➖ Remove bionty & lamindb from dependencies (#408)

* 🔥 Remove bionty from dependencies

* ✏️ Typo

* 💚 Fix dependency

* 💚 Global fixture

* 🔥 Remove unnecessary duplication

* 💚 Fix

noxfile.py

@@ -14,6 +14,6 @@ def test(session: nox.Session) -> None:
     run(session, "uv pip install --system -e .[dev]")
     run(
         session,
-        "uv pip install --system lamindb[bionty]@git+https://github.com/laminlabs/lamindb",
+        "uv pip install --system lamindb_setup@git+https://github.com/laminlabs/lamindb-setup",
     )
     run_pytest(session, coverage=False)

tests/conftest.py

@@ -0,0 +1,9 @@
+import lamindb_setup as ln_setup
+import pytest
+
+
+@pytest.fixture(scope="session")
+def setup_instance():
+    ln_setup.init(storage="./testdb")
+    yield
+    ln_setup.delete("testdb", force=True)

tests/test_integrity.py

@@ -2,16 +2,9 @@
 import pytest
 
 
-@pytest.fixture(scope="module")
-def setup_bionty_instance():
-    ln_setup.init(storage="./test-bionty-db", schema="bionty")
-    yield
-    ln_setup.delete("test-bionty-db", force=True)
-
-
-def test_migrate_check(setup_bionty_instance):
+def test_migrate_check(setup_instance):
     assert ln_setup.migrate.check()
 
 
-def test_system_check(setup_bionty_instance):
+def test_system_check(setup_instance):
     ln_setup.django("check")

tests/test_models.py

@@ -1,8 +1,6 @@
 import re
 import textwrap
 
-import lamindb as ln
-
 # The tests defined in this script use the lamindb instance defined in test_integrity
 
 
@@ -12,7 +10,9 @@ def _strip_ansi(text: str) -> str:
     return ansi_escape.sub("", text)
 
 
-def test_registry__repr__param():
+def test_registry__repr__param(setup_instance):
+    import lnschema_core.models as ln
+
     param = ln.Param
     expected_repr = textwrap.dedent("""\
     Param
@@ -33,7 +33,9 @@ def test_registry__repr__param():
     assert actual_repr.strip() == expected_repr.strip()
 
 
-def test_registry__repr__artifact():
+def test_registry__repr__artifact(setup_instance):
+    import lnschema_core.models as ln
+
     artifact = ln.Artifact
     expected_repr = textwrap.dedent("""\
     Artifact
@@ -72,22 +74,6 @@ def test_registry__repr__artifact():
         .environment_of: Run
         .collection: Collection
         .collections: Collection
-      Bionty fields
-        .organisms: bionty.Organism
-        .genes: bionty.Gene
-        .proteins: bionty.Protein
-        .cell_markers: bionty.CellMarker
-        .tissues: bionty.Tissue
-        .cell_types: bionty.CellType
-        .diseases: bionty.Disease
-        .cell_lines: bionty.CellLine
-        .phenotypes: bionty.Phenotype
-        .pathways: bionty.Pathway
-        .experimental_factors: bionty.ExperimentalFactor
-        .developmental_stages: bionty.DevelopmentalStage
-        .ethnicities: bionty.Ethnicity
-        .reference_of_source: bionty.Source
-        .reference_of_sources: bionty.Source
     """).strip()
 
     actual_repr = _strip_ansi(repr(artifact))