Merge pull request #1028 from bihealth/dev

Merge v0.11.0 release

.github/ISSUE_TEMPLATE/feature_request.md

@@ -19,6 +19,7 @@ A clear and concise description of what you want to happen and how this feature
 should work.
 
 ### Alternative Solutions
+
 A clear and concise description of any alternative solutions or features you've
 considered.
 

.github/workflows/build.yml

@@ -12,7 +12,7 @@ jobs:
           - '3.10'
     services:
       postgres:
-        image: postgres:9.6
+        image: postgres:11
         env:
           POSTGRES_DB: sodar_core
           POSTGRES_USER: sodar_core
@@ -52,15 +52,17 @@ jobs:
       - name: Run tests
         run: |
           coverage run --rcfile=.coveragerc manage.py test -v 2 --settings=config.settings.test
-          coverage xml
+          coverage lcov
           coverage report
       - name: Check linting
         run: flake8 .
+        if: ${{ matrix.python-version == '3.8' }}
       - name: Check formatting
         run: make black arg=--check
-      - name: Run Codacy coverage reporter
-        uses: codacy/codacy-coverage-reporter-action@master
+        if: ${{ matrix.python-version == '3.8' }}
+      - name: Report coverage with Coveralls
+        uses: coverallsapp/github-action@master
         with:
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: coverage.xml
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: './coverage.lcov'
         if: ${{ matrix.python-version == '3.8' }}

.gitlab-ci.yml

@@ -1,7 +1,7 @@
 image: python:3.8
 
 services:
-  - postgres:9.6
+  - postgres:11
 
 variables:
   POSTGRES_DB: sodar_core

CHANGELOG.rst

@@ -5,6 +5,68 @@ Changelog for the **SODAR Core** Django app package. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v0.11.0 (2022-09-23)
+====================
+
+Added
+-----
+
+- **General**
+    - Coverage reporting with Coveralls (#1026)
+- **Projectroles**
+    - Project modifying API in ``ProjectModifyPluginMixin`` (#387)
+    - ``PROJECTROLES_ENABLE_MODIFY_API`` Django setting (#387)
+    - ``PROJECTROLES_MODIFY_API_APPS`` Django setting (#387)
+    - ``syncmodifyapi`` management command (#387)
+    - ``SODARBaseAjaxMixin`` with ``SODARBaseAjaxView`` functionality (#994)
+    - Custom login view content via ``include/_login_extend.html`` (#982)
+
+Changed
+-------
+
+- **General**
+    - Upgrade minimum PostgreSQL version to v11 (#303)
+    - Upgrade minimum Django version to v3.2.15 (#1003)
+    - Upgrade to black v22.6.0 (#1003)
+    - Upgrade general Python dependencies (#1003, #1019)
+- **Filesfolders**
+    - Change ``public_url`` form label (#1016)
+- **Projectroles**
+    - Replace Taskflow specific code with project modifying API calls (#387)
+    - Rename ``revoke_failed_invite()`` to ``revoke_invite()``
+    - Do not return ``submit_status`` from project API views (#971)
+    - Remove required ``owner`` argument for ``ProjectUpdateAPIView`` (#1007)
+    - Remove unused owner operations from ``ProjectModifyMixin`` (#1008)
+    - Refactor and cleanup ``AppSettingAPI`` (#1024)
+- **Timeline**
+    - Deprecate ``ProjectEvent.get_current_status()``, use ``get_status()`` (#322)
+
+Fixed
+-----
+
+- **Projectroles**
+    - Crash at exception handling in ``clean_new_owner()`` (#981)
+    - Incorrect button icon in remote site form (#1001)
+    - Case-sensitive project list sorting (#1006)
+    - Project list filtering not trimmed (#1021)
+- **Timeline**
+    - Uncaught exceptions in ``get_plugin_lookup()`` (#979)
+
+Removed
+-------
+
+- **General**
+    - Codacy support (#1022)
+- **Projectroles**
+    - Taskflow specific views, tests and API calls (#387)
+    - ``get_taskflow_sync_data()`` method from ``ProjectAppPluginPoint`` (#387)
+    - ``Project.submit_status`` field and usages in code (#971)
+- **Taskflowbackend**
+    - Remove app and implement in SODAR (#387)
+- **Timeline**
+    - Taskflow API views (#387)
+
+
 v0.10.13 (2022-07-15)
 =====================
 

MANIFEST.in

@@ -8,7 +8,6 @@ recursive-include bgjobs *
 recursive-include filesfolders *
 recursive-include siteinfo *
 recursive-include sodarcache *
-recursive-include taskflowbackend *
 recursive-include timeline *
 recursive-include tokens *
 recursive-include userprofile *

Makefile

@@ -6,10 +6,8 @@ define USAGE=
 @echo -e "\tmake black [arg=--<arg>]                 -- black formatting"
 @echo -e "\tmake serve                               -- start source server"
 @echo -e "\tmake serve_target                        -- start target server"
-@echo -e "\tmake serve_taskflow [arg=sync]           -- start server with SODAR Taskflow"
 @echo -e "\tmake collectstatic                       -- run collectstatic"
 @echo -e "\tmake test [arg=<test_object>]            -- run all tests or specify module/class/function"
-@echo -e "\tmake test_taskflow [arg=<test_object>]   -- run all tests and taskflow tests or specify module/class/function"
 @echo -e "\tmake manage_target arg=<target_command>  -- run management command on target site, arg is mandatory"
 @echo -e
 endef
@@ -36,15 +34,6 @@ serve_target:
 	$(MANAGE) runserver 0.0.0.0:$(target_port) --settings=config.settings.local_target
 
 
-.PHONY: serve_taskflow
-ifeq ($(arg),sync)
-serve_taskflow: sync_taskflow
-else
-serve_taskflow:
-endif
-	$(MANAGE) runserver --settings=config.settings.local_taskflow
-
-
 .PHONY: collectstatic
 collectstatic:
 	$(MANAGE) collectstatic --no-input
@@ -55,11 +44,6 @@ test: collectstatic
 	$(MANAGE) test -v 2 --parallel --settings=config.settings.test $(arg)
 
 
-.PHONY: test_taskflow
-test_taskflow: test
-	$(MANAGE) test -v 2 --tag=Taskflow --settings=config.settings.test_taskflow $(arg)
-
-
 .PHONY: manage_target
 manage_target:
 ifeq ($(arg),)
@@ -71,11 +55,6 @@ else
 endif
 
 
-.PHONY: sync_taskflow
-sync_taskflow:
-	$(MANAGE) synctaskflow --settings=config.settings.local_taskflow
-
-
 .PHONY: usage
 usage:
 	$(USAGE)

README.rst

@@ -7,11 +7,8 @@ SODAR Core
 .. 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://app.codacy.com/project/badge/Grade/6ba6b44ee37642918c7ff7a44d413982
-    :target: https://www.codacy.com/gh/bihealth/sodar-core/dashboard
-
-.. image:: https://app.codacy.com/project/badge/Coverage/6ba6b44ee37642918c7ff7a44d413982
-    :target: https://www.codacy.com/gh/bihealth/sodar-core/dashboard
+.. image:: https://coveralls.io/repos/github/bihealth/sodar-core/badge.svg?branch=main
+    :target: https://coveralls.io/github/bihealth/sodar-core?branch=update/codacy
 
 .. image:: https://img.shields.io/badge/License-MIT-green.svg
     :target: https://opensource.org/licenses/MIT
@@ -101,8 +98,6 @@ This repository provides the following installable Django apps:
   administrators.
 - **sodarcache**: Generic caching and aggregation of data referring to external
   services.
-- **taskflowbackend**: Backend app providing an API for the optional
-  ``sodar_taskflow`` transaction service.
 - **timeline**: Project app for logging and viewing project-related activity.
 - **tokens**: Token management for API access.
 - **userprofile**: Site app for viewing user profiles.
@@ -120,7 +115,7 @@ and breaking changes are possible.
 
 .. code-block:: console
 
-    pip install django-sodar-core==0.10.13
+    pip install django-sodar-core==0.11.0
 
 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.

codemeta.json

@@ -40,12 +40,12 @@
   ],
   "identifier": "https://doi.org/10.5281/zenodo.4269346",
   "codeRepository": "https://github.com/bihealth/sodar-core",
-  "datePublished": "2022-07-15",
-  "dateModified": "2022-07-15",
+  "datePublished": "2022-09-23",
+  "dateModified": "2022-09-23",
   "dateCreated": "2019-06-26",
   "description": "SODAR Core: A Django-based framework for scientific data management and analysis web apps",
   "keywords": "Python, Django, scientific data managmenent, software library",
   "license": "MIT",
   "title": "SODAR Core",
-  "version": "v0.10.13"
+  "version": "v0.11.0"
 }

config/settings/base.py

@@ -87,8 +87,6 @@
     'siteinfo.apps.SiteinfoConfig',
     # API Tokens site app
     'tokens.apps.TokensConfig',
-    # SODAR Taskflow backend app
-    'taskflowbackend.apps.TaskflowbackendConfig',
     # Background Jobs app
     'bgjobs.apps.BgjobsConfig',
     # External Data Cache app
@@ -492,7 +490,6 @@
         'projectroles',
         'siteinfo',
         'sodarcache',
-        'taskflowbackend',
         'timeline',
     ],
 )
@@ -591,6 +588,12 @@ def set_logging(level=None):
 # Allow unauthenticated users to access public projects if set true
 PROJECTROLES_ALLOW_ANONYMOUS = env.bool('PROJECTROLES_ALLOW_ANONYMOUS', False)
 
+# Enable project modify API
+PROJECTROLES_ENABLE_MODIFY_API = False
+# List of apps for executing project modify API actions in the given order. If
+# not set, backend and project apps will execute in alphabetical order by name.
+PROJECTROLES_MODIFY_API_APPS = []
+
 # General projectroles settings
 PROJECTROLES_DISABLE_CATEGORIES = env.bool(
     'PROJECTROLES_DISABLE_CATEGORIES', False
@@ -680,10 +683,5 @@ def set_logging(level=None):
 APPALERTS_STATUS_INTERVAL = env.int('APPALERTS_STATUS_INTERVAL', 5)
 
 
-# Taskflow backend settings
-TASKFLOW_SODAR_SECRET = env.str('TASKFLOW_SODAR_SECRET', 'CHANGE ME!')
-TASKFLOW_TEST_MODE = False  # Important! Disallow cleanup() command by default
-
-
 # SODAR constants
 # SODAR_CONSTANTS = get_sodar_constants(default=True)

config/settings/test.py

@@ -85,6 +85,7 @@
 PROJECTROLES_DEFAULT_ADMIN = 'admin'
 PROJECTROLES_ALLOW_LOCAL_USERS = True
 PROJECTROLES_ALLOW_ANONYMOUS = False
+PROJECTROLES_ENABLE_MODIFY_API = True
 PROJECTROLES_DISABLE_CATEGORIES = False
 PROJECTROLES_INVITE_EXPIRY_DAYS = 14
 PROJECTROLES_SEND_EMAIL = True

docs/source/app_appalerts.rst

@@ -145,8 +145,15 @@ accompanying API documentation for details.
 Backend Django API Documentation
 ================================
 
-This is the backend API, retrievable with
-``get_backend_api('appalerts_backend')``.
+The backend API can be retrieved as follows.
+
+.. code-block:: python
+
+    from projectroles.plugins import get_backend_api
+    app_alerts = get_backend_api('appalerts_backend')
+
+Make sure to also enable ``appalerts_backend`` in the
+``ENABLED_BACKEND_PLUGINS`` Django setting.
 
 .. currentmodule:: appalerts.api
 

docs/source/app_projectroles_api_django.rst

@@ -35,7 +35,12 @@ App Settings
 ============
 
 Projectroles provides an API for getting or setting project and user specific
-settings.
+settings. The API can be invoked as follows:
+
+.. code-block:: python
+
+    from projectroles.app_settings import AppSettingAPI
+    app_settings = AppSettingAPI()
 
 .. autoclass:: projectroles.app_settings.AppSettingAPI
     :members:
@@ -119,6 +124,10 @@ Base view classes and mixins for building Ajax API views can be found in
 
 .. currentmodule:: projectroles.views_ajax
 
+.. autoclass:: SODARBaseAjaxMixin
+    :members:
+    :show-inheritance:
+
 .. autoclass:: SODARBaseAjaxView
     :members:
     :show-inheritance:

docs/source/app_projectroles_basics.rst

@@ -146,8 +146,8 @@ Other features in the projectroles app:
 - **Custom user model**: Additions to the standard Django user model
 - **Multi-domain LDAP/AD support**: Support for LDAP/AD users from multiple
   domains
-- **SODAR Taskflow and Timeline integration**: Included but disabled unless
-  backend apps for Taskflow and Timeline are integrated in the Django site
+- **SODAR Timeline integration**: Included but disabled unless the backend app
+  for Timeline is enabled in your Django site
 
 
 Templates and Styles

docs/source/app_projectroles_custom.rst

@@ -92,6 +92,15 @@ documentation links or linking to external sites. Example:
     </li>
 
 
+Extra Login View Content
+========================
+
+If you want to provide extra content in your site's login view, you can add
+custom HTML into the template file
+``{SITE_NAME}/templates/include/_login_extend.html``. The content will appear
+below the login form and its format is not restricted.
+
+
 Site Logo
 =========
 

docs/source/app_projectroles_integration.rst

@@ -86,7 +86,7 @@ desired release tag or commit ID.
 .. code-block:: console
 
     -e git+https://github.com/mikkonie/django-plugins.git@42e86e7904e5c09f1da32173862b26843eda5dd8#egg=django-plugins
-    django-sodar-core==0.10.13
+    django-sodar-core==0.11.0
 
 Install the requirements for development: