Skip to content

UPDATE.md

Latest commit

 

History

History
138 lines (92 loc) · 4.77 KB

UPDATE.md

File metadata and controls

138 lines (92 loc) · 4.77 KB
Raw

Some CATMAID versions require manual changes to an existing setup. Below these and other administration related changes are listed in order.

2019.06.20

  • A virtualenv update is required.

  • All *.pyc files in the folders django/applications/catmaid/migrations/, django/applications/performancetests/migrations/ and django/applications/pgcompat/migrations/ need to be deleted.

  • Python 3.7 is now supported.

  • Heads-up: The next CATMAID version will require Postgres 11, PostGIS 2.5 and Python 3.6 or 3.7.

  • Should migration 0057 fail due a permission error, the Postgres extension "pg_trgm" has to be installed manually into the CATMAID database using a Postgres superuser: sudo -u postgres psql -d <catmaid-db> -c 'CREATE EXTENSION pg_trgm;'

  • CATMAID's version information changes back to a plain git describe format. This results overall in a simpler setup and makes live easier for some third-party front-ends, because the commit counter is included again. The version display is now the same git describe format for both regular setups and Docker containers.

  • Tile loading is clamped to (0,0) again, i.e. there are no negative tile coordinates anymore by default. If you need them, set the respective stack's metadata field to {"clamp": false}.

  • To write to CATMAID through its API using an API token, users need to have now dedicated "API write" permission, called "Can annotate project using API token" in the admin UI. To restore the previous behavior (regular annotate permission allows API write access) the settings.py variable REQUIRE_EXTRA_TOKEN_PERMISSIONS can be set to False. This is done as a safety measure to prevent accidental changes through automation.

  • If R based NBLAST is used, make sure to execute to update all dependencies: manage.py catmaid_setup_nblast_environment.

  • The main documentation on catmaid.org has now a place for widget specific documentation as well. Only a few widgets have been updated yet, but more will follow.

2018.11.09

  • Python 3 is now required for the back-end. We recommend the use of Python 3.6.

2018.07.19

  • This is the last CATMAID version with support for Python 2.7. Starting from next version, only Python 3 will be supported.

2018.04.15

  • Postgres 10+ is now required.

2018.02.16

  • Three new OS package dependencies have been added (due to a Django framework upgrade), make sure they are installed:

    sudo apt-get install binutils libproj-dev gdal-bin

  • Python 3.6 is now supported. Make sure to update your settings.py by replacing the line

    COOKIE_SUFFIX = hashlib.md5(CATMAID_URL).hexdigest()

    with the following line:

    COOKIE_SUFFIX = hashlib.md5(CATMAID_URL.encode('utf-8')).hexdigest()

  • CATMAID extensions no longer require users to manually update their INSTALLED_APPS in settings.py. Remove if they are already in use.

  • The NODE_PROVIDER settings variable (settings.py) is replaced with the NODE_PROVIDERS variable. The new variable takes a list of node provider names, which are iterated as long as no result nodes are found. Replace the former single string value with a list with this name as single element, e.g. if the current setting reads NODE_PROVIDER = 'postgis2d', replace it with NODE_PROVIDERS = ['postgis2d'].

2017.12.07

  • PostgreSQL 9.6 and Postgis 2.4 are now required.

  • A virtualenv upgrade is required. To correctly install one updated dependency, the django-rest-swagger Python package has to be removed first from from the virtualenv, before the virtualenv is updated:

    pip uninstall django-rest-swagger
pip install -r requirements.txt

  • Requires running of: manage.py catmaid_update_project_configuration

  • Tracing data is now by default transmitted in a binary form, please make therefore sure your web-server applies GZIP not only to the application/json content type, but also to application/octet-stream. For Nginx this would be the gzip_types setting.

2017.07.28

  • The following lines have to be removed from settings.py,

    import djcelery
djcelery.setup_loader()
INSTALLED_APPs += ("kombu.transport.django")
BROKER_URL = 'django://'

2017.05.17

  • A virtualenv upgrade is required. To correctly install one updated dependency, the django-rest-swagger Python package has to be removed first from from the virtualenv, before the virtualenv is updated:

    pip uninstall django-rest-swagger
pip install -r requirements.txt

2017.04.20

  • The location of the manage.py script changed: it moved a level up into django/projects. All other configuration files remain where they are. Make sure to update your settings.py file by replacing the line from settings_base import * with from mysite.settings_base import *.