Update Python to 3.12 and dependencies

.gitlab-ci.yml

.pre-commit-config.yaml

Dockerfile

app/api/endpoints/resource_version.py

app/api/endpoints/resources.py

app/api/resource_cluster_utils.py

app/api/resource_s3_utils.py

app/tests/conftest.py

pyproject.toml

requirements-dev.txt

requirements.txt