✨ Add blank=True (#14)

laminlabs · Nov 17, 2024 · f7d75cf · f7d75cf
1 parent 0e22a39
commit f7d75cf
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Showing 8 changed files with 964 additions and 116 deletions.
diff --git a/.gitignore b/.gitignore
@@ -106,4 +106,4 @@ docs/clinicore.*
 lamin_sphinx
 docs/conf.py
 _docs_tmp*
-docs/test-clinicore/
+test-clinicore/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,20 +2,20 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.12.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.4
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         exclude: |
           (?x)(
             docs/changelog.md
           )
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.8.0
     hooks:
       - id: nbstripout
         exclude: |
@@ -24,13 +24,13 @@ repos:
               docs/notes/
           )
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.7.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
       - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
@@ -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: v1.13.0
     hooks:
       - id: mypy
         args: [--no-strict-optional, --ignore-missing-imports]

diff --git a/clinicore/__init__.py b/clinicore/__init__.py
@@ -33,6 +33,8 @@ def __getattr__(name):
 
 
 if _check_instance_setup():
+    import lamindb
+
     del __getattr__  # delete so that imports work out
     from .models import (
         Biosample,

diff --git a/clinicore/migrations/0001_initial.py b/clinicore/migrations/0001_initial.py
@@ -91,7 +91,7 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
         migrations.CreateModel(
             name="Medication",
@@ -179,7 +179,7 @@ class Migration(migrations.Migration):
             bases=(
                 models.Model,
                 lnschema_core.models.HasParents,
-                lnschema_core.models.CanValidate,
+                lnschema_core.models.CanCurate,
             ),
         ),
         migrations.CreateModel(
@@ -263,7 +263,7 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
         migrations.CreateModel(
             name="Project",
@@ -316,7 +316,7 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
         migrations.CreateModel(
             name="Treatment",
@@ -400,6 +400,6 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
     ]
diff --git a/clinicore/migrations/0004_remove_biosample_project_clinicaltrial_and_more.py b/clinicore/migrations/0004_remove_biosample_project_clinicaltrial_and_more.py
@@ -74,7 +74,7 @@ class Migration(migrations.Migration):
             options={
                 "abstract": False,
             },
-            bases=(lnschema_core.models.CanValidate, models.Model),
+            bases=(lnschema_core.models.CanCurate, models.Model),
         ),
         migrations.AddField(
             model_name="biosample",