Merge branch 'release/0.3.86' into main

.coveragerc

@@ -1,4 +1,4 @@
 [run]
 include = edc_adverse_event/*
 omit = edc_adverse_event/tests/*,edc_adverse_event/migrations/*
-branch = 1
+branch = 1

.github/workflows/build.yml

@@ -5,14 +5,16 @@ 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: ['3.12']
-        django-version: ['4.2', '5.0', '5.1', 'dev']
+        python-version: ['3.12', '3.13']
+        django-version: ['5.1', 'dev']
+        database-engine: ["mysql", "postgres"]
 
     services:
       mysql:
@@ -23,6 +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
@@ -56,7 +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

@@ -3,14 +3,14 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.9
+    rev: 1.7.10
     hooks:
       - id: bandit
         args:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         language_version: python3.12
@@ -28,18 +28,21 @@ repos:
       - id: isort
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     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: check-yaml
       - id: debug-statements
       - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: requirements-txt-fixer
+        files: requirements/.*\.txt$
+      - id: trailing-whitespace
 
   - repo: https://github.com/adrienverge/yamllint
     rev: v1.35.1

AUTHORS

@@ -1 +1 @@
-Erik van Widenfelt <ew2789@gmail.com>
+Erik van Widenfelt <ew2789@gmail.com>

edc_adverse_event/templates/edc_adverse_event/action_item_column.html

@@ -5,4 +5,3 @@
   {{ action_identifier }}
 {% endif %}
 {% if status == CANCELLED %}<span style="color: red">{{ status_display }}</span>{% else %}<span>{{ status_display }}</span>{% endif %}
-

edc_adverse_event/templates/edc_adverse_event/admin/index.html

@@ -4,4 +4,3 @@
 {% block branding %}
   {% show_navbar_for_admin_templates_b3 %}
 {% endblock %}
-

edc_adverse_event/templates/edc_adverse_event/bootstrap3/aefollowup_description.html

@@ -40,4 +40,3 @@
 {% endif %}
 <BR><B>Description:</B>
   <BR><div class="ae_description">{{ ae_description|default:ae_initial.ae_description }}</div>
-

edc_adverse_event/templates/edc_adverse_event/bootstrap3/tmg/tmg_ae_listboard.html

@@ -43,5 +43,3 @@
 
 
 {% endblock main %}
-
-

edc_adverse_event/tests/holidays.csv → edc_adverse_event/tests/etc/holidays.csv

@@ -1,15 +1,15 @@
-local_date,label,country
-2017-01-02,Public Holiday,botswana
-2017-04-14,Good Friday,botswana
-2017-04-15,Public Holiday,botswana
-2017-04-17,Easter Monday,botswana
-2017-05-01,May Day/Labour Day,botswana
-2017-05-25,Ascension Day,botswana
-2017-07-01,Sir Seretse Khama Day,botswana
-2017-07-17,President's Day,botswana
-2017-07-18,Public Holiday,botswana
-2017-09-30,Botswana Day,botswana
-2017-10-02,Public Holiday,botswana
-2017-12-25,Christmas Day,botswana
-2017-12-26,Boxing Day,botswana
-2017-01-01,New Year,botswana
+local_date,label,country
+2017-01-02,Public Holiday,botswana
+2017-04-14,Good Friday,botswana
+2017-04-15,Public Holiday,botswana
+2017-04-17,Easter Monday,botswana
+2017-05-01,May Day/Labour Day,botswana
+2017-05-25,Ascension Day,botswana
+2017-07-01,Sir Seretse Khama Day,botswana
+2017-07-17,President's Day,botswana
+2017-07-18,Public Holiday,botswana
+2017-09-30,Botswana Day,botswana
+2017-10-02,Public Holiday,botswana
+2017-12-25,Christmas Day,botswana
+2017-12-26,Boxing Day,botswana
+2017-01-01,New Year,botswana

edc_adverse_event/tests/test_settings.py

@@ -0,0 +1,87 @@
+#!/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_adverse_event"
+base_dir = Path(__file__).absolute().parent.parent.parent
+
+project_settings = DefaultTestSettings(
+    calling_file=__file__,
+    BASE_DIR=base_dir,
+    APP_NAME=app_name,
+    ETC_DIR=str(base_dir / app_name / "tests" / "etc"),
+    HOLIDAY_FILE=base_dir / app_name / "tests" / "etc" / "holidays.csv",
+    SILENCED_SYSTEM_CHECKS=["sites.E101", "edc_navbar.E002", "edc_navbar.E003"],
+    SUBJECT_VISIT_MODEL="adverse_event_app.subjectvisit",
+    ADVERSE_EVENT_APP_LABEL="adverse_event_app",
+    ADVERSE_EVENT_ADMIN_SITE="adverse_event_app_admin",
+    EMAIL_ENABLED=True,
+    EMAIL_CONTACTS={
+        "ae_reports": "aereports@example.com",
+        "data_manager": "data_manager@example.com",
+        "tmg": "tmg@example.com",
+    },
+    EDC_PROTOCOL_STUDY_OPEN_DATETIME=get_utcnow().replace(
+        microsecond=0, second=0, minute=0, hour=0
+    )
+    - relativedelta(years=2),
+    EDC_PROTOCOL_STUDY_CLOSE_DATETIME=get_utcnow().replace(
+        microsecond=999999, second=59, minute=59, hour=11
+    )
+    + relativedelta(years=2),
+    EDC_NAVBAR_DEFAULT=app_name,
+    EDC_AUTH_SKIP_SITE_AUTHS=True,
+    EDC_AUTH_SKIP_AUTH_UPDATER=True,
+    EDC_SITES_REGISTER_DEFAULT=True,
+    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.apps.AppConfig",
+        "edc_auth.apps.AppConfig",
+        "edc_action_item.apps.AppConfig",
+        "edc_adverse_event.apps.AppConfig",
+        "edc_appointment.apps.AppConfig",
+        "edc_consent.apps.AppConfig",
+        "edc_crf.apps.AppConfig",
+        "edc_data_manager.apps.AppConfig",
+        "edc_dashboard.apps.AppConfig",
+        "edc_device.apps.AppConfig",
+        "edc_facility.apps.AppConfig",
+        "edc_form_runners.apps.AppConfig",
+        "edc_identifier.apps.AppConfig",
+        "edc_lab.apps.AppConfig",
+        "edc_list_data.apps.AppConfig",
+        "edc_locator.apps.AppConfig",
+        "edc_metadata.apps.AppConfig",
+        "edc_navbar.apps.AppConfig",
+        "edc_notification.apps.AppConfig",
+        "edc_offstudy.apps.AppConfig",
+        "edc_prn.apps.AppConfig",
+        "edc_protocol.apps.AppConfig",
+        "edc_randomization.apps.AppConfig",
+        "edc_registration.apps.AppConfig",
+        "edc_review_dashboard.apps.AppConfig",
+        "edc_sites.apps.AppConfig",
+        "edc_subject_dashboard.apps.AppConfig",
+        "edc_timepoint.apps.AppConfig",
+        "edc_visit_tracking.apps.AppConfig",
+        "edc_visit_schedule.apps.AppConfig",
+        "adverse_event_app.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_adverse_event/tests/tests/mixins.py

@@ -8,8 +8,7 @@
 from model_bakery import baker
 
 from adverse_event_app.visit_schedules import visit_schedule
-
-from ...models import CauseOfDeath
+from edc_adverse_event.models import CauseOfDeath
 
 
 class DeathReportTestMixin:

edc_adverse_event/tests/tests/test_ae_and_actions.py

@@ -22,10 +22,9 @@
     StudyTerminationConclusionAction,
 )
 from adverse_event_app.models import AeFollowup, AeInitial, AeSusar, AeTmg
+from edc_adverse_event.constants import CONTINUING_UPDATE, RECOVERED, RECOVERING
 from edc_adverse_event.models import AeClassification
 
-from ...constants import CONTINUING_UPDATE, RECOVERED, RECOVERING
-
 
 @override_settings(EDC_LIST_DATA_ENABLE_AUTODISCOVER=False)
 class TestAeAndActions(TestCase):

edc_adverse_event/tests/tests/test_ae_form_validators.py

@@ -7,14 +7,13 @@
 from edc_sites.tests import SiteTestCaseMixin
 
 from adverse_event_app import list_data
-from edc_adverse_event.models import AeClassification, SaeReason
-
-from ...constants import AE_WITHDRAWN
-from ...form_validators import (
+from edc_adverse_event.constants import AE_WITHDRAWN
+from edc_adverse_event.form_validators import (
     AeFollowupFormValidator,
     AeInitialFormValidator,
     AeTmgFormValidator,
 )
+from edc_adverse_event.models import AeClassification, SaeReason
 
 
 @override_settings(EDC_LIST_DATA_ENABLE_AUTODISCOVER=False)

edc_adverse_event/tests/tests/test_notifications.py

@@ -7,6 +7,10 @@
 from model_bakery import baker
 
 from adverse_event_app import list_data
+from edc_adverse_event.notifications import (
+    AeInitialG3EventNotification,
+    AeInitialG4EventNotification,
+)
 
 from ...action_items import (
     AeFollowupAction,
@@ -16,7 +20,6 @@
     DeathReportAction,
     DeathReportTmgAction,
 )
-from ...notifications import AeInitialG3EventNotification, AeInitialG4EventNotification
 from .mixins import DeathReportTestMixin
 
 

edc_adverse_event/view_utils/tmg_button.py

@@ -4,7 +4,7 @@
 from typing import TYPE_CHECKING
 
 from django.utils.translation import gettext as _
-from edc_subject_dashboard.view_utils import ModelButton
+from edc_view_utils import ModelButton
 
 if TYPE_CHECKING:
     from edc_action_item.models import ActionItem

pyproject.toml

@@ -1,8 +1,9 @@
 [build-system]
 requires = ["setuptools>=60", "setuptools-scm>=8.0"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-version_file="_version.py"
+version_file = "_version.py"
 
 [tool.black]
 line-length = 95
@@ -35,35 +36,33 @@ exclude_lines = [
 legacy_tox_ini = """
 [tox]
 envlist =
-    py{312}-dj{42,50,51,dev},
+    py{312,313}-dj{51,dev},
     lint
+    pre-commit
 
 isolated_build = true
 
 [gh-actions]
 python =
-    3.12: py312, lint
+    3.12: py312, lint, pre-commit
+    3.13: py313
 
 [gh-actions:env]
 DJANGO =
-    4.2: dj42
-    5.0: dj50
     5.1: dj51
-    dev: djdev, lint
+    dev: djdev, lint, pre-commit
 
 [testenv]
 deps =
     -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/tox.txt
     -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/test_utils.txt
     -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,<5.1
-    dj51: Django>=5.1
+    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
+    python --version
     pip --version
     pip freeze
     coverage run -a runtests.py
@@ -72,7 +71,19 @@ commands =
 [testenv:lint]
 deps = -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/lint.txt
 commands =
+    python --version
+    pip --version
+    pip freeze
     isort --profile=black --check --diff .
     black --check --diff .
     flake8 .
+
+[testenv:pre-commit]
+deps = pre-commit
+commands =
+    python --version
+    pip --version
+    pip freeze
+    pre-commit autoupdate
+    pre-commit run --all-files
 """