Merge branch 'release/0.3.85'

clinicedc · Sep 18, 2024 · 2713419 · 2713419
2 parents 3211d89 + bc330d4
commit 2713419
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Showing 7 changed files with 68 additions and 68 deletions.
diff --git a/.github/workflows/build.yml b/.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

diff --git a/.pre-commit-config.yaml b/.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 +28,27 @@ 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: detect-private-key
+        exclude: |
+              (?x)^(
+                edc_consent/tests/crypto_keys/user-rsa-local-private.pem|
+                edc_consent/tests/crypto_keys/user-rsa-restricted-private.pem
+              )$
+      - 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:

diff --git a/edc_consent/consent_definition.py b/edc_consent/consent_definition.py
@@ -174,16 +174,21 @@ def check_date_within_study_period(self) -> None:
         protocol = ResearchProtocolConfig()
         study_open_datetime = protocol.study_open_datetime
         study_close_datetime = protocol.study_close_datetime
-        for index, attr in enumerate(["start", "end"]):
+        for attr in ["start", "end"]:
             if not (
                 floor_secs(study_open_datetime)
                 <= getattr(self, attr)
                 <= ceil_secs(study_close_datetime)
             ):
-                date_string = formatted_datetime(getattr(self, attr))
+                open_date_string = formatted_datetime(study_open_datetime)
+                close_date_string = formatted_datetime(study_close_datetime)
+                attr_date_string = formatted_datetime(getattr(self, attr))
                 raise ConsentDefinitionError(
-                    f"Invalid {attr} date. Cannot be before study start date. "
-                    f"See {self}. Got {date_string}."
+                    f"Invalid {attr} date. "
+                    f"Must be within the opening and closing dates of the protocol. "
+                    f"See {self}. "
+                    f"Got {open_date_string=}, {close_date_string=}, "
+                    f"{attr=}, {attr_date_string=}."
                 )
 
     def get_previous_consent(

diff --git a/edc_consent/tests/test_settings.py b/edc_consent/tests/test_settings.py
@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import sys
 from pathlib import Path
 
@@ -6,13 +7,11 @@
 from edc_utils import get_utcnow
 
 app_name = "edc_consent"
-base_dir = Path(__file__).absolute().parent
+base_dir = Path(__file__).absolute().parent.parent.parent
 
 project_settings = DefaultTestSettings(
     calling_file=__file__,
     BASE_DIR=base_dir,
-    DJANGO_CRYPTO_FIELDS_KEY_PATH=base_dir / "crypto_keys",
-    GIT_DIR=base_dir.parent.parent,
     APP_NAME=app_name,
     SILENCED_SYSTEM_CHECKS=[
         "edc_consent.E001",
@@ -21,17 +20,16 @@
         "edc_navbar.E003",
         "edc_sites.E001",
     ],
-    ETC_DIR=str(base_dir / app_name / "tests" / "etc"),
     EDC_NAVBAR_DEFAULT="edc_consent",
     EDC_PROTOCOL_STUDY_OPEN_DATETIME=get_utcnow() - relativedelta(years=1),
     EDC_PROTOCOL_STUDY_CLOSE_DATETIME=get_utcnow() + relativedelta(years=1),
-    EDC_SITES_REGISTER_DEFAULT=True,
     SUBJECT_SCREENING_MODEL="consent_app.subjectscreening",
     SUBJECT_CONSENT_MODEL="consent_app.subjectconsent",
     SUBJECT_VISIT_MODEL="consent_app.subjectvisit",
     SUBJECT_VISIT_MISSED_MODEL="consent_app.subjectvisitmissed",
     SUBJECT_REQUISITION_MODEL="consent_app.subjectrequisition",
     SUBJECT_REFUSAL_MODEL="consent_app.subjectrefusal",
+    EDC_SITES_REGISTER_DEFAULT=True,
     INSTALLED_APPS=[
         "django.contrib.admin",
         "django.contrib.auth",
@@ -40,30 +38,31 @@
         "django.contrib.messages",
         "django.contrib.staticfiles",
         "django.contrib.sites",
-        "multisite",
-        "simple_history",
         "django_crypto_fields.apps.AppConfig",
         "django_revision.apps.AppConfig",
+        "multisite",
+        "adverse_event_app.apps.AppConfig",
+        "edc_action_item.apps.AppConfig",
+        "edc_adverse_event.apps.AppConfig",
         "edc_appointment.apps.AppConfig",
-        "edc_visit_schedule.apps.AppConfig",
-        "edc_export.apps.AppConfig",
+        "edc_auth.apps.AppConfig",
         "edc_crf.apps.AppConfig",
-        "edc_sites.apps.AppConfig",
-        "edc_form_runners.apps.AppConfig",
-        "edc_timepoint.apps.AppConfig",
+        "edc_dashboard.apps.AppConfig",
         "edc_data_manager.apps.AppConfig",
         "edc_device.apps.AppConfig",
+        "edc_form_runners.apps.AppConfig",
         "edc_identifier.apps.AppConfig",
-        "edc_action_item.apps.AppConfig",
         "edc_lab.apps.AppConfig",
-        "edc_locator.apps.AppConfig",
         "edc_metadata.apps.AppConfig",
         "edc_notification.apps.AppConfig",
-        "edc_protocol.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_schedule.apps.AppConfig",
         "edc_visit_tracking.apps.AppConfig",
         "edc_consent.apps.AppConfig",
-        "edc_auth.apps.AppConfig",
         "consent_app.apps.AppConfig",
         "edc_appconfig.apps.AppConfig",
     ],

diff --git a/pyproject.toml b/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

diff --git a/runtests.py b/runtests.py
@@ -1,20 +1,5 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-
-import os
-import sys
+from edc_test_settings.func_main import func_main2
 
 if __name__ == "__main__":
-    os.environ["DJANGO_SETTINGS_MODULE"] = "edc_consent.tests.test_settings"
-    import django
-
-    django.setup()
-    from django.test.runner import DiscoverRunner
-
-    tags = [t.split("=")[1] for t in sys.argv if t.startswith("--tag")]
-    failfast = any([True for t in sys.argv if t.startswith("--failfast")])
-    keepdb = any([True for t in sys.argv if t.startswith("--keepdb")])
-    opts = dict(failfast=failfast, tags=tags, keepdb=keepdb)
-    failures = DiscoverRunner(**opts).run_tests(["edc_consent.tests"], **opts)
-    sys.exit(failures)
+    func_main2("edc_consent.tests.test_settings", "edc_consent.tests")
diff --git a/setup.cfg b/setup.cfg
@@ -13,15 +13,15 @@ classifiers=
     Environment :: Web Environment
     Framework :: Django
     Framework :: Django :: 4.2
+    Framework :: Django :: 5.1
     Intended Audience :: Developers
     Intended Audience :: Science/Research
     Operating System :: OS Independent
-    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 
-
 [options]
-python_requires = >=3.11
+python_requires = >=3.12
 zip_safe = False
 include_package_data = True
 packages = find: