Csse pyd2 internal classes

.github/workflows/CI.yml

@@ -163,14 +163,17 @@ jobs:
       run: |
         sed -i s/from\ pydantic\ /from\ pydantic.v1\ /g ${CONDA_PREFIX}/lib/python${{ matrix.cfg.python-version }}/site-packages/psi4/driver/*py
 
+    - name: Install QCEngine
+      run: |
+        python -m pip install . --no-deps
+
     - name: Environment Information
       run: |
         conda info
         conda list
-
-    - name: Install QCEngine
-      run: |
-        python -m pip install . --no-deps
+        python -c "import qcelemental as q;print(q.__file__, q.__version__)"
+        python -c "import qcengine as q;print(q.__file__, q.__version__)"
+        git describe
 
     - name: QCEngineRecords
       if: "(matrix.cfg.label != 'Psi4-1.6')"
@@ -197,7 +200,7 @@ jobs:
       matrix:
         cfg:
           - conda-env: docs-cf
-            python-version: 3.8
+            python-version: "3.10"
             label: Sphinx
             runs-on: ubuntu-latest
 

devtools/conda-envs/adcc.yaml

@@ -13,6 +13,7 @@ dependencies:
   - psutil
   - qcelemental >=0.24.0
   - pydantic=2
+  - pydantic-settings
   - msgpack-python
 
     # Testing

devtools/conda-envs/aimnet2.yaml

@@ -11,6 +11,7 @@ dependencies:
   - psutil
   - qcelemental >=0.12.0
   - pydantic>=2.0.0
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/base.yaml

@@ -9,6 +9,7 @@ dependencies:
   - psutil
   - qcelemental >=0.12.0
   - pydantic>=2.0.0
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/docs-cf.yaml

@@ -5,7 +5,8 @@ channels:
 dependencies:
   - python
   - networkx
-  - pydantic=1
+  - pydantic=2
+  - pydantic-settings
   - numpy
   - pint
 
@@ -18,7 +19,7 @@ dependencies:
   - sphinx-autodoc-typehints
   - sphinx-automodapi
   - sphinx_rtd_theme
-  - autodoc-pydantic
+  - autodoc-pydantic=2
 
     # testing
   - pytest>=4.0.0

devtools/conda-envs/mace.yaml

@@ -9,6 +9,7 @@ dependencies:
   - psutil
   - qcelemental >=0.12.0
   - pydantic>=2.0.0
+  - pydantic-settings
 
   # mace deps
   - pymace

devtools/conda-envs/mrchem.yaml

@@ -14,6 +14,7 @@ dependencies:
   - psutil
   - qcelemental>=0.24
   - pydantic=2
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/nwchem-cf.yaml

@@ -12,6 +12,7 @@ dependencies:
   - qcelemental >=0.24.0
   - pydantic>=2.0.0
   - networkx>=2.4.0
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/nwchem.yaml

@@ -10,6 +10,7 @@ dependencies:
   - qcelemental >=0.24.0
   - pydantic>=2.0.0
   - networkx>=2.4.0
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/openmm.yaml

@@ -17,6 +17,7 @@ dependencies:
   - psutil
   - qcelemental >=0.11.1
   - pydantic >=2
+  - pydantic-settings
   - pint <0.22
 
     # Testing

devtools/conda-envs/opt-disp-cf.yaml

@@ -22,6 +22,7 @@ dependencies:
   - psutil
   - qcelemental >=0.26.0
   - pydantic=2
+  - pydantic-settings
   - msgpack-python
 
     # Testing

devtools/conda-envs/opt-disp.yaml

@@ -9,6 +9,7 @@ dependencies:
   #- intel-openmp!=2019.5
   - rdkit
   - mopac
+  - pydantic-settings
 
     # Mixed Tests
   - dftd3 3.2.1

devtools/conda-envs/psi-cf.yaml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   - psi4=1.8
   - numpy<2
+  - pydantic-settings
 
     # Core
   - python

devtools/conda-envs/psi-nightly.yaml

@@ -13,6 +13,7 @@ dependencies:
   - psutil
   - qcelemental >=0.26.0
   - pydantic>=2.0.0
+  - pydantic-settings
   - msgpack-python
   - numpy=1
 

devtools/conda-envs/rdkit.yaml

@@ -12,6 +12,7 @@ dependencies:
   - psutil
   - qcelemental >=0.12.0
   - pydantic>=2
+  - pydantic-settings
 
     # Testing
   - pytest

devtools/conda-envs/torchani.yaml

@@ -12,6 +12,7 @@ dependencies:
   - psutil
   - qcelemental >=0.12.0
   - pydantic>=2
+  - pydantic-settings
 
   - pytorch
 

devtools/conda-envs/xtb.yaml

@@ -12,6 +12,7 @@ dependencies:
   - psutil
   - qcelemental >=0.11.1
   - pydantic >=2
+  - pydantic-settings
 
     # Extras
   - gcp-correction

docs/source/changelog.rst

@@ -28,6 +28,41 @@ Changelog
 .. - UNSOLVED (:issue:`397`) extras failed
 
 
+vX.Y.0 / 2024-MM-DD (Unreleased)
+--------------------
+
+Breaking Changes
+++++++++++++++++
+- (:pr:`453`) Deps - Require pydantic v2 dependency (don't worry, this isn't
+  changing QCEngine's role as QCSchema I/O runner. Also require pydantic-settings
+  for CLI. @loriab
+
+New Features
+++++++++++++
+
+Enhancements
+++++++++++++
+- (:pr:`453`) Maint - Convert internal (non-QCSchema) pydantic classes to
+  pydantic v2 API, namely `NodeDescriptor`, `TaskConfig`, `ProgramHarness`,
+  `ProcedureHarness`. @loriab
+
+Bug Fixes
++++++++++
+- (:pr:`453`) Maint - Fix a warning thrown by `execute` about unclosed files. @loriab
+
+Misc.
++++++
+- (:pr:`452`) Maint - Set up pre-commit and run over repository. @loriab
+- (:pr:`453`) CI - Dropped Entos/QCore and Psi4 v1.5 as too hard to solve with
+  pydantic v2 and modern python versions. @loriab
+
+MUST (Unmerged)
++++++++++++++++
+
+WIP (Unmerged)
+++++++++++++++
+
+
 v0.30.0 / 2024-06-25
 --------------------
 

docs/source/single_compute.rst

@@ -74,13 +74,19 @@ The results contain a complete record of the computation:
 Input Fields
 -------------
 
-.. autopydantic_model:: qcelemental.models.AtomicInput
+Note this is QCSchema v2 ``AtomicInput``. See the QCElemental docs for the
+longstanding v1 model.
+
+.. autopydantic_model:: qcelemental.models.v2.AtomicInput
    :noindex:
 
 Returned Fields
 ---------------
 
-.. autopydantic_model:: qcelemental.models.AtomicResult
+Note this is QCSchema v2 ``AtomicResult``. See the QCElemental docs for the
+longstanding v1 model.
+
+.. autopydantic_model:: qcelemental.models.v2.AtomicResult
    :noindex:
 
 FAQ

qcengine/compute.py

@@ -13,10 +13,7 @@
 from .util import compute_wrapper, environ_context, handle_output_metadata, model_wrapper
 
 if TYPE_CHECKING:
-    try:
-        from pydantic.v1.main import BaseModel
-    except ImportError:
-        from pydantic.main import BaseModel
+    from pydantic.main import BaseModel
     from qcelemental.models import AtomicResult
 
 

qcengine/config.py

@@ -9,10 +9,8 @@
 import socket
 from typing import Any, Dict, Optional, Union
 
-try:
-    import pydantic.v1 as pydantic
-except ImportError:
-    import pydantic
+from pydantic import BaseModel, ConfigDict, Field
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from .extras import get_information
 
@@ -69,7 +67,7 @@ def get_global(key: Optional[str] = None) -> Union[str, Dict[str, Any]]:
         return _global_values[key]
 
 
-class NodeDescriptor(pydantic.BaseModel):
+class NodeDescriptor(BaseModel):
     """
     Description of an individual node
     """
@@ -83,7 +81,7 @@ class NodeDescriptor(pydantic.BaseModel):
     memory_safety_factor: int = 10  # Percentage of memory as a safety factor
 
     # Specifications
-    ncores: Optional[int] = pydantic.Field(
+    ncores: Optional[int] = Field(
         None,
         description="""Number of cores accessible to each task on this node
 
@@ -93,9 +91,9 @@ class NodeDescriptor(pydantic.BaseModel):
     retries: int = 0
 
     # Cluster options
-    is_batch_node: bool = pydantic.Field(
+    is_batch_node: bool = Field(
         False,
-        help="""Whether the node running QCEngine is a batch node
+        description="""Whether the node running QCEngine is a batch node
 
     Some clusters are configured such that tasks are launched from a special "batch" or "MOM" onto the compute nodes.
     The compute nodes on such clusters often have a different CPU architecture than the batch nodes and 
@@ -108,7 +106,7 @@ class NodeDescriptor(pydantic.BaseModel):
     ``mpiexec_command`` must always be used even for serial jobs (e.g., getting the version number)
     """,
     )
-    mpiexec_command: Optional[str] = pydantic.Field(
+    mpiexec_command: Optional[str] = Field(
         None,
         description="""Invocation for launching node-parallel tasks with MPI
 
@@ -145,31 +143,27 @@ def __init__(self, **data: Dict[str, Any]):
             if "{ranks_per_node}" not in self.mpiexec_command:
                 raise ValueError("mpiexec_command must explicitly state the number of ranks per node")
 
-    class Config:
-        extra = "forbid"
+    model_config = ConfigDict(extra="forbid")
 
 
-class TaskConfig(pydantic.BaseSettings):
+class TaskConfig(BaseSettings):
     """Description of the configuration used to launch a task."""
 
     # Specifications
-    ncores: int = pydantic.Field(None, description="Number cores per task on each node")
-    nnodes: int = pydantic.Field(None, description="Number of nodes per task")
-    memory: float = pydantic.Field(
-        None, description="Amount of memory in GiB (2^30 bytes; not GB = 10^9 bytes) per node."
-    )
+    ncores: int = Field(None, description="Number cores per task on each node")
+    nnodes: int = Field(None, description="Number of nodes per task")
+    memory: float = Field(None, description="Amount of memory in GiB (2^30 bytes; not GB = 10^9 bytes) per node.")
     scratch_directory: Optional[str]  # What location to use as scratch
     retries: int  # Number of retries on random failures
     mpiexec_command: Optional[str]  # Command used to launch MPI tasks, see NodeDescriptor
     use_mpiexec: bool = False  # Whether it is necessary to use MPI to run an executable
-    cores_per_rank: int = pydantic.Field(1, description="Number of cores per MPI rank")
-    scratch_messy: bool = pydantic.Field(
-        False, description="Leave scratch directory and contents on disk after completion."
-    )
+    cores_per_rank: int = Field(1, description="Number of cores per MPI rank")
+    scratch_messy: bool = Field(False, description="Leave scratch directory and contents on disk after completion.")
 
-    class Config(pydantic.BaseSettings.Config):
-        extra = "forbid"
-        env_prefix = "QCENGINE_"
+    model_config = SettingsConfigDict(
+        extra="forbid",
+        env_prefix="QCENGINE_",
+    )
 
 
 def _load_defaults() -> None:

qcengine/procedures/berny.py

@@ -2,7 +2,7 @@
 import sys
 import traceback
 from io import StringIO
-from typing import Any, Dict, Union
+from typing import Any, ClassVar, Dict, Union
 
 import numpy as np
 from qcelemental.models import FailedOperation, OptimizationInput, OptimizationResult
@@ -16,7 +16,7 @@
 
 
 class BernyProcedure(ProcedureHarness):
-    _defaults = {"name": "Berny", "procedure": "optimization"}
+    _defaults: ClassVar[Dict[str, Any]] = {"name": "Berny", "procedure": "optimization"}
 
     def found(self, raise_error: bool = False) -> bool:
         return which_import(

qcengine/procedures/geometric.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, Union
+from typing import Any, ClassVar, Dict, Union
 
 from qcelemental.models import OptimizationInput, OptimizationResult
 from qcelemental.util import safe_version, which_import
@@ -8,13 +8,10 @@
 
 class GeometricProcedure(ProcedureHarness):
 
-    _defaults = {"name": "geomeTRIC", "procedure": "optimization"}
+    _defaults: ClassVar[Dict[str, Any]] = {"name": "geomeTRIC", "procedure": "optimization"}
 
     version_cache: Dict[str, str] = {}
 
-    class Config(ProcedureHarness.Config):
-        pass
-
     def found(self, raise_error: bool = False) -> bool:
         return which_import(
             "geometric",