🎨 Rename CanValidate to CanCurate

laminlabs · Nov 15, 2024 · 457050c · 457050c
1 parent 626d35c
commit 457050c
Show file tree

Hide file tree

Showing 5 changed files with 21 additions and 23 deletions.
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/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",

diff --git a/clinicore/models.py b/clinicore/models.py
@@ -21,7 +21,7 @@
 )
 from lnschema_core.models import (
     Artifact,
-    CanValidate,
+    CanCurate,
     Collection,
     Feature,
     LinkORM,
@@ -31,7 +31,7 @@
 )
 
 
-class ClinicalTrial(Record, CanValidate, TracksRun, TracksUpdates):
+class ClinicalTrial(Record, CanCurate, TracksRun, TracksUpdates):
     """Models a ClinicalTrials.
 
     Example:
@@ -85,7 +85,7 @@ class ArtifactClinicalTrial(Record, LinkORM, TracksRun):
     feature_ref_is_name: bool | None = BooleanField(null=True, default=None)
 
 
-class Biosample(Record, CanValidate, TracksRun, TracksUpdates):
+class Biosample(Record, CanCurate, TracksRun, TracksUpdates):
     """Models a specimen derived from an patient, such as tissue, blood, or cells.
 
     Examples:
@@ -144,7 +144,7 @@ class ArtifactBiosample(Record, LinkORM, TracksRun):
     feature_ref_is_name: bool | None = BooleanField(null=True, default=None)
 
 
-class Patient(Record, CanValidate, TracksRun, TracksUpdates):
+class Patient(Record, CanCurate, TracksRun, TracksUpdates):
     """Models a patient in a clinical study.
 
     Examples:
@@ -255,15 +255,13 @@ def __init__(
         description: str | None,
         parents: list[Medication],
         source: Source | None,
-    ):
-        ...
+    ): ...
 
     @overload
     def __init__(
         self,
         *db_args,
-    ):
-        ...
+    ): ...
 
     def __init__(
         self,
@@ -290,7 +288,7 @@ class ArtifactMedication(Record, LinkORM, TracksRun):
     feature_ref_is_name: bool | None = BooleanField(null=True, default=None)
 
 
-class Treatment(Record, CanValidate, TracksRun, TracksUpdates):
+class Treatment(Record, CanCurate, TracksRun, TracksUpdates):
     """Models compound treatments such as drugs.
 
     Examples:

diff --git a/pyproject.toml b/pyproject.toml
@@ -116,7 +116,7 @@ ignore = [
     # subprocess` call: check for execution of untrusted input - https://github.com/PyCQA/bandit/issues/333
     "S603",
     # Starting a process with a partial executable path
-    "S607"
+    "S607",
 ]
 
 [tool.ruff.pydocstyle]