🎨 Clean up (#15)

clinicore/migrations/0007_alter_artifactbiosample_artifact_and_more.py

@@ -10,7 +10,6 @@
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("bionty", "0041_alter_artifactcellline_artifact_and_more"),
         ("clinicore", "0006_artifactbiosample_artifactclinicaltrial_and_more"),

clinicore/models.py

@@ -48,13 +48,13 @@ class Meta(Record.Meta, TracksRun.Meta, TracksUpdates.Meta):
     """Internal id, valid only in one DB instance."""
     uid: str = CharField(unique=True, max_length=8, default=ids.base62_8)
     """Universal id, valid across DB instances."""
-    name: str | None = CharField(max_length=255, default=None, db_index=True)
+    name: str | None = CharField(max_length=255, db_index=True)
     """ClinicalTrials.gov ID, the format is "NCT" followed by an 8-digit number."""
-    title: str | None = TextField(null=True, default=None)
+    title: str | None = TextField(null=True)
     """Official title of the clinical trial."""
-    objective: str | None = TextField(null=True, default=None)
+    objective: str | None = TextField(null=True)
     """Objective of the clinical trial."""
-    description: str | None = TextField(null=True, default=None)
+    description: str | None = TextField(null=True)
     """Description of the clinical trial."""
     collections: Collection = models.ManyToManyField(
         Collection, related_name="clinical_trials"
@@ -99,11 +99,11 @@ class Biosample(Record, CanCurate, TracksRun, TracksUpdates):
     """Internal id, valid only in one DB instance."""
     uid: str = CharField(unique=True, max_length=12, default=ids.base62_12)
     """Universal id, valid across DB instances."""
-    name: str | None = CharField(max_length=255, default=None, db_index=True, null=True)
+    name: str | None = CharField(db_index=True, null=True)
     """Name of the biosample."""
-    batch: str | None = CharField(max_length=60, default=None, null=True, db_index=True)
+    batch: str | None = CharField(max_length=60, null=True, db_index=True)
     """Batch label of the biosample."""
-    description: str | None = TextField(null=True, default=None)
+    description: str | None = TextField(null=True)
     """Description of the biosample."""
     patient: Patient = ForeignKey(
         "Patient", PROTECT, related_name="biosamples", null=True, default=None
@@ -167,12 +167,12 @@ class Patient(Record, CanCurate, TracksRun, TracksUpdates):
     """Internal id, valid only in one DB instance."""
     uid: str = CharField(unique=True, max_length=12, default=ids.base62_12)
     """Universal id, valid across DB instances. Use this field to model internal patient IDs."""
-    name: str | None = CharField(max_length=255, default=None, db_index=True)
+    name: str | None = CharField(db_index=True)
     """Name of the patient."""
     age: int | None = IntegerField(null=True, default=None, db_index=True)
     """Age of the patient."""
     gender: str | None = CharField(
-        max_length=10, choices=GENDER_CHOICES, null=True, default=None, db_index=True
+        max_length=10, choices=GENDER_CHOICES, null=True, db_index=True
     )
     """Gender of the patient."""
     ethnicity: Ethnicity = ForeignKey(Ethnicity, PROTECT, null=True, default=None)
@@ -220,21 +220,15 @@ class Meta(BioRecord.Meta, TracksRun.Meta, TracksUpdates.Meta):
     """A universal id (hash of selected field)."""
     name: str = CharField(max_length=256, db_index=True)
     """Name of the medication."""
-    ontology_id: str | None = CharField(
-        max_length=32, db_index=True, null=True, default=None
-    )
+    ontology_id: str | None = CharField(max_length=32, db_index=True, null=True)
     """Ontology ID of the medication."""
-    chembl_id: str | None = CharField(
-        max_length=32, db_index=True, null=True, default=None
-    )
+    chembl_id: str | None = CharField(max_length=32, db_index=True, null=True)
     """ChEMBL ID of the medication."""
-    abbr: str | None = CharField(
-        max_length=32, db_index=True, unique=True, null=True, default=None
-    )
+    abbr: str | None = CharField(max_length=32, db_index=True, unique=True, null=True)
     """A unique abbreviation of medication."""
-    synonyms: str | None = TextField(null=True, default=None)
+    synonyms: str | None = TextField(null=True)
     """Bar-separated (|) synonyms that correspond to this medication."""
-    description: str | None = TextField(null=True, default=None)
+    description: str | None = TextField(null=True)
     """Description of the medication."""
     parents: Medication = models.ManyToManyField(
         "self", symmetrical=False, related_name="children"
@@ -311,27 +305,25 @@ class Treatment(Record, CanCurate, TracksRun, TracksUpdates):
     """Internal id, valid only in one DB instance."""
     uid: str = CharField(unique=True, max_length=12, default=ids.base62_12)
     """Universal id, valid across DB instances."""
-    name: str | None = CharField(max_length=255, default=None, db_index=True)
+    name: str | None = CharField(db_index=True)
     """Name of the treatment."""
-    status: str | None = CharField(
-        max_length=16, choices=STATUS_CHOICES, null=True, default=None
-    )
+    status: str | None = CharField(max_length=16, choices=STATUS_CHOICES, null=True)
     """Status of the treatment."""
     medication: Medication | None = ForeignKey(
         Medication, PROTECT, null=True, default=None
     )
     """Medications linked to the treatment."""
     dosage: float | None = FloatField(null=True, default=None)
     """Dosage of the treatment."""
-    dosage_unit: str | None = CharField(max_length=32, null=True, default=None)
+    dosage_unit: str | None = CharField(max_length=32, null=True)
     """Unit of the dosage."""
     administered_datetime: datetime | None = DateTimeField(null=True, default=None)
     """Date and time the treatment was administered."""
     duration: DurationField = DurationField(null=True, default=None)
     """Duration of the treatment."""
-    route: str | None = CharField(max_length=32, null=True, default=None)
+    route: str | None = CharField(max_length=32, null=True)
     """Route of administration of the treatment."""
-    site: str | None = CharField(max_length=32, null=True, default=None)
+    site: str | None = CharField(max_length=32, null=True)
     """Body site of administration of the treatment."""
     artifacts: Artifact = models.ManyToManyField(
         Artifact, through="ArtifactTreatment", related_name="treatments"

docs/quickstart.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "7f26a335-cf1c-4e69-be3b-0c26b154606a",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Quickstart"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f37ebcaa",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a51faaf3-ee27-43c6-b48d-13be1adb5c46",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a1e61ead",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,17 +41,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c71693bf",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
-    "clinical_trail = cl.ClinicalTrial(name=\"NCT00000000\", title=\"This is a test clinical trial\").save()"
+    "clinical_trail = cl.ClinicalTrial(\n",
+    "    name=\"NCT00000000\", title=\"This is a test clinical trial\"\n",
+    ").save()"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5d3f489d",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -61,7 +63,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7f19edc5",
+   "id": "6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +76,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "47078824",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +86,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "81d079b6",
+   "id": "8",
    "metadata": {},
    "outputs": [],
    "source": [

pyproject.toml

@@ -8,7 +8,7 @@ authors = [{name = "Lamin Labs", email = "[email protected]"}]
 readme = "README.md"
 dynamic = ["version", "description"]
 dependencies = [
-    "lamindb[bionty,aws]",
+    "lamindb[bionty]>=0.77.0",
 ]
 
 [project.urls]
@@ -31,7 +31,7 @@ testpaths = [
 [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
@@ -48,7 +48,7 @@ select = [
     "PTH",  # Use pathlib
     "S"  # Security
 ]
-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.
@@ -119,10 +119,10 @@ ignore = [
     "S607",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "google"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "docs/*" = ["I"]
 "tests/**/*.py" = [
     "D",  # docstrings are allowed to look a bit off