Django update to 3.2, Python 3.10

varfish-org · Feb 1, 2024 · 1d8f0d8 · 1d8f0d8
1 parent a95e73b
commit 1d8f0d8
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -13,17 +13,15 @@ jobs:
         with:
           conda-channels: defaults,bioconda,conda-forge
       - name: Install mamba.
-        run: conda install -y mamba python=3.8
+        run: conda install -y mamba
       - name: Install the cadd-scripts package from bioconda
         run: mamba install -y cadd-scripts
 
       - name: Checkout repository
         uses: actions/checkout@v2
       - name: Install project Python dependencies
         run: |
-          pip install -r requirements/base.txt
           pip install -r requirements/test.txt
-          pip install -r requirements/production.txt
       - name: Run tests
         run: |
           coverage run --rcfile=.coveragerc manage.py test -v 2 --settings=config.settings.test

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -1,27 +1,26 @@
-pytz==2019.2  # https://github.com/stub42/pytz
-python-slugify==3.0.3  # https://github.com/un33k/python-slugify
-Pillow==6.1.0  # https://github.com/python-pillow/Pillow
-argon2-cffi==19.1.0  # https://github.com/hynek/argon2_cffi
-redis==3.3.8  # https://github.com/antirez/redis
-celery==4.3.1  # pyup: < 5.0  # https://github.com/celery/celery
-django-celery-beat==1.5.0  # https://github.com/celery/django-celery-beat
+pytz
+python-slugify
+Pillow
+argon2-cffi
+redis
+celery
 
-Werkzeug==0.14.1  # pyup: < 0.15 # https://github.com/pallets/werkzeug
-Sphinx==2.2.0  # https://github.com/sphinx-doc/sphinx
+Werkzeug
+Sphinx
 
 # Django
 # ------------------------------------------------------------------------------
-django<2.0  # pyup: < 3.0  # https://www.djangoproject.com/
-django-environ==0.4.5  # https://github.com/joke2k/django-environ
-django-model-utils==3.2.0  # https://github.com/jazzband/django-model-utils
-django-allauth==0.40.0  # https://github.com/pennersr/django-allauth
-django-crispy-forms==1.7.2  # https://github.com/django-crispy-forms/django-crispy-forms
-django-redis==4.10.0  # https://github.com/niwinz/django-redis
-django-debug-toolbar==2.0  # https://github.com/jazzband/django-debug-toolbar
+django==3.2
+django-environ
+django-model-utils
+django-allauth
+django-crispy-forms
+django-redis
+django-debug-toolbar
 
 # Django REST Framework
-djangorestframework==3.10.3  # https://github.com/encode/django-rest-framework
-coreapi==2.3.3  # https://github.com/core-api/python-client
+djangorestframework
+coreapi
 
-jsonfield==2.1.1
-ipdb==0.12.2  # https://github.com/gotcha/ipdb
+jsonfield
+ipdb
diff --git a/requirements/production.txt b/requirements/production.txt
@@ -2,9 +2,9 @@
 
 -r ./base.txt
 
-gunicorn==19.9.0  # https://github.com/benoitc/gunicorn
-Collectfast==1.0.0  # https://github.com/antonagestam/collectfast
+gunicorn
+Collectfast
 
 # Django
 # ------------------------------------------------------------------------------
-django-anymail[mailgun]==6.1.0  # https://github.com/anymail/django-anymail
+django-anymail[mailgun]
diff --git a/requirements/test.txt b/requirements/test.txt
@@ -2,22 +2,23 @@
 
 # Testing
 # ------------------------------------------------------------------------------
-mypy==0.720  # https://github.com/python/mypy
-pytest==5.1.2  # https://github.com/pytest-dev/pytest
-pytest-sugar==0.9.2  # https://github.com/Frozenball/pytest-sugar
+mypy
+pytest
+pytest-sugar
 
 # Code quality
 # ------------------------------------------------------------------------------
-flake8==3.7.8  # https://github.com/PyCQA/flake8
-coverage==4.5.4  # https://github.com/nedbat/coveragepy
-black==22.3.0  # https://github.com/ambv/black
-pylint-django==2.0.11  # https://github.com/PyCQA/pylint-django
-pylint-celery==0.3  # https://github.com/PyCQA/pylint-celery
+flake8
+coverage
+black
+pylint-django
+pylint-celery
 
 # Django
 # ------------------------------------------------------------------------------
-factory-boy==2.12.0  # https://github.com/FactoryBoy/factory_boy
+factory-boy
 
-django-extensions==2.2.1  # https://github.com/django-extensions/django-extensions
-django-coverage-plugin==1.6.0  # https://github.com/nedbat/django_coverage_plugin
-pytest-django==3.5.1  # https://github.com/pytest-dev/pytest-django
+django-extensions
+django-coverage-plugin
+django-test-plus
+pytest-django
diff --git a/restapi/tests.py b/restapi/tests.py
@@ -2,7 +2,7 @@
 from unittest.mock import patch
 import uuid
 
-from django.test import TestCase
+from test_plus.test import TestCase
 from django.urls import reverse
 
 from restapi.models import AnnotateBackgroundJob

diff --git a/restapi/views.py b/restapi/views.py
@@ -25,7 +25,7 @@ def post(self, *args, **kwargs):
             "genome_build": genomebuild,
             "cadd_release": self.request.data.get("cadd_release"),
             "variants": [
-                var for var in self.request.data.getlist("variant") if re.search(RE_VAR, var)
+                var for var in self.request.data.get("variant") if re.search(RE_VAR, var)
             ],
         }
         try:

diff --git a/utils/docker/Dockerfile b/utils/docker/Dockerfile
@@ -4,7 +4,7 @@
 # Base
 # ---------------------------------------------------------------------------
 
-FROM python:3.8 AS base
+FROM python:3.10-bookworm AS base
 
 ENV LANG C.UTF-8
 ENV LC_ALL C.UTF-8

diff --git a/utils/docker/docker-entrypoint.sh b/utils/docker/docker-entrypoint.sh
@@ -50,8 +50,9 @@ if [[ "$1" == wsgi ]]; then
 elif [[ "$1" == celeryd ]]; then
   cd $APP_DIR
 
-  exec celery worker \
+  exec celery \
     --app config.celery_app \
+    worker \
     -Q "${CELERY_QUEUES}" \
     --concurrency "${CELERY_WORKERS}" \
     --loglevel info