build(python): upgrade to Flask 3.x

[tiborsimko]

Upgrade Flask from <2.3.0 to >=3.0.0 and Werkzeug from <2.3.0 to >=3.0.0, in line with the Invenio package upgrade in reana-server. Bump marshmallow from <3.0.0 to >=3.5.0,<4.0.0 and webargs to >=8.0, since the new Invenio stack requires marshmallow 3 and the corresponding webargs 8.

Adapt the REST endpoints to the new marshmallow 3 and webargs 8 APIs. Replace the deprecated missing= keyword on schema fields with load_default=. Add unknown=marshmallow.EXCLUDE to all @use_kwargs and @use_args decorators that parse query parameters, so that REANA-specific extras such as access_token are silently ignored, matching the pre-upgrade webargs 5 behaviour.

Replace all remaining Model.query call sites in the REST handlers, the workflow run manager, and the test suite with explicit Session.query(Model) queries, since SQLAlchemy 2.x no longer supports the Base.query shortcut.

Replace the deprecated FLASK_ENV setting with FLASK_DEBUG, both in the runtime checks of the workflow run manager and in the DEBUG_ENV_VARS injected into spawned workflow engine containers. Update the test configuration to use DEBUG instead of FLASK_ENV.

Remove pinned reana-commons, reana-db, and kubernetes entries from requirements.txt so that pip install . resolves them freshly from setup.py against the locally-mounted modules/reana-db and modules/reana-commons shared sources during development, avoiding version conflicts with PyPI versions that still carry the old pins.

Closes reanahub/reana-server#770.

[michaelbuchar]

AI Review

Workspace-limit tests still mock the pre-migration query API

_mock_workspace_access() still monkeypatches workflows_workspace.User.query, but the migrated handlers now look users up via Session.query(User). On this branch that means the helper no longer intercepts anything, and the PR's python-tests job fails with five tests/test_workspace_limits.py cases returning 500 instead of their expected 200/400 responses. Please update the helper to stub Session.query(...) or use a real session-backed user fixture.

reana-workflow-controller/tests/test_workspace_limits.py:45-55

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.51%. Comparing base (dc8bb22) to head (324f4ad).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #678      +/-   ##
==========================================
+ Coverage   74.46%   74.51%   +0.04%     
==========================================
  Files          17       17              
  Lines        2044     2048       +4     
==========================================
+ Hits         1522     1526       +4     
  Misses        522      522              

Files with missing lines	Coverage Δ
reana_workflow_controller/config.py	95.45% <ø> (ø)
reana_workflow_controller/rest/utils.py	84.70% <100.00%> (ø)
reana_workflow_controller/rest/workflows.py	68.83% <100.00%> (+0.10%)	⬆️
...eana_workflow_controller/rest/workflows_session.py	72.34% <100.00%> (+0.60%)	⬆️
reana_workflow_controller/rest/workflows_status.py	83.90% <100.00%> (+0.18%)	⬆️
...na_workflow_controller/rest/workflows_workspace.py	63.57% <100.00%> (+0.26%)	⬆️
reana_workflow_controller/workflow_run_manager.py	80.32% <100.00%> (ø)

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[tiborsimko]

_mock_workspace_access() still monkeypatches workflows_workspace.User.query, but the migrated handlers now look users up via Session.query(User). On this branch that means the helper no longer intercepts anything, and the PR's python-tests job fails with five tests/test_workspace_limits.py cases returning 500 instead of their expected 200/400 responses.

Thanks — fixed in this branch. _mock_workspace_access() now patches workflows_workspace.Session.query (returning a fake query that yields a stub user) instead of the obsolete User.query, so the helper intercepts the migrated Session.query(User).filter(...).first() lookup. The five tests/test_workspace_limits.py cases pass locally and in CI.