Merge branch 'release/0.1.15' into main

.github/workflows/build.yml

@@ -11,11 +11,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11']
-        django-version: ['4.1', '4.2', 'dev']
-        exclude:
-          - python-version: '3.10'
-            django-version: 'dev'
+        python-version: ['3.11']
+        django-version: ['4.2', 'dev']
     services:
       mysql:
         image: mysql:latest

.pre-commit-config.yaml

@@ -10,13 +10,13 @@ repos:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3.10
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         args:
@@ -42,7 +42,7 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.31.0
+    rev: v1.32.0
     hooks:
       - id: yamllint
         args:

edc_microbiology/tests/tests/test_form.py

@@ -1,14 +1,16 @@
-from decimal import Decimal
-
 from django import forms
 from django.core.exceptions import ValidationError
 from django.test import TestCase
+from edc_appointment.models import Appointment
+from edc_appointment.tests.helper import Helper
 from edc_constants.constants import NO, NOT_APPLICABLE, OTHER, POS, YES
 from edc_crf.crf_form_validator_mixins import BaseFormValidatorMixin
 from edc_form_validators import FormValidator
-from edc_registration.models import RegisteredSubject
+from edc_reference import site_reference_configs
 from edc_utils import get_utcnow
-from edc_visit_schedule.constants import DAY1
+from edc_visit_schedule.site_visit_schedules import site_visit_schedules
+from edc_visit_tracking.constants import SCHEDULED
+from edc_visit_tracking.models import SubjectVisit
 
 from edc_microbiology.constants import (
     BACTERIA,
@@ -17,8 +19,7 @@
     NO_GROWTH,
 )
 from edc_microbiology.form_validators import MicrobiologyFormValidatorMixin
-
-from ..models import Appointment, SubjectVisit
+from microbiology_app.visit_schedule import visit_schedule
 
 
 class MicrobiologyFormValidator(
@@ -32,22 +33,31 @@ class MicrobiologyFormValidator(
 
 
 class TestMicrobiologyFormValidator(TestCase):
+    helper_cls = Helper
+
     def setUp(self):
-        self.subject_identifier = "1234"
-        RegisteredSubject.objects.create(
-            subject_identifier=self.subject_identifier,
-            randomization_datetime=get_utcnow(),
+        self.subject_identifier = "1235"
+        self.helper = self.helper_cls(subject_identifier=self.subject_identifier)
+        self.visit_schedule_name = "visit_schedule"
+        self.schedule_name = "schedule"
+
+        site_visit_schedules._registry = {}
+        site_visit_schedules.loaded = False
+        site_visit_schedules.register(visit_schedule)
+
+        site_reference_configs.registry = {}
+        site_reference_configs.register_from_visit_schedule(
+            visit_models={"edc_appointment.appointment": "edc_visit_tracking.subjectvisit"}
         )
-        appointment = Appointment.objects.create(
-            subject_identifier=self.subject_identifier,
-            appt_datetime=get_utcnow(),
-            visit_code=DAY1,
-            visit_schedule_name="visit_schedule",
-            schedule_name="schedule",
-            timepoint=Decimal("0.0"),
+
+        self.helper.consent_and_put_on_schedule(
+            visit_schedule_name="visit_schedule", schedule_name="schedule"
         )
+        appointment = Appointment.objects.all().order_by("timepoint_datetime")[0]
         self.subject_visit = SubjectVisit.objects.create(
-            appointment=appointment, subject_identifier=self.subject_identifier
+            appointment=appointment,
+            subject_identifier=self.subject_identifier,
+            reason=SCHEDULED,
         )
 
     def test_urine_culture_performed_yes_require_urine_culture_result(self):

microbiology_app/apps.py

@@ -0,0 +1,5 @@
+from django.apps import AppConfig as DjangoAppConfig
+
+
+class AppConfig(DjangoAppConfig):
+    name = "microbiology_app"

microbiology_app/models.py

@@ -0,0 +1,61 @@
+from datetime import date
+
+from django.db import models
+from django.db.models import PROTECT
+from edc_crf.model_mixins import CrfModelMixin
+from edc_identifier.managers import SubjectIdentifierManager
+from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
+from edc_model.models import BaseUuidModel
+from edc_registration.model_mixins import UpdatesOrCreatesRegistrationModelMixin
+from edc_screening.model_mixins import ScreeningModelMixin
+from edc_sites.models import SiteModelMixin
+from edc_utils import get_utcnow
+from edc_visit_schedule.model_mixins import OffScheduleModelMixin, OnScheduleModelMixin
+from edc_visit_tracking.models import SubjectVisit
+
+
+class SubjectScreening(ScreeningModelMixin, BaseUuidModel):
+    objects = SubjectIdentifierManager()
+
+
+class SubjectConsent(
+    SiteModelMixin,
+    NonUniqueSubjectIdentifierFieldMixin,
+    UpdatesOrCreatesRegistrationModelMixin,
+    BaseUuidModel,
+):
+    report_datetime = models.DateTimeField(default=get_utcnow)
+
+    consent_datetime = models.DateTimeField(default=get_utcnow)
+
+    version = models.CharField(max_length=25, default="1")
+
+    identity = models.CharField(max_length=25)
+
+    confirm_identity = models.CharField(max_length=25)
+
+    dob = models.DateField(default=date(1995, 1, 1))
+
+
+class OnSchedule(SiteModelMixin, OnScheduleModelMixin, BaseUuidModel):
+    pass
+
+
+class OffSchedule(SiteModelMixin, OffScheduleModelMixin, BaseUuidModel):
+    pass
+
+
+class CrfOne(CrfModelMixin, BaseUuidModel):
+    subject_visit = models.ForeignKey(SubjectVisit, on_delete=PROTECT)
+
+    report_datetime = models.DateTimeField(default=get_utcnow)
+
+    f1 = models.CharField(max_length=50, null=True, blank=True)
+
+    f2 = models.CharField(max_length=50, null=True, blank=True)
+
+    f3 = models.CharField(max_length=50, null=True, blank=True)
+
+    next_appt_date = models.DateField(null=True, blank=True)
+
+    next_visit_code = models.CharField(max_length=50, null=True, blank=True)

microbiology_app/urls.py

@@ -0,0 +1,15 @@
+from django.contrib import admin
+from django.urls import include, path
+from django.views.generic import RedirectView
+
+app_name = "microbiology_app"
+
+
+urlpatterns = []
+
+
+urlpatterns += [
+    path("admin/", admin.site.urls),
+    path("i18n/", include("django.conf.urls.i18n")),
+    path("", RedirectView.as_view(url="admin/"), name="logout"),
+]

microbiology_app/visit_schedule.py

@@ -0,0 +1,67 @@
+from dateutil.relativedelta import relativedelta
+from edc_visit_schedule.schedule import Schedule
+from edc_visit_schedule.visit import Crf, FormsCollection, Visit
+from edc_visit_schedule.visit_schedule import VisitSchedule
+
+crfs = FormsCollection(Crf(show_order=1, model="microbiology_app.crfone", required=True))
+
+visit0 = Visit(
+    code="1000",
+    title="Day 1",
+    timepoint=0,
+    rbase=relativedelta(days=0),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+visit1 = Visit(
+    code="2000",
+    title="Day 2",
+    timepoint=1,
+    rbase=relativedelta(days=1),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+visit2 = Visit(
+    code="3000",
+    title="Day 3",
+    timepoint=2,
+    rbase=relativedelta(days=2),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+visit3 = Visit(
+    code="4000",
+    title="Day 4",
+    timepoint=3,
+    rbase=relativedelta(days=3),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+schedule = Schedule(
+    name="schedule",
+    onschedule_model="microbiology_app.onschedule",
+    offschedule_model="microbiology_app.offschedule",
+    appointment_model="edc_appointment.appointment",
+    consent_model="microbiology_app.subjectconsent",
+)
+
+schedule.add_visit(visit0)
+schedule.add_visit(visit1)
+schedule.add_visit(visit2)
+schedule.add_visit(visit3)
+
+visit_schedule = VisitSchedule(
+    name="visit_schedule",
+    offstudy_model="edc_offstudy.subjectoffstudy",
+    death_report_model="edc_adverse_event.deathreport",
+)
+
+visit_schedule.add_schedule(schedule)

pyproject.toml

@@ -1,18 +1,17 @@
 [build-system]
-requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
-build-backend = "setuptools.build_meta"
+requires = ["setuptools>=60", "setuptools-scm>=8.0"]
 
 [tool.setuptools_scm]
-write_to = "_version.py"
+version_file="_version.py"
 
 [tool.black]
 line-length = 95
-target-version = ["py310"]
+target-version = ["py311"]
 extend-exclude = '''^(.*\/)*\b(migrations)\b($|\/.*$)'''
 
 [tool.isort]
 profile = "black"
-py_version = "310"
+py_version = "311"
 skip = [".tox", ".eggs", "migrations"]
 
 [tool.coverage.run]
@@ -36,15 +35,13 @@ exclude_lines = [
 legacy_tox_ini = """
 [tox]
 envlist =
-    py{310}-dj{41,42},
     py{311}-dj{41,42,dev},
     lint
 
 isolated_build = true
 
 [gh-actions]
 python =
-    3.10: py310
     3.11: py311, lint
 
 [gh-actions:env]

runtests.py

@@ -7,19 +7,26 @@
 import django
 from django.conf import settings
 from django.test.runner import DiscoverRunner
+from edc_constants.constants import IGNORE
 from edc_test_utils import DefaultTestSettings
 
 app_name = "edc_microbiology"
 base_dir = dirname(abspath(__file__))
 
 DEFAULT_SETTINGS = DefaultTestSettings(
     calling_file=__file__,
-    template_dirs=[os.path.join(base_dir, app_name, "tests", "templates")],
     BASE_DIR=base_dir,
     APP_NAME=app_name,
-    ETC_DIR=os.path.join(base_dir, app_name, "tests", "etc"),
-    SUBJECT_VISIT_MODEL="edc_microbiology.subjectvisit",
-    SUBJECT_VISIT_MISSED_MODEL="edc_appointment.subjectvisitmissed",
+    ETC_DIR=os.path.join(base_dir, "edc_microbiology", "tests", "etc"),
+    SUBJECT_VISIT_MODEL="edc_visit_tracking.subjectvisit",
+    SUBJECT_VISIT_MISSED_MODEL="edc_visit_tracking.subjectvisitmissed",
+    SUBJECT_SCREENING_MODEL="microbiology_app.subjectscreening",
+    SUBJECT_CONSENT_MODEL="microbiology_app.subjectconsent",
+    SUBJECT_REQUISITION_MODEL="microbiology_app.subjectrequisition",
+    SUBJECT_APP_LABEL="microbiology_app",
+    EDC_NAVBAR_DEFAULT=app_name,
+    EDC_NAVBAR_VERIFY_ON_LOAD=IGNORE,
+    EDC_AUTH_SKIP_SITE_AUTHS=True,
     INSTALLED_APPS=[
         "django.contrib.admin",
         "django.contrib.auth",
@@ -32,17 +39,27 @@
         "multisite",
         "django_crypto_fields.apps.AppConfig",
         "edc_auth.apps.AppConfig",
+        "edc_action_item.apps.AppConfig",
         "edc_appointment.apps.AppConfig",
         "edc_notification.apps.AppConfig",
         "edc_export.apps.AppConfig",
         "edc_crf.apps.AppConfig",
+        "edc_device.apps.AppConfig",
+        "edc_identifier.apps.AppConfig",
         "edc_timepoint.apps.AppConfig",
         "edc_registration.apps.AppConfig",
         "edc_metadata.apps.AppConfig",
+        "edc_facility.apps.AppConfig",
+        "edc_offstudy.apps.AppConfig",
+        "edc_reference.apps.AppConfig",
         "edc_sites.apps.AppConfig",
+        "edc_visit_schedule.apps.AppConfig",
+        "edc_visit_tracking.apps.AppConfig",
         "edc_microbiology.apps.AppConfig",
+        "microbiology_app.apps.AppConfig",
     ],
     add_dashboard_middleware=True,
+    use_test_urls=False,
 ).settings