Merge pull request #795 from MolSSI/rel_52

Release v0.52
MolSSI · Nov 29, 2023 · 1ca10b9 · 1ca10b9
2 parents 63ace1b + 57e9465
commit 1ca10b9
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diff --git a/docs/source/release_notes.rst b/docs/source/release_notes.rst
@@ -1,6 +1,22 @@
 Release Notes
 =============
 
+0.52 / 2023-11-29
+-----------------
+
+Some improvements and bugfixes, but no breaking changes. Upgrading qcportal is recommended
+due to fixes related to JWTs, but is not required. The same is true with compute managers.
+
+Notable pull requests and features:
+
+- (:pr:`781`) Fixes issues related to shutdown of snowflakes, particularly with Python 3.12
+- (:pr:`783`, :pr:`793`) Fixes JWT refresh issues that cause errors in clients
+- (:pr:`785`) Some cleanups related to Python 3.12 (including removing use of removing `pkg_resources` module)
+- (:pr:`787`) Pydantic v1/v2 dual compatibility (L. Naden :contrib:`lnaden`, M. Thompson `mattwthompson`, L. Burns `loriab`)
+- (:pr:`792`) Add ability to get status overview of child records (such as optimizations of a torsiondrive)
+- (:pr:`794`) Remove use of now-deprecated `utctime` function and improve handling of timezones
+
+
 0.51 / 2023-10-19
 -----------------
 

diff --git a/qcarchivetesting/qcarchivetesting/data_generator.py b/qcarchivetesting/qcarchivetesting/data_generator.py
@@ -34,7 +34,6 @@ def clean_conda_env(d: Dict[str, Any]):
 
 class DataGeneratorManager(ComputeManager):
     def __init__(self, qcf_config: FractalConfig, result_queue: queue.Queue, n_workers: int = 2):
-
         self._qcf_config = qcf_config
         self._result_queue = result_queue
         self._record_id_map = {}  # Maps task id to record id

diff --git a/qcarchivetesting/qcarchivetesting/helpers.py b/qcarchivetesting/qcarchivetesting/helpers.py
@@ -190,7 +190,6 @@ def caplog_handler_at_level(caplog_fixture, level, logger=None):
 
 def terminate_process(proc):
     if proc.poll() is None:
-
         # Interrupt (SIGINT)
         if sys.platform.startswith("win"):
             proc.send_signal(signal.CTRL_BREAK_EVENT)

diff --git a/qcarchivetesting/qcarchivetesting/test_full_reaction.py b/qcarchivetesting/qcarchivetesting/test_full_reaction.py
@@ -23,7 +23,6 @@
 
 
 def test_reaction_full_1(fulltest_client: PortalClient):
-
     sp_spec = {"program": "psi4", "driver": "energy", "method": "b3lyp", "basis": "def2-tzvp", "keywords": {}}
 
     rxn_keywords = {}

diff --git a/qcarchivetesting/qcarchivetesting/testing_classes.py b/qcarchivetesting/qcarchivetesting/testing_classes.py
@@ -33,7 +33,6 @@
 
 class QCATestingPostgresHarness(PostgresHarness):
     def __init__(self, config: DatabaseConfig):
-
         PostgresHarness.__init__(self, config)
         self.db_name = self.config.database_name
         self.template_name = self.db_name + "_template"
@@ -108,7 +107,6 @@ def __init__(
         log_access=True,
         extra_config=None,
     ):
-
         self.pg_harness = pg_harness
         self.encoding = encoding
 

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-10-963822c28879_molecule_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-10-963822c28879_molecule_msgpack_1.py
@@ -39,7 +39,6 @@
 
 
 def transformer(old_data):
-
     row = {}
     for k, v in old_data.items():
         if k == "id":

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-84c94a48e491_results_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-84c94a48e491_results_msgpack_1.py
@@ -27,7 +27,6 @@
 
 
 def transformer(old_data):
-
     arr = old_data["return_result"]
     if arr is None:
         pass

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-11-8b0cd9accaf2_base_records_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-11-8b0cd9accaf2_base_records_msgpack_1.py
@@ -26,7 +26,6 @@
 
 
 def transformer(old_data):
-
     extras = old_data["extras"]
     extras.pop("_qcfractal_tags", None)  # cleanup old tags
 

diff --git a/qcfractal/qcfractal/alembic/versions/2019-08-12-da7c6f141bcb_extras_msgpack_1.py b/qcfractal/qcfractal/alembic/versions/2019-08-12-da7c6f141bcb_extras_msgpack_1.py
@@ -25,21 +25,18 @@
 
 
 def transformer(old_data):
-
     extras = old_data["extras"]
     extras.pop("_qcfractal_tags", None)  # cleanup old tags
 
     return {"extras_": msgpackext_dumps(extras)}
 
 
 def upgrade():
-
     ## Task Queue
     table_name = "task_queue"
     update_columns = {"spec"}
 
     def transformer(old_data):
-
         spec = old_data["spec"]
 
         return {"spec_": msgpackext_dumps(spec)}
@@ -51,7 +48,6 @@ def transformer(old_data):
     update_columns = {"extra"}
 
     def transformer(old_data):
-
         spec = old_data["extra"]
 
         return {"extra_": msgpackext_dumps(spec)}
@@ -60,7 +56,6 @@ def transformer(old_data):
 
 
 def downgrade():
-
     ## Task Queue
     table_name = "task_queue"
     update_columns = {"spec"}

diff --git a/qcfractal/qcfractal/alembic/versions/2019-11-01-159ba85908fd_add_contributed_values_table.py b/qcfractal/qcfractal/alembic/versions/2019-11-01-159ba85908fd_add_contributed_values_table.py
@@ -22,7 +22,6 @@
 
 
 def migrate_contributed_values_data():
-
     bind = op.get_bind()
     session = orm.Session(bind=bind)
 
@@ -41,7 +40,6 @@ def migrate_contributed_values_data():
             continue
 
         for key, dict_values in ds_contrib.items():
-
             idx, vals = [], []
             for key, value in dict_values["values"].items():
                 idx.append(key)
@@ -59,7 +57,6 @@ def migrate_contributed_values_data():
 
 
 def upgrade():
-
     # rename old column with data
     op.alter_column("dataset", "contributed_values", new_column_name="contributed_values_data")
     op.alter_column("reaction_dataset", "contributed_values", new_column_name="contributed_values_data")

diff --git a/...qcfractal/alembic/versions/2020-07-02-1604623c481a_id_pirmary_key_for_torsion_init_mol.py b/...qcfractal/alembic/versions/2020-07-02-1604623c481a_id_pirmary_key_for_torsion_init_mol.py
@@ -17,7 +17,6 @@
 
 
 def upgrade():
-
     # Removes (harmless) duplicate rows
     op.execute(
         "DELETE FROM torsion_init_mol_association a USING \

diff --git a/qcfractal/qcfractal/alembic/versions/2021-07-13-651954cbdec6_migrate_services.py b/qcfractal/qcfractal/alembic/versions/2021-07-13-651954cbdec6_migrate_services.py
@@ -83,7 +83,6 @@ def upgrade():
     services = session.query(service_table).all()
 
     for service in services:
-
         if "torsiondrive_state" in service.extra:
             # We have a torsiondrive
             service_state = {}

diff --git a/qcfractal/qcfractal/alembic/versions/2021-12-17-bb4804242cea_refactor_torsiondrive.py b/qcfractal/qcfractal/alembic/versions/2021-12-17-bb4804242cea_refactor_torsiondrive.py
@@ -314,7 +314,6 @@ def upgrade():
     services = session.query(service_table).all()
 
     for service in services:
-
         if "torsiondrive_state" not in service.service_state:
             continue
 

diff --git a/qcfractal/qcfractal/alembic/versions/2022-01-03-0f6d9e6ef312_refactoring_gridoptimization.py b/qcfractal/qcfractal/alembic/versions/2022-01-03-0f6d9e6ef312_refactoring_gridoptimization.py
@@ -311,7 +311,6 @@ def upgrade():
     services = session.query(service_table).all()
 
     for service in services:
-
         if "torsiondrive_state" in service.service_state:
             continue
 

diff --git a/qcfractal/qcfractal/alembic/versions/2022-03-15-0b31ab4244de_migrate_reaction_dataset.py b/qcfractal/qcfractal/alembic/versions/2022-03-15-0b31ab4244de_migrate_reaction_dataset.py
@@ -30,7 +30,6 @@
 
 
 def create_reaction_record(conn, ds_id, created_on, modified_on, spec_id, stoichiometries, records):
-
     # We do this allllll by hand. We don't want to depend on the real ORM code
     # First, add a base record
     r = conn.execute(
@@ -119,7 +118,6 @@ def create_reaction_record(conn, ds_id, created_on, modified_on, spec_id, stoich
 
 
 def create_manybody_record(conn, ds_id, created_on, modified_on, spec_id, mol_id, record):
-
     # We do this allllll by hand. We don't want to depend on the real ORM code
     # First, add a base record
     r = conn.execute(

diff --git a/qcfractal/qcfractal/alembic/versions/2022-12-12-c0fba229aaa8_make_molecules_unique.py b/qcfractal/qcfractal/alembic/versions/2022-12-12-c0fba229aaa8_make_molecules_unique.py
@@ -33,7 +33,7 @@ def upgrade():
         )
     )
 
-    for (mol_hash, mol_ids, _) in duplicates:
+    for mol_hash, mol_ids, _ in duplicates:
         mol_ids = sorted(mol_ids)
 
         # Keep the first id, merge the rest

diff --git a/...actal/qcfractal/alembic/versions/2023-03-03-c23b3ba12869_finalize_migration_of_outputs.py b/...actal/qcfractal/alembic/versions/2023-03-03-c23b3ba12869_finalize_migration_of_outputs.py
@@ -37,7 +37,6 @@ def decompress_old_string(compressed_data: bytes, compression_type: CompressionE
 
 
 def upgrade():
-
     # Table with output data
     old_output_table = table(
         "output_store",

diff --git a/qcfractal/qcfractal/alembic/versions/migration_helpers/msgpack_migrations.py b/qcfractal/qcfractal/alembic/versions/migration_helpers/msgpack_migrations.py
@@ -23,7 +23,6 @@ def _get_colnames(columns):
 
 
 def _intermediate_table(table_name, columns, read_columns=None):
-
     column_pairs, old_names, new_names = _get_colnames(columns)
     table_data = [table_name, sa.MetaData(), sa.Column("id", sa.Integer, primary_key=True)]
     table_data.extend([sa.Column(x, old_type) for x in old_names])
@@ -41,7 +40,6 @@ def _intermediate_table(table_name, columns, read_columns=None):
 
 
 def json_to_msgpack_table(table_name, block_size, update_columns, transformer, read_columns=None):
-
     if read_columns is None:
         read_columns = {}
 
@@ -67,7 +65,6 @@ def json_to_msgpack_table(table_name, block_size, update_columns, transformer, r
 
     logger.info("Converting data, this may take some time...")
     for block in tqdm.tqdm(range(0, num_records, block_size)):
-
         # Pull chunk to migrate
         data = connection.execute(
             sa.select([*read_columns], order_by=table.c.id.asc(), offset=block, limit=block_size)
@@ -84,14 +81,12 @@ def json_to_msgpack_table(table_name, block_size, update_columns, transformer, r
 
 
 def json_to_msgpack_table_dropcols(table_name, block_size, update_columns):
-
     column_pairs, old_names, new_names = _get_colnames(update_columns)
     for col in new_names:
         op.drop_column(table_name, col)
 
 
 def json_to_msgpack_table_altercolumns(table_name, update_columns, nullable_true=None):
-
     if nullable_true is None:
         nullable_true = set()
 

diff --git a/qcfractal/qcfractal/components/auth/auth_socket.py b/qcfractal/qcfractal/components/auth/auth_socket.py
@@ -27,7 +27,9 @@ def __init__(self, root_socket: SQLAlchemySocket):
         self.unauth_read_permissions = self.root_socket.roles.get("read")["permissions"]
         self.protected_resources = {"users", "roles", "me"}
 
-    def authenticate(self, username: str, password: str, *, session: Optional[Session] = None) -> Tuple[UserInfo, RoleInfo]:
+    def authenticate(
+        self, username: str, password: str, *, session: Optional[Session] = None
+    ) -> Tuple[UserInfo, RoleInfo]:
         """
         Authenticates a given username and password, returning info about the user and their role
 
@@ -166,7 +168,6 @@ def assert_authorized(
             raise AuthorizationFailure(msg)
 
     def allowed_actions(self, subject: Any, resources: Any, actions: Any, policies: Any) -> List[Tuple[str, str]]:
-
         allowed: List[Tuple[str, str]] = []
 
         # if no auth required, always allowed, except for protected endpoints

diff --git a/qcfractal/qcfractal/components/auth/user_socket.py b/qcfractal/qcfractal/components/auth/user_socket.py
@@ -415,7 +415,6 @@ def get_owner_ids(
     def assert_group_member(
         self, user_id: Optional[int], group_id: Optional[int], *, session: Optional[Session] = None
     ):
-
         # No user and group - ok
         if user_id is None and group_id is None:
             return

diff --git a/qcfractal/qcfractal/components/create_view.py b/qcfractal/qcfractal/components/create_view.py
@@ -43,7 +43,6 @@ def _serialize_orm(orm, exclude=None):
 
 
 def create_dataset_view(dataset_id: int, socket: SQLAlchemySocket, view_file_path: str):
-
     if os.path.exists(view_file_path):
         raise RuntimeError(f"File {view_file_path} exists - will not overwrite")
 

diff --git a/qcfractal/qcfractal/components/dataset_routes.py b/qcfractal/qcfractal/components/dataset_routes.py
@@ -32,7 +32,6 @@ def list_dataset_v1():
 @api_v1.route("/datasets/<int:dataset_id>", methods=["GET"])
 @wrap_route("READ")
 def get_general_dataset_v1(dataset_id: int, url_params: ProjURLParameters):
-
     with storage_socket.session_scope(True) as session:
         ds_type = storage_socket.datasets.lookup_type(dataset_id, session=session)
         ds_socket = storage_socket.datasets.get_socket(ds_type)
@@ -73,13 +72,13 @@ def delete_dataset_v1(dataset_id: int, url_params: DatasetDeleteParams):
 # are different
 #################################################################
 
+
 ########################
 # Adding a dataset
 ########################
 @api_v1.route("/datasets/<string:dataset_type>", methods=["POST"])
 @wrap_route("WRITE")
 def add_dataset_v1(dataset_type: str, body_data: DatasetAddBody):
-
     ds_socket = storage_socket.datasets.get_socket(dataset_type)
     return ds_socket.add(
         name=body_data.name,

diff --git a/qcfractal/qcfractal/components/dataset_socket.py b/qcfractal/qcfractal/components/dataset_socket.py
@@ -400,7 +400,6 @@ def add(
         )
 
         with self.root_socket.optional_session(session) as session:
-
             user_id, group_id = self.root_socket.users.get_owner_ids(owner_user, owner_group)
             self.root_socket.users.assert_group_member(user_id, group_id, session=session)
 
@@ -452,7 +451,6 @@ def update_metadata(
                 raise MissingDataError(f"Could not find dataset with type={self.dataset_type} and id={dataset_id}")
 
             if ds.name != new_metadata.name:
-
                 # If only change in case, no need to check if it already exists
                 if ds.name.lower() != new_metadata.name.lower():
                     stmt2 = select(self.dataset_orm.id)
@@ -1285,7 +1283,6 @@ def modify_records(
         """
 
         with self.root_socket.optional_session(session) as session:
-
             record_ids = self._lookup_record_ids(
                 session,
                 dataset_id,

diff --git a/qcfractal/qcfractal/components/gridoptimization/dataset_socket.py b/qcfractal/qcfractal/components/gridoptimization/dataset_socket.py
@@ -23,7 +23,6 @@
 
 
 class GridoptimizationDatasetSocket(BaseDatasetSocket):
-
     # Used by the base class
     dataset_orm = GridoptimizationDatasetORM
     specification_orm = GridoptimizationDatasetSpecificationORM
@@ -47,7 +46,6 @@ def _add_specification(
     def _create_entries(
         self, session: Session, dataset_id: int, new_entries: Sequence[GridoptimizationDatasetNewEntry]
     ):
-
         all_entries = []
         for entry in new_entries:
             meta, mol_ids = self.root_socket.molecules.add_mixed([entry.initial_molecule], session=session)