Merge branch 'release/0.3.10' into main

.github/workflows/build.yml

@@ -5,20 +5,17 @@ on: [push, pull_request]
 
 jobs:
   build:
-    name: build (Python ${{ matrix.python-version }}, Django ${{ matrix.django-version }})
+    name: |
+      build (Python ${{ matrix.python-version }}, Django ${{ matrix.django-version }}, ${{ matrix.database-engine }})
     runs-on: ubuntu-latest
 
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11', '3.12']
-        django-version: ['4.2', '5.0', 'dev']
+        python-version: ['3.12']
+        django-version: ['4.2', '5.1', 'dev']
+        database-engine: ["mysql", "postgres"]
 
-        exclude:
-          - python-version: '3.12'
-            django-version: '4.2'
-          - python-version: '3.11'
-            django-version: 'dev'
     services:
       mysql:
         image: mysql:latest
@@ -28,6 +25,17 @@ jobs:
         ports:
           - 3306:3306
         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
+      postgres:
+        image: postgres:latest
+        env:
+          POSTGRES_PASSWORD: postgres
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
 
     steps:
       - name: Install pycups and words dependency
@@ -61,7 +69,6 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/tox.txt
 
-
       - name: Tox tests
         run: |
           tox -v

.pre-commit-config.yaml

@@ -3,20 +3,20 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.7
+    rev: 1.7.9
     hooks:
       - id: bandit
         args:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 24.2.0
+    rev: 24.8.0
     hooks:
       - id: black
-        language_version: python3.11
+        language_version: python3.12
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         args:
@@ -28,21 +28,22 @@ repos:
       - id: isort
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
-      - id: requirements-txt-fixer
-        files: requirements/.*\.txt$
-      - id: trailing-whitespace
       - id: check-added-large-files
-      - id: fix-byte-order-marker
       - id: check-docstring-first
       - id: check-executables-have-shebangs
       - id: check-merge-conflict
+      - id: check-toml
       - id: debug-statements
       - id: detect-private-key
+      - id: fix-byte-order-marker
+      - id: requirements-txt-fixer
+        files: requirements/.*\.txt$
+      - id: trailing-whitespace
 
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.34.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args:

edc_pharmacy/migrations/0023_remove_rx_edc_pharmac_modifie_986021_idx_and_more.py

@@ -0,0 +1,27 @@
+# Generated by Django 5.1 on 2024-09-09 14:04
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_action_item", "0037_remove_actionitem_reference_model_and_more"),
+        ("edc_pharmacy", "0022_alter_historicalproduct_site_alter_historicalrx_site_and_more"),
+        ("sites", "0002_alter_domain_unique"),
+    ]
+
+    operations = [
+        migrations.RemoveIndex(
+            model_name="rx",
+            name="edc_pharmac_modifie_986021_idx",
+        ),
+        migrations.RemoveIndex(
+            model_name="rx",
+            name="edc_pharmac_user_mo_b9ac53_idx",
+        ),
+        migrations.AddIndex(
+            model_name="rx",
+            index=models.Index(fields=["rando_sid"], name="edc_pharmac_rando_s_0bcc84_idx"),
+        ),
+    ]

edc_pharmacy/models/rx.py

@@ -2,7 +2,7 @@
 
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import models
-from django.db.models import PROTECT
+from django.db.models import PROTECT, Index
 from edc_action_item.models import ActionModelMixin
 from edc_constants.constants import NEW
 from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
@@ -133,3 +133,4 @@ def description(self):
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Prescription"
         verbose_name_plural = "Prescriptions"
+        indexes = [Index(fields=["rando_sid"])]

edc_pharmacy/tests/__init__.py

@@ -1 +0,0 @@
-from .models import OffSchedule, OnSchedule, StudyMedication

edc_pharmacy/tests/consents.py

@@ -1,5 +1,4 @@
 from edc_consent.consent_definition import ConsentDefinition
-from edc_consent.site_consents import site_consents
 from edc_constants.constants import FEMALE, MALE
 from edc_protocol.research_protocol_config import ResearchProtocolConfig
 
@@ -13,4 +12,3 @@
     age_max=64,
     gender=[MALE, FEMALE],
 )
-site_consents.register(consent_v1)

edc_pharmacy/tests/test_settings.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python
+import sys
+from pathlib import Path
+
+from dateutil.relativedelta import relativedelta
+from edc_test_settings.default_test_settings import DefaultTestSettings
+from edc_utils import get_utcnow
+
+app_name = "edc_pharmacy"
+base_dir = Path(__file__).absolute().parent.parent.parent
+
+project_settings = DefaultTestSettings(
+    calling_file=__file__,
+    SILENCED_SYSTEM_CHECKS=["sites.E101", "edc_navbar.E002", "edc_navbar.E003"],
+    EDC_AUTH_CODENAMES_WARN_ONLY=True,
+    EDC_AUTH_SKIP_SITE_AUTHS=True,
+    EDC_AUTH_SKIP_AUTH_UPDATER=True,
+    BASE_DIR=base_dir,
+    APP_NAME=app_name,
+    EDC_SITES_REGISTER_DEFAULT=True,
+    EDC_PROTOCOL_STUDY_OPEN_DATETIME=(
+        get_utcnow().replace(microsecond=0, second=0, minute=0, hour=0)
+        - relativedelta(years=6)
+    ),
+    EDC_PROTOCOL_STUDY_CLOSE_DATETIME=(
+        get_utcnow().replace(microsecond=999999, second=59, minute=59, hour=11)
+        + relativedelta(years=6)
+    ),
+    INSTALLED_APPS=[
+        "django.contrib.admin",
+        "django.contrib.auth",
+        "django.contrib.contenttypes",
+        "django.contrib.sessions",
+        "django.contrib.messages",
+        "django.contrib.staticfiles",
+        "django.contrib.sites",
+        "django_crypto_fields.apps.AppConfig",
+        "multisite",
+        "edc_action_item.apps.AppConfig",
+        "edc_adverse_event.apps.AppConfig",
+        "adverse_event_app.apps.AppConfig",
+        "edc_appointment.apps.AppConfig",
+        "edc_device.apps.AppConfig",
+        "edc_facility.apps.AppConfig",
+        "edc_identifier.apps.AppConfig",
+        "edc_list_data.apps.AppConfig",
+        "edc_metadata.apps.AppConfig",
+        "edc_notification.apps.AppConfig",
+        "edc_offstudy.apps.AppConfig",
+        "edc_randomization.apps.AppConfig",
+        "edc_registration.apps.AppConfig",
+        "edc_sites.apps.AppConfig",
+        "edc_timepoint.apps.AppConfig",
+        "edc_visit_schedule.apps.AppConfig",
+        "edc_visit_tracking.apps.AppConfig",
+        "edc_dashboard.apps.AppConfig",
+        "edc_subject_dashboard.apps.AppConfig",
+        "edc_review_dashboard.apps.AppConfig",
+        "edc_pharmacy.apps.AppConfig",
+        "edc_appconfig.apps.AppConfig",
+    ],
+    add_dashboard_middleware=True,
+).settings
+
+
+for k, v in project_settings.items():
+    setattr(sys.modules[__name__], k, v)

edc_pharmacy/tests/tests/test_stock.py

@@ -1,5 +1,6 @@
 from dateutil.relativedelta import relativedelta
 from django.test import TestCase
+from edc_consent import site_consents
 from edc_list_data import site_list_data
 from edc_utils import get_utcnow
 
@@ -22,11 +23,16 @@
     get_shelf,
 )
 
+from ..consents import consent_v1
+
 
 class TestPrescription(TestCase):
     def setUp(self):
         site_list_data.initialize()
         site_list_data.autodiscover()
+        site_consents.registry = {}
+        site_consents.loaded = False
+        site_consents.register(consent_v1)
 
         self.medication = Medication.objects.create(
             name="METFORMIN",

edc_pharmacy/tests/tests/test_study_medication_crf.py

@@ -11,6 +11,7 @@
 from edc_appointment.models import Appointment
 from edc_appointment.tests.helper import Helper
 from edc_appointment.utils import get_next_appointment
+from edc_consent import site_consents
 from edc_constants.constants import YES
 from edc_facility import import_holidays
 from edc_protocol.research_protocol_config import ResearchProtocolConfig
@@ -32,6 +33,7 @@
     Units,
 )
 
+from ..consents import consent_v1
 from ..forms import StudyMedicationForm
 from ..models import StudyMedication, SubjectVisit
 from ..visit_schedule import visit_schedule
@@ -47,6 +49,10 @@ def setUpTestData(cls):
         pre_save.disconnect(dispatch_uid="requires_consent_on_pre_save")
 
     def setUp(self) -> None:
+        site_consents.registry = {}
+        site_consents.loaded = False
+        site_consents.register(consent_v1)
+
         site_visit_schedules._registry = {}
         site_visit_schedules.loaded = False
         site_visit_schedules.register(visit_schedule)

pyproject.toml

@@ -6,12 +6,12 @@ version_file="_version.py"
 
 [tool.black]
 line-length = 95
-target-version = ["py311"]
+target-version = ["py312"]
 extend-exclude = '''^(.*\/)*\b(migrations)\b($|\/.*$)'''
 
 [tool.isort]
 profile = "black"
-py_version = "311"
+py_version = "312"
 skip = [".tox", ".eggs", "migrations"]
 
 [tool.coverage.run]
@@ -35,21 +35,19 @@ exclude_lines = [
 legacy_tox_ini = """
 [tox]
 envlist =
-    py{311}-dj{42,50},
-    py{312}-dj{50,dev},
+    py{312}-dj{42,51,dev},
     lint
 
 isolated_build = true
 
 [gh-actions]
 python =
-    3.11: py311
     3.12: py312, lint
 
 [gh-actions:env]
 DJANGO =
     4.2: dj42
-    5.0: dj50
+    5.1: dj51
     dev: djdev, lint
 
 [testenv]
@@ -59,11 +57,11 @@ deps =
     -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/edc.txt
     -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/third_party_dev.txt
     dj42: Django>=4.2,<5.0
-    dj50: Django>=5.0
+    dj51: Django>=5.1,<5.2
     djdev: https://github.com/django/django/tarball/main
 
 commands =
-    pip install -U pip coverage[toml]
+    pip install -U pip
     pip --version
     pip freeze
     coverage run -a runtests.py