merge v1.3.2 release

Author: mikkonie

.github/ISSUE_TEMPLATE/dependency_upgrade.md

@@ -0,0 +1,16 @@
+---
+name: Dependency Upgrade
+about: Checklist for manual dependency upgrades for a release
+title: 'Upgrade dependencies for RELEASE_VERSION'
+labels: environment
+assignees: 'mikkonie'
+
+---
+
+## Dependencies
+
+- [ ] TODO
+
+## Notes
+
+N/A

CHANGELOG.rst

@@ -5,6 +5,28 @@ Changelog for the **SODAR Core** Django app package. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
+v1.3.2 (2026-01-12)
+===================
+
+Added
+-----
+
+- **General**
+    - Dependency upgrade issue template (#1856)
+- **Timeline**
+    - Debug logging for event creation and updating (#449)
+
+Changed
+-------
+
+- **General**
+    - Upgrade to Django v5.2.10 (#1857)
+    - Refactor relative imports into absolute imports (#392)
+    - Update ``dev_core_install.rst`` for ``sodar-core-docker-compose`` (#1852)
+- **Timeline**
+    - Refactor object creation (#1858)
+
+
 v1.3.1 (2025-12-12)
 ===================
 

README.rst

@@ -117,7 +117,7 @@ and breaking changes are possible.
 
 .. code-block:: console
 
-    pip install django-sodar-core==1.3.1
+    pip install django-sodar-core==1.3.2
 
 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.

adminalerts/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from .models import AdminAlert
+from adminalerts.models import AdminAlert
 
 # Register your models here.
 admin.site.register(AdminAlert)

bgjobs/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from .models import BackgroundJob, BackgroundJobLogEntry
+from bgjobs.models import BackgroundJob, BackgroundJobLogEntry
 
 # Register your models here.
 admin.site.register(BackgroundJob)

codemeta.json

@@ -40,12 +40,12 @@
   ],
   "identifier": "https://doi.org/10.5281/zenodo.4269346",
   "codeRepository": "https://github.com/bihealth/sodar-core",
-  "datePublished": "2025-12-12",
-  "dateModified": "2025-12-12",
+  "datePublished": "2026-01-12",
+  "dateModified": "2026-01-12",
   "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": "v1.3.1"
+  "version": "v1.3.2"
 }

docs/source/conf.py

@@ -23,13 +23,13 @@
 # -- Project information -----------------------------------------------------
 
 project = 'SODAR Core'
-copyright = '2018-2025, Berlin Institute of Health'
+copyright = '2018-2026, Berlin Institute of Health'
 author = 'BIH Core Unit Bioinformatics'
 
 # The short X.Y version
 version = '1.3'
 # The full version, including alpha/beta/rc tags
-release = '1.3.1'
+release = '1.3.2'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/dev_core_install.rst

@@ -6,44 +6,46 @@ Development Installation
 Instructions on how to install a local development version of SODAR Core are
 detailed here. Ubuntu 24.04 LTS is the supported OS for development. For
 deployment, the same Ubuntu version or a corresponding Debian release are
-recommended. Other Linux variants can be used, but some system dependencies may
-vary for different OS versions or distributions.
-
-Installation and development should be possible on most recent versions of
-Linux, Mac and Windows (WSL2 recommended). However, this may require extra work
-and your mileage may vary.
-
-If you need to set up the accompanying example site in Docker, please see online
-for up-to-date Docker setup tutorials for Django related to your operating
-system of choice.
+recommended. Other Linux variants can be used for development or deployment, but
+some system dependencies may vary for different OS versions or distributions.
 
 .. note::
 
-    These instructions are also valid for the
+    These instructions are also valid for developing the
     `sodar-django-site <https://github.com/bihealth/sodar-django-site>`_
     repository.
 
 
-System Dependencies
-===================
+.. _dev_core_install_database:
 
-To get started, install the OS dependencies, Python >=3.11 (3.13 recommended)
-and PostgreSQL >=12 (16 recommended).
+1. Setup Database Servers
+=========================
 
-.. code-block:: console
+Developing SODAR Core requires PostgreSQL v12+ (v16 recommended) and Redis.
+There are two options for setting up the databases: bringing up the
+pre-configured Docker Compose network or manual setup.
 
-    $ sudo utility/install_os_dependencies.sh
-    $ sudo utility/install_python.sh
-    $ sudo utility/install_postgres.sh
+Setup with Docker Compose (Recommended)
+---------------------------------------
 
+The easiest way to set up the database servers is by cloning
+`sodar-core-docker-compose <https://github.com/bihealth/sodar-core-docker-compose>`_.
+This repository sets up a Docker Compose network with the database servers as
+containers. Follow the instructions in the repository readme to bring up the
+network. The SODAR Core database and user will be set up automatically on
+initial launch.
 
-.. _dev_core_install_database:
+Manual Setup
+------------
 
-Database Setup
-==============
+It is also possible to set up a server manually or use an existing server. To
+install PostgreSQL prerequisites, run the following script:
 
-Next you need to setup the database and PostgreSQL user. You need to enter the
-following SQL in ``psql``:
+.. code-block:: console
+
+    $ sudo utility/install_postgres.sh
+
+Once you have a PostgreSQL server running, you'll need to run the following SQL:
 
 .. code-block:: sql
 
@@ -52,41 +54,58 @@ following SQL in ``psql``:
     ALTER DATABASE sodar_core OWNER TO sodar_core;
     ALTER USER sodar_core CREATEDB;
 
-Alternatively, if PostgreSQL is running directly on your development host, you
-can use the following utility script (this does not work with a Docker setup):
+If your PostgreSQL is running directly on your development host, you can also
+use the following utility script:
 
 .. code-block:: console
 
     $ sudo utility/setup_database.sh
 
-You have to set the database URL and credentials for Django in the environment
-variable ``DATABASE_URL``. For development it is recommended to place
-environment variables in file ``.env`` located in your project root. To enable
-loading the file in Django, set ``DJANGO_READ_DOT_ENV_FILE=1`` in your
-environment variables when running SODAR or any of its management commands.
-See ``config/settings/base.py`` for more information and the ``env.example``
-file for an example environment file.
+To install Redis manually, run the following script:
+
+.. code-block:: console
+
+    $ sudo utility/install_redis.sh
 
-Example of the database URL variable as set within an ``.env`` file:
+
+2. Setup Repository
+===================
+
+Clone the SODAR Core repository from GitHub and create yourself a ``.env``
+environment configuration file.
 
 .. code-block:: console
 
-    DATABASE_URL="postgres://sodar_core:sodar_core@127.0.0.1/sodar_core"
+    $ git clone https://github.com/bihealth/sodar-core.git
+    $ cd sodar-core
+    $ cp env.example .env
+
+.. important::
 
-Asynchronous Celery tasks require running a Redis server. For development, you
-can install it with the following script:
+    To enable loading environment variables from the ``.env`` file, make sure to
+    set ``DJANGO_READ_DOT_ENV_FILE=1`` in the environment variables of the
+    development host.
+
+
+3. Install OS Dependencies
+==========================
+
+For development, you are expected to run the Django server and possible Celery
+worker locally. To get started, install the OS dependencies and Python >=3.11
+(3.13 recommended).
 
 .. code-block:: console
 
-    $ sudo utility/install_redis.sh
+    $ sudo utility/install_os_dependencies.sh
+    $ sudo utility/install_python.sh
 
 
-Repository and Environment Setup
-================================
+4. Install Python Dependencies
+==============================
 
-Clone the repository, setup and activate the virtual environment. Once within
-the repository and an active virtual environment, install Python requirements
-for the project. Example:
+To set up Python dependencies for the repository, you'll first need to activate
+a virtual environment. Once within an active virtual environment, use the
+provided script to install the Python dependencies for development. Example:
 
 .. code-block:: console
 
@@ -95,21 +114,21 @@ for the project. Example:
     $ utility/install_python_dependencies.sh
 
 
-LDAP Setup (Optional)
-=====================
+5. Install LDAP Dependencies (Optional)
+=======================================
 
-If you will be using LDAP/AD auth on your site, make sure to also run:
+If you will be using LDAP/AD auth when developing, make sure to also run:
 
 .. code-block:: console
 
     $ sudo utility/install_ldap_dependencies.sh
     $ pip install -r requirements/ldap.txt
 
 
-Final Setup
-===========
+6. Setup Django
+===============
 
-Initialize the database (this will also synchronize django-plugins):
+Initialize the SODAR Core Django database (this will also synchronize plugins):
 
 .. code-block:: console
 
@@ -150,20 +169,20 @@ terminal.
     process is not necessary.
 
 
-Optional Steps
-==============
+7. Create Development Users (Optional)
+======================================
 
-For creating a group of example users for your development site, you can run the
-``createdevusers`` management command. This creates the users "alice", "bob",
-"carol", "dan" and "erin". The users will be created with the password
-"sodarpass", unless a custom password is supplied via the ``-p`` or
+For creating a group of example users for your development site, it is
+recommended to run the ``createdevusers`` management command. This creates the
+users "alice", "bob", "carol", "dan" and "erin". The users will be created with
+the password "sodarpass", unless a custom password is supplied via the ``-p`` or
 ``--password`` argument.
 
 .. code-block:: console
 
     $ ./manage.py createdevusers
 
-.. note::
+.. hint::
 
     Having multiple non-admin user accounts is useful for developing and trying
     out project and member access management features. It is recommended to log

docs/source/major_changes.rst

@@ -10,6 +10,26 @@ older SODAR Core version. For a complete list of changes in current and previous
 releases, see the :ref:`full changelog<changelog>`.
 
 
+v1.3.2 (2026-01-12)
+*******************
+
+Release Highlights
+==================
+
+- Add timeline API debug logging
+- Add depdendency upgrade issue template
+- Upgrade critical dependencies
+
+Breaking Changes
+================
+
+System Prerequisites
+--------------------
+
+Django Version
+    The minimum Django version has been bumped to v5.2.10.
+
+
 v1.3.1 (2025-12-12)
 *******************
 

filesfolders/admin.py

@@ -2,7 +2,8 @@
 from django.contrib import admin
 
 from db_file_storage.form_widgets import DBAdminClearableFileInput
-from .models import File, Folder, HyperLink
+
+from filesfolders.models import File, Folder, HyperLink
 
 
 class FileForm(forms.ModelForm):