feat: upgrade to sodar core v1 (#1973)

.github/workflows/main.yml

@@ -14,7 +14,7 @@ jobs:
           - 6379:6379
 
       postgres:
-        image: postgres:14
+        image: postgres:16
         env:
           POSTGRES_DB: varfish_web
           POSTGRES_USER: varfish_web

backend/Makefile

@@ -109,13 +109,16 @@ ci: \
 docs:
 	pipenv run $(MAKE) -C ../docs clean html
 
-.PHONY: _migrate
-_migrate:
+.PHONY: _makemigrations
+_makemigrations:
 	pipenv run $(MANAGE) makemigrations
-	pipenv run $(MANAGE) migrate
+
+.PHONY: makemigrations
+makemigrations: _makemigrations format
 
 .PHONY: migrate
-migrate: _migrate format
+migrate:
+	pipenv run $(MANAGE) migrate
 
 .PHONY: shell
 shell:

backend/Pipfile

@@ -7,20 +7,21 @@ name = "pypi"
 aldjemy = "~=2.2"
 altamisa = "~=0.2.5"
 attrs = "~=24.2"
-beautifulsoup4 = "~=4.9"
+beautifulsoup4 = "~=4.12.3"
 cattrs = "*"
 django = "*"  # whatever django-sodar-core enforces
 django-clone = "*"
 django-cryptographic-fields-bihealth = "~=0.6.0"
 django-debug-toolbar = "*"
 django-extensions = "~=3.2"
 django-postgres-copy = "~=2.3.5"  # there are issues above 2.3
-django-plugins-bihealth = "~=0.4.0"
-django-sodar-core = "~=0.13.4"
+django-plugins-bihealth = "~=0.5.2"
+django-sodar-core = "~=1.0.2"
 django-su = "~=1.0.0"
 djangorestframework-httpsignature = "~=1.0"
+djangorestframework = "~=3.15"
 djproxy = "~=2.3"
-drf-keyed-list-bihealth = "~=0.1.1"
+drf-keyed-list-bihealth = "~=0.2.1"
 httpsig = "~=1.3"
 interval-binning = "~=1.0"
 intervaltree = "~=3.1"
@@ -51,10 +52,10 @@ wrapt = "~=1.16"
 xlsxwriter = "~=3.2"
 django-pydantic-field = "*"
 pydantic = "*"
+typing-extensions="*"
 universal-pathlib = "*"
 s3fs = "*"
 toml = "*"
-black = "*"
 rich = "*"
 drf-writable-nested = "*"
 django-modelcluster = "*"
@@ -96,7 +97,7 @@ django-types = "*"
 [ldap-packages]
 # Dependencies for enabling LDAP support.  You will need the system library
 # named `libldap` (or similar).
-django-auth-ldap = "~=4.1"
+django-auth-ldap = "~=4.6"
 python-ldap = "~=3.4"
 # Packages needed in production.
 
@@ -109,4 +110,4 @@ django-storages = "*"
 django_redis = "*"
 
 [requires]
-python_version = "3.10"
+python_version = "3.11"