🎨 Order artifact collections

.github/workflows/build.yml

@@ -14,16 +14,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ['3.10']
     timeout-minutes: 15
 
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
-          cache-dependency-path: ".github/workflows/build.yml" # See dependencies below
+          cache: 'pip'
+          cache-dependency-path: '.github/workflows/build.yml' # See dependencies below
       - name: cache pre-commit
         uses: actions/cache@v3
         with:

.pre-commit-config.yaml

@@ -34,6 +34,11 @@ repos:
     rev: v2.6.2
     hooks:
       - id: prettier
+        exclude: |
+          (?x)(
+              build.yml|
+              .pre-commit-config.yaml
+          )
   - repo: https://github.com/kynan/nbstripout
     rev: 0.3.9
     hooks:
@@ -53,7 +58,7 @@ repos:
     hooks:
       - id: isort
         name: isort (python)
-        args: ["--profile", "black"]
+        args: ['--profile', 'black']
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.940
     hooks:

lnschema_core/migrations/0039_remove_collection_artifacts_collectionartifact_and_more.py

@@ -0,0 +1,39 @@
+# Generated by Django 5.1 on 2024-01-07 19:08
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+import lnschema_core.models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("lnschema_core", "0038_alter_collection_artifact_alter_collection_artifacts_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="CollectionArtifact",
+            fields=[
+                ("id", models.BigAutoField(primary_key=True, serialize=False)),
+                ("collection", models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="lnschema_core.collection")),
+                ("artifact", models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="lnschema_core.artifact")),
+            ],
+            options={
+                "unique_together": {("collection", "artifact")},
+            },
+            bases=(models.Model, lnschema_core.models.LinkORM),
+        ),
+        migrations.AddField(
+            model_name="collection",
+            name="unordered_artifacts",
+            field=models.ManyToManyField(related_name="collections", through="lnschema_core.CollectionArtifact", to="lnschema_core.artifact"),
+        ),
+        migrations.RunSQL(
+            "INSERT INTO lnschema_core_collectionartifact (id, collection_id, artifact_id) SELECT id, collection_id, artifact_id FROM lnschema_core_collection_artifacts"
+        ),
+        migrations.RemoveField(
+            model_name="collection",
+            name="artifacts",
+        ),
+    ]

lnschema_core/models.py

@@ -1913,7 +1913,7 @@ class Collection(Registry, Data, IsVersioned):
     """Runs that use this collection as an input."""
     artifact = models.OneToOneField("Artifact", on_delete=PROTECT, null=True, unique=True, related_name="collection")
     """Storage of collection as a one artifact."""
-    artifacts = models.ManyToManyField("Artifact", related_name="collections")
+    unordered_artifacts = models.ManyToManyField("Artifact", related_name="collections", through="CollectionArtifact")
     """Storage of collection as multiple artifacts."""
     visibility = models.SmallIntegerField(db_index=True, choices=VisibilityChoice.choices, default=1)
     """Visibility of record,  0-default, 1-hidden, 2-trash."""
@@ -1924,6 +1924,11 @@ class Collection(Registry, Data, IsVersioned):
     created_by = models.ForeignKey(User, PROTECT, default=current_user_id, related_name="created_collections")
     """Creator of record, a :class:`~lamindb.User`."""
 
+    @property
+    def artifacts(self) -> "QuerySet":
+        """Ordered QuerySet of artifacts."""
+        pass
+
     @overload
     def __init__(
         self,
@@ -2046,7 +2051,7 @@ def from_anndata(
     def mapped(
         self,
         label_keys: Optional[Union[str, List[str]]] = None,
-        join: Optional[Literal["inner", "outer"]] = "outer",
+        join: Optional[Literal["inner", "outer"]] = "inner",
         encode_labels: bool = True,
         cache_categories: bool = True,
         parallel: bool = False,
@@ -2160,6 +2165,15 @@ class Meta:
         unique_together = ("collection", "feature_set")
 
 
+class CollectionArtifact(Registry, LinkORM):
+    id = models.BigAutoField(primary_key=True)
+    collection = models.ForeignKey(Collection, on_delete=models.CASCADE)
+    artifact = models.ForeignKey(Artifact, on_delete=models.CASCADE)
+
+    class Meta:
+        unique_together = ("collection", "artifact")
+
+
 class ArtifactULabel(Registry, LinkORM):
     id = models.BigAutoField(primary_key=True)
     artifact = models.ForeignKey(Artifact, on_delete=models.CASCADE)

noxfile.py

@@ -12,5 +12,4 @@ def lint(session: nox.Session) -> None:
 @nox.session
 def test(session: nox.Session) -> None:
     session.run(*"pip install -e .[dev]".split())
-    login_testuser1(session)
     run_pytest(session, coverage=False)

pyproject.toml

@@ -21,7 +21,7 @@ Home = "https://github.com/laminlabs/lnschema-core"
 
 [project.optional-dependencies]
 dev = [
-    "lamindb_setup>=0.55.0",  # not possible on PyPI:  @ git+https://github.com/laminlabs/lamindb-setup
+    "lamindb_setup@git+https://github.com/laminlabs/lamindb-setup",
     "pre-commit",
     "nox",
     "laminci",