Merge pull request #978 from MolSSI/pydv2

[Pydantic v2] Update server and compute config to use pydantic v2

Author: bennybp

docs/requirements.txt

@@ -1,9 +1,7 @@
-sphinx<8.0
+sphinx
 sphinx_design
 sphinx-copybutton
 pydata_sphinx_theme
-pydantic<2.0a0
-autodoc-pydantic<2.0a0
 myst-nb
 nglview
 -e ../qcportal

docs/source/admin_guide/managers/index.rst

@@ -128,25 +128,15 @@ Configuration for different HPC schedulers
 HPC cluster schedulers vary in behavior, so you will need to adapt your ``qcfractal-manager-config.yml`` to the scheduler of the HPC cluster you intend to use.
 The configuration keys available for each ``type`` of record in the ``executors`` list are referenced here.
 
-----
 
-.. autopydantic_model:: qcfractalcompute.config.SlurmExecutorConfig
-   :model-show-config-summary: false
-   :model-show-field-summary: false
+.. autoclass:: qcfractalcompute.config.SlurmExecutorConfig
 
-----
 
-.. autopydantic_model:: qcfractalcompute.config.TorqueExecutorConfig
-   :model-show-config-summary: false
-   :model-show-field-summary: false
+.. autoclass:: qcfractalcompute.config.TorqueExecutorConfig
 
-----
 
-.. autopydantic_model:: qcfractalcompute.config.LSFExecutorConfig
-   :model-show-config-summary: false
-   :model-show-field-summary: false
+.. autoclass:: qcfractalcompute.config.LSFExecutorConfig
 
-----
 
 .. _compute-manager-local:
 
@@ -178,6 +168,4 @@ Using the ``local`` executor type is also recommended for running a compute mana
 
 ----
 
-.. autopydantic_model:: qcfractalcompute.config.LocalExecutorConfig
-   :model-show-config-summary: false
-   :model-show-field-summary: false
+.. autoclass:: qcfractalcompute.config.LocalExecutorConfig

docs/source/conf.py

@@ -49,7 +49,7 @@
     "sphinx.ext.napoleon",
     "sphinx.ext.extlinks",
     "sphinx_design",
-    "sphinxcontrib.autodoc_pydantic",
+#    "sphinxcontrib.autodoc_pydantic",
     "sphinx_copybutton",
     "myst_nb",
 ]
@@ -65,8 +65,8 @@
     "show-inheritance": True,
     "member-order": "bysource",
 }
-autodoc_pydantic_model_show_json = False
-autodoc_pydantic_settings_show_json = False
+#autodoc_pydantic_model_show_json = False
+#autodoc_pydantic_settings_show_json = False
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = [

qcarchivetesting/conda-envs/fulltest_server.yaml

@@ -13,6 +13,7 @@ dependencies:
   - requests
   - pyyaml
   - pydantic
+  - pydantic-settings
   - zstandard
   - apsw>=3.42
   - qcelemental<0.70a0

qcarchivetesting/conda-envs/fulltest_snowflake.yaml

@@ -13,6 +13,7 @@ dependencies:
   - requests
   - pyyaml
   - pydantic
+  - pydantic-settings
   - zstandard
   - apsw>=3.42
   - qcelemental<0.70a0

qcarchivetesting/conda-envs/fulltest_testing.yaml

@@ -13,6 +13,7 @@ dependencies:
   - requests
   - pyyaml
   - pydantic
+  - pydantic-settings
   - zstandard
   - apsw>=3.42
   - qcelemental<0.70a0

qcarchivetesting/conda-envs/fulltest_worker.yaml

@@ -11,6 +11,7 @@ dependencies:
   - requests
   - pyyaml
   - pydantic
+  - pydantic-settings
   - zstandard
   - apsw>=3.42
   - qcelemental<0.70a0

qcarchivetesting/qcarchivetesting/config_files/gha_fractal_compute.yaml

@@ -17,5 +17,5 @@ executors:
     max_workers: 1
     cores_per_worker: 2
     memory_per_worker: 2
-    queue_tags:
+    compute_tags:
       - '*'

qcarchivetesting/qcarchivetesting/testing_classes.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-from copy import deepcopy
 
 from qcarchivetesting import geoip_path, geoip_filename, ip_tests_enabled
 from qcfractal.config import DatabaseConfig
@@ -78,10 +77,8 @@ def __init__(self, db_path: str):
         assert self.harness.is_alive() and not self.harness.can_connect()
 
     def get_new_harness(self, db_name: str) -> QCATestingPostgresHarness:
-        harness_config = deepcopy(self.harness.config.dict())
-        harness_config["database_name"] = db_name
-
-        new_harness = QCATestingPostgresHarness(DatabaseConfig(**harness_config))
+        db_config = self.harness.config.model_copy(deep=True, update={"database_name": db_name})
+        new_harness = QCATestingPostgresHarness(db_config)
         new_harness.create_database(create_tables=True)
         return new_harness
 
@@ -170,7 +167,7 @@ def __init__(
             extra_config=qcf_config,
         )
 
-        self._original_config = self._qcf_config.copy(deep=True)
+        self._original_config = self._qcf_config.model_copy(deep=True)
 
         if create_users:
             self.create_users()
@@ -192,7 +189,7 @@ def reset(self):
         self._stop_job_runner()
         self._stop_compute()
         self._all_completed = set()
-        self._qcf_config = self._original_config.copy(deep=True)
+        self._qcf_config = self._original_config.model_copy(deep=True)
 
         if self._api_thread is None:
             self.start_api(wait=True)

qcarchivetesting/qcarchivetesting/testing_fixtures.py

@@ -27,7 +27,7 @@ def _generate_default_config(pg_harness, extra_config=None) -> FractalConfig:
     cfg_dict = {}
     cfg_dict["base_folder"] = pg_harness.config.base_folder
     cfg_dict["loglevel"] = "DEBUG"
-    cfg_dict["database"] = pg_harness.config.dict()
+    cfg_dict["database"] = pg_harness.config.model_dump()
     cfg_dict["database"]["pool_size"] = 0
     cfg_dict["log_access"] = True