🚚 Integrate ourprojects into lamindb (#2342)

.gitmodules

@@ -13,6 +13,3 @@
 [submodule "sub/clinicore"]
 	path = sub/clinicore
 	url = https://github.com/laminlabs/clinicore
-[submodule "sub/ourprojects"]
-	path = sub/ourprojects
-	url = https://github.com/laminlabs/ourprojects

docs/api.md

@@ -26,7 +26,6 @@ rest
 :hidden:
 
 bionty
-ourprojects
 wetlab
 clinicore
 cellregistry

docs/faq/validate-fields.ipynb

@@ -6,9 +6,7 @@
    "source": [
     "# Django field validation\n",
     "\n",
-    "[Django field validation](https://docs.djangoproject.com/en/5.1/ref/validators/) are enabled for models that inherit the `ValidateFields` class.\n",
-    "\n",
-    "For instance: [`ourprojects.Reference`](https://docs.lamin.ai/ourprojects.reference)"
+    "[Django field validation](https://docs.djangoproject.com/en/5.1/ref/validators/) are enabled for models that inherit the `ValidateFields` class."
    ]
   },
   {
@@ -17,8 +15,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# !pip install lamindb[ourprojects]\n",
-    "!lamin init --storage ./test-django-validation --modules ourprojects"
+    "# pip install lamindb\n",
+    "!lamin init --storage ./test-django-validation"
    ]
   },
   {
@@ -27,7 +25,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import ourprojects as pj\n",
+    "import lamindb as ln\n",
     "from lamindb.base.validation import FieldValidationError"
    ]
   },
@@ -38,7 +36,7 @@
    "outputs": [],
    "source": [
     "try:\n",
-    "    pj.Reference(name=\"my ref\", doi=\"abc.ef\", url=\"myurl.com\")\n",
+    "    ln.Reference(name=\"my ref\", doi=\"abc.ef\", url=\"myurl.com\")\n",
     "except FieldValidationError as e:\n",
     "    print(e)"
    ]

docs/storage/prepare-transfer-local-to-cloud.ipynb

@@ -34,7 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ln.setup.init(storage=\"./test-transfer-to-cloud\", modules=\"bionty,wetlab,ourprojects\")\n",
+    "ln.setup.init(storage=\"./test-transfer-to-cloud\", modules=\"bionty,wetlab\")\n",
     "ln.setup.settings.auto_connect = False"
    ]
   },

lamindb/__init__.py

@@ -1,28 +1,37 @@
 """A data framework for biology.
 
-Core registries.
+Tracking notebooks & scripts.
+
+.. autosummary::
+   :toctree: .
+
+   track
+   finish
+
+Registries.
 
 .. autosummary::
    :toctree: .
 
    Artifact
-   Collection
    Transform
+   ULabel
    Run
    User
    Storage
-   ULabel
    Feature
    FeatureSet
    Param
+   Collection
+   Project
+   Reference
+   Person
 
 Key functionality.
 
 .. autosummary::
    :toctree: .
 
-   track
-   finish
    connect
    Curator
    view
@@ -44,7 +53,7 @@
 """
 
 # denote a release candidate for 0.1.0 with 0.1rc1, 0.1a1, 0.1b1, etc.
-__version__ = "1.0a2"
+__version__ = "1.0a3"
 
 from lamindb_setup._check_setup import InstanceNotSetupError as _InstanceNotSetupError
 from lamindb_setup._check_setup import _check_instance_setup
@@ -87,6 +96,9 @@ def __getattr__(name):
         Feature,
         FeatureSet,
         Param,
+        Person,
+        Project,
+        Reference,
         Run,
         Storage,
         Transform,

lamindb/base/validation.py

@@ -21,9 +21,12 @@ def validate_literal_fields(record: "Record", kwargs) -> None:
     Raises:
         ValidationError: If any field value is not in its Literal's allowed values
     """
+    # check is based on string to avoid circular imports
     if record.__class__.__name__ == "Feature":
         # the FeatureDtype is more complicated than a simple literal
         # because it allows constructs like cat[ULabel] etc.
+        # the User model is used at startup and throws a datetime-related error otherwise
+        # simmilar for Storage & Source
         return None
     try:
         type_hints = get_type_hints(record.__class__)