Cleanup warnings in tests (#6911)

* Only show 5 slowest test durations
* Remove deprecation warning in cmd_node.py
* Remove deprecation warnings in tests/cmdline/commands/test_node.py
* Add stacklevel to warn_deprecation
* Ignore plumpy get_event_loop deprecation warning
* Fix fixture in tests/cmdline/commands/test_process.py
* Ignore 'dict interface' spglib deprecation warning
* Fix pymatgen deprecation warning
tests/test_dataclasses.py::TestStructureDataFromPymatgen::test_1
  tests/test_dataclasses.py:2098: FutureWarning: get_structures is deprecated;
use parse_structures in pymatgen.io.cif instead.
The only difference is that primitive defaults to False in the new parse_structures method.
So parse_structures(primitive=True) is equivalent to the old behavior of get_structures().
  pymatgen_struct = pymatgen_parser.get_structures()[0]

Author: danielhollas

pyproject.toml

@@ -378,7 +378,7 @@ ignore_errors = true
 module = 'plumpy'
 
 [tool.pytest.ini_options]
-addopts = '--benchmark-skip --durations=50 --durations-min=1 --strict-config --strict-markers -ra --cov-report xml --cov-append '
+addopts = '--benchmark-skip --durations=5 --durations-min=1 --strict-config --strict-markers -ra --cov-report xml --cov-append '
 filterwarnings = [
   'ignore:.*and will be removed in NumPy 2.0.*:DeprecationWarning:ase:',
   'ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:pytz|dateutil|tqdm|aio_pika:',
@@ -398,6 +398,10 @@ filterwarnings = [
   'ignore:Identity map already had an identity for .* inside of an event handler within the flush?:sqlalchemy.exc.SAWarning',
   'ignore:The `aiida.orm.nodes.data.upf` module is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
   'ignore:The `Code` class is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
+  # https://github.com/aiidateam/plumpy/issues/283
+  'ignore:There is no current event loop:DeprecationWarning:plumpy',
+  # spglib deprecation
+  'ignore:dict interface is deprecated:DeprecationWarning',
   'default::ResourceWarning'
 ]
 markers = [

src/aiida/cmdline/commands/cmd_node.py

@@ -372,7 +372,7 @@ def _perform_delete():
         from aiida.orm.utils.remote import clean_mapping_remote_paths, get_calcjob_remote_paths
         from aiida.tools.graph.graph_traversers import get_nodes_delete
 
-        backend = get_manager().get_backend()
+        backend = get_manager().get_profile_storage()
         # For here we ignore missing nodes will be raised via func:``delete_nodes`` in the next block
         pks_set_to_delete = get_nodes_delete(
             pks, get_links=False, missing_callback=lambda missing_pks: None, backend=backend, **traversal_rules

src/aiida/manage/manager.py

@@ -248,7 +248,7 @@ def get_backend(self) -> 'StorageBackend':
         """
         from aiida.common.warnings import warn_deprecation
 
-        warn_deprecation('get_backend() is deprecated, use get_profile_storage() instead', version=3)
+        warn_deprecation('get_backend() is deprecated, use get_profile_storage() instead', version=3, stacklevel=3)
         return self.get_profile_storage()
 
     def get_profile_storage(self) -> 'StorageBackend':

tests/cmdline/commands/test_node.py

@@ -606,7 +606,7 @@ def _setup(n_workflows=1, n_calcjobs=1, n_remotes=1):
 
                 for i in range(n_calcjobs):
                     calcjob_node = CalcJobNode(computer=aiida_localhost)
-                    calcjob_node.add_incoming(workflow_node, link_type=LinkType.CALL_CALC, link_label='call')
+                    calcjob_node.base.links.add_incoming(workflow_node, link_type=LinkType.CALL_CALC, link_label='call')
 
                     workdir = tmp_path / f'calcjob_{uuid.uuid4()}'
                     workdir.mkdir()
@@ -637,22 +637,22 @@ def verify_deletion(self, nodes_deleted=True, folders_deleted=True):
         if nodes_deleted:
             for workflow_pk in self.workflow_pks:
                 with pytest.raises(NotExistent):
-                    WorkflowNode.objects.get(pk=workflow_pk)
+                    WorkflowNode.collection.get(pk=workflow_pk)
 
             for calcjob_pk in self.calcjob_pks:
                 with pytest.raises(NotExistent):
-                    CalcJobNode.objects.get(pk=calcjob_pk)
+                    CalcJobNode.collection.get(pk=calcjob_pk)
 
             for remote_pk in self.remote_pks:
                 with pytest.raises(NotExistent):
-                    RemoteData.objects.get(pk=remote_pk)
+                    RemoteData.collection.get(pk=remote_pk)
         else:
             for workflow_pk in self.workflow_pks:
-                WorkflowNode.objects.get(pk=workflow_pk)
+                WorkflowNode.collection.get(pk=workflow_pk)
             for calcjob_pk in self.calcjob_pks:
-                CalcJobNode.objects.get(pk=calcjob_pk)
+                CalcJobNode.collection.get(pk=calcjob_pk)
             for remote_pk in self.remote_pks:
-                RemoteData.objects.get(pk=remote_pk)
+                RemoteData.collection.get(pk=remote_pk)
 
         for remote_folder in self.remote_folders:
             if folders_deleted:

tests/cmdline/commands/test_process.py

@@ -95,14 +95,11 @@ async def exponential_backoff_retry_fail_kill(fct: t.Callable[..., t.Any], *args
 
 
 @pytest.fixture(scope='function')
-@pytest.mark.usefixtures('started_daemon_client')
-def fork_worker_context(aiida_profile):
+def fork_worker_context(aiida_profile, started_daemon_client):
     """Runs daemon worker on a new process with redirected stdout and stderr streams."""
     import multiprocessing
 
-    from aiida.engine.daemon.client import get_daemon_client
-
-    client = get_daemon_client(aiida_profile)
+    client = started_daemon_client
     nb_workers = client.get_number_of_workers()
     # The workers are decreased to zero to ensure that the worker that is
     # subsequently started through this fixture is the one that receives all

tests/test_dataclasses.py

@@ -2095,7 +2095,7 @@ def test_1(self):
             )
             tmpf.flush()
             pymatgen_parser = CifParser(tmpf.name)
-            pymatgen_struct = pymatgen_parser.get_structures()[0]
+            pymatgen_struct = pymatgen_parser.parse_structures(primitive=True)[0]
 
         structs_to_test = [StructureData(pymatgen=pymatgen_struct), StructureData(pymatgen_structure=pymatgen_struct)]