merge v1.0.0 release

bihealth · Jul 19, 2024 · 47ef9dc · 47ef9dc
2 parents be012e5 + 9d52958
commit 47ef9dc
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diff --git a/.github/ISSUE_TEMPLATE/release_cleanup.md b/.github/ISSUE_TEMPLATE/release_cleanup.md
@@ -20,13 +20,14 @@ TBA
 - [ ] Review code style and cleanup if needed
 - [ ] Review and update doc entries if needed
 - [ ] Ensure all relevant updates are in `CHANGELOG` and major changes doc
-- [ ] Ensure new version is in `CORE_API_ALLOWED_VERSIONS`
+- [ ] Ensure REST API versions are up to date and documented
 - [ ] Upgrade version number of pypi package references in `README` and docs
 - [ ] Upgrade docs config version number (usually at `x.y.z-WIP` when developing)
 - [ ] Update latest version info in `codemeta.json`
 - [ ] Update version number and date in `CHANGELOG`
 - [ ] Update version number and date in `Major Changes` doc
 - [ ] Ensure docs can be built without errors
+- [ ] Ensure `generateschema` runs without errors or warnings (until in CI)
 
 ## Notes
 

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -7,12 +7,12 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - '3.8'
           - '3.9'
           - '3.10'
+          - '3.11'
     services:
       postgres:
-        image: postgres:11
+        image: postgres:16
         env:
           POSTGRES_DB: sodar_core
           POSTGRES_USER: sodar_core
@@ -44,7 +44,7 @@ jobs:
         run: git fetch --prune --unshallow
       - name: Install project Python dependencies
         run: |
-          pip install "wheel>=0.38.4, <0.39"
+          pip install "wheel>=0.42.0, <0.43"
           pip install -r requirements/local.txt
           pip install -r requirements/test.txt
       - name: Download icons
@@ -58,13 +58,13 @@ jobs:
           coverage report
       - name: Check linting
         run: flake8 .
-        if: ${{ matrix.python-version == '3.8' }}
+        if: ${{ matrix.python-version == '3.11' }}
       - name: Check formatting
         run: make black arg=--check
-        if: ${{ matrix.python-version == '3.8' }}
+        if: ${{ matrix.python-version == '3.11' }}
       - name: Report coverage with Coveralls
         uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: './coverage.lcov'
-        if: ${{ matrix.python-version == '3.8' }}
+        if: ${{ matrix.python-version == '3.11' }}
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,7 +1,7 @@
-image: python:3.8
+image: python:3.11
 
 services:
-  - postgres:11
+  - postgres:16
 
 variables:
   POSTGRES_DB: sodar_core

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -8,7 +8,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: '3.8'
+    python: '3.11'
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -5,6 +5,150 @@ Changelog for the **SODAR Core** Django app package. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v1.0.0 (2024-07-19)
+===================
+
+Added
+-----
+
+- **General**
+    - Python v3.11 support (#1157)
+    - Flake8 rule in ``Makefile`` (#1387)
+    - OpenID Connect (OIDC) authentication support (#1367)
+- **Adminalerts**
+    - Admin alert email sending (#415)
+    - ``notify_email_alert`` app setting (#415)
+- **Filesfolders**
+    - Optional pagination for REST API list views (#1313)
+- **Projectroles**
+    - ``full_title`` field in ``ProjectSerializer`` and API views (#1314)
+    - Custom password argument in ``createdevusers`` management command (#1393)
+    - ``PluginObjectLink`` data class in plugins (#1343)
+    - ``PluginSearchResult`` data class in plugins (#1399)
+    - Target user ``sodar_uuid`` updating in remote sync (#1316, #1317)
+    - Update local user data in remote sync (#1407)
+    - ``USER`` scope settings in remote sync (#1322)
+    - ``AppLinkContent`` utility class (#1380, #1381)
+    - ``checkusers`` management command (#1410)
+    - ``SODARPageNumberPagination`` pagination class (#1313)
+    - Optional pagination for REST API list views (#1313)
+    - Email notification opt-out settings (#1417, #1418)
+    - CC and BCC field support in sending generic emails (#415)
+    - ``SODARUserAdditionalEmail`` model (#874)
+    - ``is_source_site()`` and ``is_target_site()`` rule predicates
+    - ``settings_link`` kwarg in ``send_generic_email()`` (#1418)
+    - ``addremotesite`` and ``syncgroups`` command tests (#352)
+    - ``RemoteSite.owner_modifiable`` field (#817)
+    - ``assert_displayed()`` UI test helper
+    - ``RemoteProjectAccessAjaxView`` Ajax view (#1358)
+    - Remote project access status updating in project detail view (#1358)
+    - ``SidebarContentAjaxView`` for sidebar and project dropdown content retrieval (#1366)
+    - ``UserDropdownContentAjaxView`` for user dropdown content retrieval (#1366, #1392)
+    - ``SODARUser.get_auth_type()`` helper (#1367)
+    - ``ProjectInvite.is_ldap()`` helper (#1367)
+    - ``AppSettingAPI.is_set()`` helper (#1450)
+    - ``checks`` module for Django checks (#504)
+    - Django check for enabled auth methods (#1451)
+- **Timeline**
+    - ``sodar_uuid`` field in ``TimelineEventObjectRef`` model (#1415)
+    - REST API views (#1350)
+    - ``get_project()`` helpers in ``TimelineEvent`` and ``TimelineEventObjectRef`` (#1350)
+    - Optional pagination for REST API list views (#1313)
+- **Userprofile**
+    - Additional email address management and verification (#874)
+
+Changed
+-------
+
+- **General**
+    - Upgrade to Django v4.2 (#880)
+    - Upgrade minimum PostgreSQL version to v12 (#1074)
+    - Upgrade to PostgreSQL v16 in CI (#1074)
+    - Upgrade general Python dependencies (#1374)
+    - Reformat with black v24.3.0 (#1374)
+    - Update download URL in ``get_chromedriver_url.py`` (#1385)
+    - Add ``AUTH_LDAP_USER_SEARCH_BASE`` as a Django setting (#1410)
+    - Change ``ATOMIC_REQUESTS`` recommendation and default to ``True`` (#1281)
+    - Add OpenAPI dependencies (#1444)
+    - Squash migrations (#1446)
+- **Filesfolders**
+    - Add migration required by Django v4.2 (#1396)
+    - Add app specific media type and versioning (#1278)
+- **Projectroles**
+    - Rename ``AppSettingAPI`` ``app_name`` arguments to ``plugin_name`` (#1285)
+    - Default password in ``createdevusers`` management command (#1390)
+    - Deprecate ``local`` in app settings, use ``global`` instead (#1319)
+    - Enforce optional handling of app settings ``global`` attributes (#1395)
+    - Expect ``get_object_link()`` plugin methods to return ``PluginObjectLink`` (#1343)
+    - Deprecate returning ``dict`` from ``get_object_link()`` (#1343)
+    - Expect ``search()`` plugin methods to return list of ``PluginSearchResult`` objects (#1399)
+    - Deprecate returning ``dict`` from ``search()`` (#1399)
+    - Update core API view media type and versioning (#1278, #1406)
+    - Separate projectroles and remote sync API media types and versioning (#1278)
+    - Rename base test classes for consistency (#1259)
+    - Prevent setting global user app settings on target site in ``AppSettingAPI`` (#1329)
+    - Move project app link logic in ``AppLinkContent`` (#1380)
+    - Move user dropdown link logic in ``AppLinkContent`` (#1381, #1413)
+    - Do not recreate ``AppSetting`` objects on remote sync update (#1409)
+    - Enforce project and site uniqueness in ``RemoteProject`` model (#1433)
+    - Remove redundant permission check in ``project_detail.html`` (#1438)
+    - Move sidebar, project dropdown and user dropdown creation to ``utils`` (#1366)
+    - Refactor ``ProjectInviteProcessMixin.get_invite_type()`` into ``ProjectInvite.is_ldap()`` (#1367)
+- **Sodarcache**
+    - Rewrite REST API views (#498, #1389)
+    - Raise ``update_cache()`` exception for ``synccache`` in debug mode (#1375)
+- **Timeline**
+    - Update ``get_object_link()`` usage for ``PluginObjectLink`` return data (#1343)
+    - Rename ``ProjectEvent*`` models to ``TimelineEvent*`` (#1414)
+    - Move event name from separate column into badge (#1370)
+    - Use constants for event status types (#973)
+- **Userprofile**
+    - Disable global user settings on target site in ``UserSettingsForm`` (#1329)
+
+Fixed
+-----
+
+- **General**
+    - ``README.rst`` badge rendering (#1402)
+- **Filesfolders**
+    - OpenAPI ``generateschema`` errors and warnings (#1442)
+- **Projectroles**
+    - ``SODARUser.update_full_name()`` not working with existing name (#1371)
+    - Legacy public guest access in child category breaks category updating (#1404)
+    - Incorrect DAL widget highlight colour after upgrade (#1412)
+    - ``ProjectStarringAjaxView`` creating redundant database objects (#1416)
+    - ``addremotesite`` crash in ``TimelineAPI.add_event()`` (#1425)
+    - ``addremotesite`` allows creation of site with mode identical to host (#1426)
+    - Public guest access field not correctly hidden in project form (#1429)
+    - Revoked remote projects displayed in project detail view (#1432)
+    - Invalid URLs for remote peer projects in project detail view (#1435)
+    - Redundant ``Project.get_source_site()`` calls in project detail view (#1436)
+    - ``RemoteSite.get_access_date()`` invalid date sorting (#1437)
+    - OpenAPI ``generateschema`` compatibility (#1440, #1442)
+    - ``ProjectCreateView`` allows ``POST`` with disabled target project creation (#1448)
+    - Plugin existence not explicitly checked in ``AppSettingAPI.set()`` update query (#1452)
+    - ``search_advanced.html`` header layout (#1453)
+- **Sodarcache**
+    - REST API set view ``app_name`` incorrectly set (#1405)
+- **Timeline**
+    - OpenAPI ``generateschema`` warnings (#1442)
+
+Removed
+-------
+
+- **General**
+    - SAML support (#1368)
+    - Python v3.8 support (#1382)
+- **Projectroles**
+    - ``PROJECTROLES_HIDE_APP_LINKS`` setting (#1143)
+    - ``CORE_API_*`` Django settings (#1278)
+    - Project starring timeline event creation (#1294)
+    - ``user_email_additional`` app setting (#874)
+    - ``get_visible_projects()`` template tag (#1432)
+    - App setting value max length limit (#1443)
+    - Redundant project permission in ``UserSettingRetrieveAPIView`` (#1449)
+
+
 v0.13.4 (2024-02-16)
 ====================
 

diff --git a/Makefile b/Makefile
@@ -4,6 +4,7 @@ define USAGE=
 @echo -e
 @echo -e "Usage:"
 @echo -e "\tmake black [arg=--<arg>]                 -- black formatting"
+@echo -e "\tmake flake                               -- run flake8"
 @echo -e "\tmake celery                              -- start celery worker"
 @echo -e "\tmake serve                               -- start source server"
 @echo -e "\tmake serve_target                        -- start target server"
@@ -25,6 +26,11 @@ black:
 	black . -l 80 --skip-string-normalization --exclude ".git|.venv|.tox|build|env|src|docs|migrations|versioneer.py" $(arg)
 
 
+.PHONY: flake
+flake:
+	flake8 .
+
+
 .PHONY: celery
 celery:
 	celery -A config worker -l info --beat

diff --git a/README.rst b/README.rst
@@ -1,28 +1,30 @@
 SODAR Core
 ^^^^^^^^^^
 
-.. image:: https://badge.fury.io/py/django-sodar-core.svg
+.. |b1| image:: https://badge.fury.io/py/django-sodar-core.svg
     :target: https://badge.fury.io/py/django-sodar-core
 
-.. image:: https://github.com/bihealth/sodar-core/actions/workflows/build.yml/badge.svg
+.. |b2| image:: https://github.com/bihealth/sodar-core/actions/workflows/build.yml/badge.svg
     :target: https://github.com/bihealth/sodar-core/actions?query=workflow%3ABuild
 
-.. image:: https://coveralls.io/repos/github/bihealth/sodar-core/badge.svg?branch=main
+.. |b3| image:: https://coveralls.io/repos/github/bihealth/sodar-core/badge.svg?branch=main
     :target: https://coveralls.io/github/bihealth/sodar-core?branch=main
 
-.. image:: https://img.shields.io/badge/License-MIT-green.svg
+.. |b4| image:: https://img.shields.io/badge/License-MIT-green.svg
     :target: https://opensource.org/licenses/MIT
 
-.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
+.. |b5| image:: https://img.shields.io/badge/code%20style-black-000000.svg
     :target: https://github.com/ambv/black
 
-.. image:: https://readthedocs.org/projects/sodar-core/badge/?version=latest
+.. |b6| image:: https://readthedocs.org/projects/sodar-core/badge/?version=latest
     :target: https://sodar-core.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4269346.svg
+.. |b7| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4269346.svg
     :target: https://doi.org/10.5281/zenodo.4269346
 
+|b1| |b2| |b3| |b4| |b5| |b6| |b7|
+
 SODAR Core is a framework for Django web application development.
 
 It was conceived to facilitate the creation of scientific data management and
@@ -115,7 +117,7 @@ and breaking changes are possible.
 
 .. code-block:: console
 
-    pip install django-sodar-core==0.13.4
+    pip install django-sodar-core==1.0.0
 
 For installing a development version you can point your dependency to a specific
 commit ID in GitHub. Note that these versions may not be stable.

diff --git a/adminalerts/forms.py b/adminalerts/forms.py
@@ -9,16 +9,28 @@
 from adminalerts.models import AdminAlert
 
 
+# Local constants
+EMAIL_HELP_CREATE = 'Send alert as email to all users on this site'
+EMAIL_HELP_UPDATE = 'Send updated alert as email to all users on this site'
+
+
 class AdminAlertForm(SODARModelForm):
     """Form for AdminAlert creation/updating"""
 
+    send_email = forms.BooleanField(
+        initial=True,
+        label='Send alert as email',
+        required=False,
+    )
+
     class Meta:
         model = AdminAlert
         fields = [
             'message',
             'date_expire',
             'active',
             'require_auth',
+            'send_email',
             'description',
         ]
 
@@ -40,13 +52,17 @@ def __init__(self, current_user=None, *args, **kwargs):
 
         # Creation
         if not self.instance.pk:
-            self.fields[
-                'date_expire'
-            ].initial = timezone.now() + timezone.timedelta(days=1)
+            self.initial['date_expire'] = timezone.now() + timezone.timedelta(
+                days=1
+            )
+            self.fields['send_email'].help_text = EMAIL_HELP_CREATE
         # Updating
         else:  # self.instance.pk
             # Set description value as raw markdown
             self.initial['description'] = self.instance.description.raw
+            self.fields['send_email'].help_text = EMAIL_HELP_UPDATE
+            # Sending email for update should be false by default
+            self.initial['send_email'] = False
 
     def clean(self):
         """Custom form validation and cleanup"""