🐛 Simplify __repr__ and test for __repr__

.github/workflows/build.yml

@@ -14,16 +14,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     timeout-minutes: 15
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: "pip"
-          cache-dependency-path: ".github/workflows/build.yml" # See dependencies below
       - name: cache pre-commit
         uses: actions/cache@v3
         with:

lnschema_core/models.py

@@ -621,11 +621,11 @@ def _get_related_field_type(field) -> str:
             )
 
         non_external_schema_fields_formatted = [
-            f"    .{field.name.replace('_links', '')}: {_get_related_field_type(field)}\n"
+            f"    .{field.name}: {_get_related_field_type(field)}\n"
             for field in non_external_schema_fields
         ]
         external_schema_fields_formatted = [
-            f"    .{field.name.replace('_links', '')}: {_get_related_field_type(field)}\n"
+            f"    .{field.name}: {_get_related_field_type(field)}\n"
             for field in external_schema_fields
         ]
 

noxfile.py

@@ -1,5 +1,5 @@
 import nox
-from laminci.nox import login_testuser1, run, run_pre_commit, run_pytest
+from laminci.nox import run, run_pre_commit, run_pytest
 
 nox.options.default_venv_backend = "none"
 
@@ -11,9 +11,9 @@ def lint(session: nox.Session) -> None:
 
 @nox.session
 def test(session: nox.Session) -> None:
-    run(session, "pip install -e .[dev]")
+    run(session, "uv pip install --system -e .[dev]")
     run(
         session,
-        "pip install lamindb_setup@git+https://github.com/laminlabs/lamindb-setup",
+        "uv pip install --system lamindb[bionty]@git+https://github.com/laminlabs/lamindb",
     )
     run_pytest(session, coverage=False)

pyproject.toml

@@ -12,6 +12,7 @@ classifiers = [
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
 ]
 # mandate zero dependencies
 dependencies = [
@@ -44,7 +45,7 @@ omit = [
 [tool.ruff]
 src = ["src"]
 line-length = 88
-select = [
+lint.select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
     "W",  # Warning detected by Pycodestyle
@@ -60,7 +61,7 @@ select = [
     "NPY",  # Numpy specific rules
     "PTH"  # Use pathlib
 ]
-ignore = [
+lint.ignore = [
     # Do not catch blind exception: `Exception`
     "BLE001",
     # Errors from function calls in argument defaults. These are fine when the result is immutable.
@@ -129,10 +130,10 @@ ignore = [
     "PTH123",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "google"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]

tests/test_integrity.py

@@ -3,15 +3,15 @@
 
 
 @pytest.fixture(scope="module")
-def setup_instance():
-    ln_setup.init(storage="./testdb")
+def setup_bionty_instance():
+    ln_setup.init(storage="./test-bionty-db", schema="bionty")
     yield
-    ln_setup.delete("testdb", force=True)
+    ln_setup.delete("test-bionty-db", force=True)
 
 
-def test_migrate_check(setup_instance):
+def test_migrate_check(setup_bionty_instance):
     assert ln_setup.migrate.check()
 
 
-def test_system_check(setup_instance):
+def test_system_check(setup_bionty_instance):
     ln_setup.django("check")

tests/test_models.py

@@ -0,0 +1,94 @@
+import re
+import textwrap
+
+import lamindb as ln
+
+# The tests defined in this script use the lamindb instance defined in test_integrity
+
+
+def _strip_ansi(text: str) -> str:
+    """Remove ANSI escape sequences from a string."""
+    ansi_escape = re.compile(r"\x1B(?:[@-Z\\-_]|\[[0-?]*[ -/]*[@-~])")
+    return ansi_escape.sub("", text)
+
+
+def test_registry__repr__param():
+    param = ln.Param
+    expected_repr = textwrap.dedent("""\
+    Param
+      Basic fields
+        .id: BigAutoField
+        .name: CharField
+        .dtype: CharField
+        .created_at: DateTimeField
+        .updated_at: DateTimeField
+      Relational fields
+        .created_by: User
+        .run: Run
+        .previous_runs: Run
+        .paramvalue: ParamValue
+    """).strip()
+
+    actual_repr = _strip_ansi(repr(param))
+    assert actual_repr.strip() == expected_repr.strip()
+
+
+def test_registry__repr__artifact():
+    artifact = ln.Artifact
+    expected_repr = textwrap.dedent("""\
+    Artifact
+      Basic fields
+        .id: AutoField
+        .uid: CharField
+        .description: CharField
+        .key: CharField
+        .suffix: CharField
+        .type: CharField
+        .accessor: CharField
+        .size: BigIntegerField
+        .hash: CharField
+        .hash_type: CharField
+        .n_objects: BigIntegerField
+        .n_observations: BigIntegerField
+        .visibility: SmallIntegerField
+        .key_is_virtual: BooleanField
+        .version: CharField
+        .created_at: DateTimeField
+        .updated_at: DateTimeField
+      Relational fields
+        .created_by: User
+        .storage: Storage
+        .transform: Transform
+        .run: Run
+        .ulabels: ULabel
+        .input_of: Run
+        .previous_runs: Run
+        .feature_sets: FeatureSet
+        .feature_values: FeatureValue
+        .param_values: ParamValue
+        .latest_report_of: Transform
+        .source_code_of: Transform
+        .report_of: Run
+        .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))
+    assert actual_repr.strip() == expected_repr.strip()