sunnyosun)
diff --git a/docs/changelog/soon/lamindb.md b/docs/changelog/soon/lamindb.md
@@ -1,23 +0,0 @@
-- 🚸 Do not evaluate filter on feature annotations in `.df(features=True`) [PR](https://github.com/laminlabs/lamindb/pull/2542) [@falexwolf](https://github.com/falexwolf)
-- ⬆️  Upgrade nbproject [PR](https://github.com/laminlabs/lamindb/pull/2541) [@Koncopd](https://github.com/Koncopd)
-- 🐛 Fix passing a path manually when no path found by `nbproject` [PR](https://github.com/laminlabs/lamindb/pull/2537) [@Koncopd](https://github.com/Koncopd)
-- ✨ Add `.load()` for artifacts holding `SpatialData` objects [PR](https://github.com/laminlabs/lamindb/pull/2532) [@Zethson](https://github.com/Zethson)
-- 🩹 Do not overwrite `._state_db` of models when the current instance is passed to `.using` [PR](https://github.com/laminlabs/lamindb/pull/2534) [@Koncopd](https://github.com/Koncopd)
-- ✨ Read fine_grained_access column from the instances table [PR](https://github.com/laminlabs/lamindb-setup/pull/983) [@Koncopd](https://github.com/Koncopd)
-- 🚸 Introduce `.slots` in `Schema`, `Curator`, and `FeatureManager` to access schemas and curators by dataset slot [PR](https://github.com/laminlabs/lamindb/pull/2530) [@sunnyosun](https://github.com/sunnyosun)
-- ⬆️ Bump django to >= 5.1 [PR](https://github.com/laminlabs/lamindb-setup/pull/982) [@Koncopd](https://github.com/Koncopd)
-- ✨ Enable `ln.track(project="My project")` to auto-link entities to projects [PR](https://github.com/laminlabs/lamindb/pull/2529) [@falexwolf](https://github.com/falexwolf)
-- 💚 Fix CI [PR](https://github.com/laminlabs/lamindb-setup/pull/981) [@Koncopd](https://github.com/Koncopd)
-- ⬆️ Upgrade Bionty [PR](https://github.com/laminlabs/lamindb/pull/2518) [@Zethson](https://github.com/Zethson)
-- ♻️ Refactor internals of legacy feature logic in `Collection` [PR](https://github.com/laminlabs/lamindb/pull/2528) [@falexwolf](https://github.com/falexwolf)
-- 🚸 Ignore Dask legacy DataFrame warning [PR](https://github.com/laminlabs/lamindb/pull/2525) [@Zethson](https://github.com/Zethson)
-- 🔊 Do not show track warning for read-only connections [PR](https://github.com/laminlabs/lamindb/pull/2527) [@Koncopd](https://github.com/Koncopd)
-- ♻️ Re-export link models [PR](https://github.com/laminlabs/lamindb/pull/2523) [@falexwolf](https://github.com/falexwolf)
-- ✅ Test fine-grained permissions [PR](https://github.com/laminlabs/lamindb/pull/2512) [@Koncopd](https://github.com/Koncopd)
-- 🏗️ Re-structure internal API away from monkey-patching Django models [PR](https://github.com/laminlabs/lamindb/pull/2516) [@falexwolf](https://github.com/falexwolf)
-- ✨ Prepare for permission management [PR](https://github.com/laminlabs/lamindb-setup/pull/974) [@Koncopd](https://github.com/Koncopd)
-- ✨ Introduce `Artifact.from_spatialdata()` and re-factor validation of `spatialdata` stores [PR](https://github.com/laminlabs/lamindb/pull/2461) [@Zethson](https://github.com/Zethson)
-- 🎨 When re-creating an `Artifact`, link subsequent runs instead of updating `.run` and linking previous runs [PR](https://github.com/laminlabs/lamindb/pull/2515) [@falexwolf](https://github.com/falexwolf)
-- 🚸 Raise `NotImplementedError` in `Artifact.load()` if there is no loader [PR](https://github.com/laminlabs/lamindb/pull/2514) [@Koncopd](https://github.com/Koncopd)
-- ✨ Support R2 [PR](https://github.com/laminlabs/lamindb-setup/pull/979) [@Koncopd](https://github.com/Koncopd)
-- ✨ Allow to use `Artifact.open()` and `Artifact.load()` for `.gz` files [PR](https://github.com/laminlabs/lamindb/pull/2506) [@Koncopd](https://github.com/Koncopd)
diff --git a/docs/glossary.md b/docs/glossary.md
@@ -30,7 +30,7 @@ observation
 record
     A record is a data structure that consists in a sequence of typed [fields](https://en.wikipedia.org/wiki/Field_(computer_science)) that hold values [[Wikipedia](https://en.wikipedia.org/wiki/Record_(computer_science))].
 
-    In LaminDB, a metadata record is modeled as a {class}`~lamindb.core.Record`.
+    In LaminDB, a metadata record is modeled as a {class}`~lamindb.models.Record`.
 
 sample
     In biology, a sample is an instance or part of a biological system.
diff --git a/docs/includes/features-lamindb.md b/docs/includes/features-lamindb.md
@@ -4,8 +4,8 @@ The following detailed specs are for the Python package `lamindb`. For the analo
 
 **Manage data & metadata with a unified API (“lakehouse”).**
 
-- Query & search across data & metadata: {class}`~lamindb.core.Record.filter`, {class}`~lamindb.core.Record.search`
-- Model entities as an {term}`ORM` which their own registry: {class}`~lamindb.core.Record`
+- Query & search across data & metadata: {class}`~lamindb.models.Record.filter`, {class}`~lamindb.models.Record.search`
+- Model entities as an {term}`ORM` which their own registry: {class}`~lamindb.models.Record`
 - Model files and folders as datasets & models via one class: {class}`~lamindb.Artifact`
 - Slice large array stores: {class}`~lamindb.Artifact.open` → [guide](cellxgene)
 - Cache & load artifacts: {class}`~lamindb.Artifact.cache`, {class}`~lamindb.Artifact.load`
@@ -32,9 +32,9 @@ The following detailed specs are for the Python package `lamindb`. For the analo
 
 **Validate, standardize & annotate.**
 
-- Validate & standardize metadata: {class}`~lamindb.core.CanCurate.validate`, {class}`~lamindb.core.CanCurate.standardize`.
+- Validate & standardize metadata: {class}`~lamindb.models.CanCurate.validate`, {class}`~lamindb.models.CanCurate.standardize`.
 - High-level curation flow including annotation: {class}`~lamindb.Curator`
-- Inspect validation failures: {class}`~lamindb.core.CanCurate.inspect`
+- Inspect validation failures: {class}`~lamindb.models.CanCurate.inspect`
 
 **Organize and share data across a mesh of LaminDB instances.**
 
diff --git a/docs/introduction.ipynb b/docs/introduction.ipynb
@@ -524,9 +524,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "LaminDB's central classes are registries that store records ({class}`~lamindb.core.Record` objects).\n",
+    "LaminDB's central classes are registries that store records ({class}`~lamindb.models.Record` objects).\n",
     "\n",
-    "The easiest way to see the latest records for a registry is to call the _class method_ {class}`~lamindb.core.Record.df`."
+    "The easiest way to see the latest records for a registry is to call the _class method_ {class}`~lamindb.models.Record.df`."
    ]
   },
   {
@@ -568,7 +568,7 @@
    "source": [
     "### Query & search\n",
     "\n",
-    "You can write arbitrary relational queries using the class methods {class}`~lamindb.core.Record.get` and {class}`~lamindb.core.Record.filter`.\n",
+    "You can write arbitrary relational queries using the class methods {class}`~lamindb.models.Record.get` and {class}`~lamindb.models.Record.filter`.\n",
     "The syntax for it is Django's query syntax."
    ]
   },
@@ -597,7 +597,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The class methods {class}`~lamindb.core.Record.search` and {class}`~lamindb.core.Record.lookup` help with approximate matches."
+    "The class methods {class}`~lamindb.models.Record.search` and {class}`~lamindb.models.Record.lookup` help with approximate matches."
    ]
   },
   {
diff --git a/docs/tutorial.ipynb b/docs/tutorial.ipynb
@@ -314,7 +314,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can get an overview of all artifacts in the database by calling {meth}`~lamindb.core.Record.df`:"
+    "We can get an overview of all artifacts in the database by calling {meth}`~lamindb.models.Record.df`:"
    ]
   },
   {
@@ -606,9 +606,9 @@
    "source": [
     "```{note}\n",
     "\n",
-    "You can look up, filter & search any registry ({class}`~lamindb.core.Record`).\n",
+    "You can look up, filter & search any registry ({class}`~lamindb.models.Record`).\n",
     "\n",
-    "You can chain {meth}`~lamindb.core.Record.filter` statements and {meth}`~lamindb.core.QuerySet.search`: `ln.Artifact.filter(suffix=\".jpg\").search(\"my image\")`\n",
+    "You can chain {meth}`~lamindb.models.Record.filter` statements and {meth}`~lamindb.core.QuerySet.search`: `ln.Artifact.filter(suffix=\".jpg\").search(\"my image\")`\n",
     "\n",
     "An empty filter returns the entire registry: `ln.Artifact.filter()`\n",
     "```"

Original file line number	Diff line number	Diff line change
`@@ -524,9 +524,9 @@`
`524`	`524`	`"cell_type": "markdown",`
`525`	`525`	`"metadata": {},`
`526`	`526`	`"source": [`
`527`		- "LaminDB's central classes are registries that store records ({class}`~lamindb.core.Record` objects).\n",
	`527`	+ "LaminDB's central classes are registries that store records ({class}`~lamindb.models.Record` objects).\n",
`528`	`528`	`"\n",`
`529`		- "The easiest way to see the latest records for a registry is to call the _class method_ {class}`~lamindb.core.Record.df`."
	`529`	+ "The easiest way to see the latest records for a registry is to call the _class method_ {class}`~lamindb.models.Record.df`."
`530`	`530`	`]`
`531`	`531`	`},`
`532`	`532`	`{`
`@@ -568,7 +568,7 @@`
`568`	`568`	`"source": [`
`569`	`569`	`"### Query & search\n",`
`570`	`570`	`"\n",`
`571`		- "You can write arbitrary relational queries using the class methods {class}`~lamindb.core.Record.get` and {class}`~lamindb.core.Record.filter`.\n",
	`571`	+ "You can write arbitrary relational queries using the class methods {class}`~lamindb.models.Record.get` and {class}`~lamindb.models.Record.filter`.\n",
`572`	`572`	`"The syntax for it is Django's query syntax."`
`573`	`573`	`]`
`574`	`574`	`},`
`@@ -597,7 +597,7 @@`
`597`	`597`	`"cell_type": "markdown",`
`598`	`598`	`"metadata": {},`
`599`	`599`	`"source": [`
`600`		- "The class methods {class}`~lamindb.core.Record.search` and {class}`~lamindb.core.Record.lookup` help with approximate matches."
	`600`	+ "The class methods {class}`~lamindb.models.Record.search` and {class}`~lamindb.models.Record.lookup` help with approximate matches."
`601`	`601`	`]`
`602`	`602`	`},`
`603`	`603`	`{`