🚚 Rename validation.Validator to Validator.from_df

laminlabs · Mar 26, 2024 · 64b09ff · 64b09ff
1 parent 603b31e
commit 64b09ff
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Showing 13 changed files with 1,219 additions and 1,240 deletions.
diff --git a/docs/introduction.ipynb b/docs/introduction.ipynb
@@ -342,9 +342,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lamindb.validation import Validator\n",
-    "\n",
-    "validator = Validator(\n",
+    "validator = ln.Validate.from_df(\n",
     "    df, \n",
     "    fields={\"perturbation\": ln.ULabel.name}, # validate categories in the perturbation column\n",
     "    feature_field=ln.Feature.name, # validate features using the Feature registry\n",
@@ -505,11 +503,10 @@
    "outputs": [],
    "source": [
     "import anndata as ad\n",
-    "from lamindb.validation import AnnDataValidator\n",
     "\n",
     "adata = ad.AnnData(df[[\"CD8A\", \"CD4\", \"CD14\"]], obs=df[[\"perturbation\"]])\n",
     "\n",
-    "validator = AnnDataValidator(adata, \n",
+    "validator = ln.Validate.from_anndata(adata, \n",
     "                      obs_fields={\"perturbation\": ln.ULabel.name}, \n",
     "                      var_field=bt.Gene.symbol, # note that we are using the Gene registry\n",
     "                      organism=\"human\") # specify the organism for the Gene registry\n",
@@ -623,7 +620,7 @@
     "adata = ad.AnnData(df[[\"CD8A\", \"CD4\", \"CD38\"]], obs=df[[\"perturbation\"]])\n",
     "\n",
     "# Validate, annotate and register a new artifact\n",
-    "validator = AnnDataValidator(adata, \n",
+    "validator = ln.Validate.from_anndata(adata, \n",
     "                      obs_fields={\"perturbation\": ln.ULabel.name}, \n",
     "                      var_field=bt.Gene.symbol, \n",
     "                      organism=\"human\")\n",

diff --git a/lamindb/__init__.py b/lamindb/__init__.py
@@ -31,7 +31,7 @@
 .. autosummary::
    :toctree: .
 
-   validation
+   Validate
    settings
    setup
    UPath
@@ -72,6 +72,7 @@ def __getattr__(name):
 
     from . import (
         _artifact,
+        _can_validate,
         _collection,
         _feature,
         _feature_set,
@@ -89,6 +90,7 @@ def __getattr__(name):
     dev = core  # backward compat
     from ._finish import finish
     from ._save import save
+    from ._validate import Validate
     from ._view import view
     from .core._run_context import run_context as _run_context
     from .core._settings import settings