Merge branch 'main' into tdrive_task

# Conflicts:
#	openff/qcsubmit/common_structures.py

.git-blame-ignore-revs

@@ -1,2 +1,3 @@
 # Black 23
 94875c5bb13a5734b720f99b181e0d6b8639ba39
+9c9f44942e6d6164e4a014491134937b36299d1e

.github/workflows/CI.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - 3.8
+          - "3.9"
         cfg:
           - os: ubuntu-latest
             conda-env: basic
@@ -60,7 +60,7 @@ jobs:
 
       - name: Install Package
         run: |
-          python setup.py develop --no-deps
+          python -m pip install .
 
       - name: Conda Environment Information
         run: |

.gitignore

@@ -103,4 +103,7 @@ ENV/
 .mypy_cache/
 
 # PyCharm
-.idea
+.idea
+
+# macOS
+.DS_Store

devtools/conda-envs/psi4.yaml

@@ -1,10 +1,9 @@
 name: qcsubmit-test-psi4
 
 channels:
-  - psi4
   - conda-forge
+  - conda-forge/label/libint_dev  # needed for psi4/libint2
   - openeye
-  - defaults
 
 dependencies:
 
@@ -25,26 +24,18 @@ dependencies:
 
   - openeye-toolkits
 
-  # Psi4 dependencies
-  - psi4 =1.5
-  - libint2=*=hc9558a2_9
-  - intel-openmp!=2019.5
-  - gau2grid >=2.0
+  - psi4 =1.8
 
   ### Core dependencies.
 
   - openff-toolkit-base >= 0.11.3
-  # argcomplete (brought in via BSE) pulls down totally incorrect builds of `importlib_metadata`,
-  - importlib_metadata >=4
-  - importlib-metadata >=4
   - rdkit
-  - pydantic
+  - pydantic =1
   - pyyaml
   - qcportal>=0.15.7
   - torsiondrive
   - basis_set_exchange
   - typing-extensions
-  - cachetools
   - h5py>=3.6.0
 
   # Optional

openff/qcsubmit/common_structures.py

@@ -6,7 +6,19 @@
 import re
 from datetime import date, datetime
 from enum import Enum
-from typing import TYPE_CHECKING, Any, ClassVar, Dict, List, Optional, Set, Tuple, Union
+from typing import (
+    TYPE_CHECKING,
+    AbstractSet,
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Mapping,
+    Optional,
+    Set,
+    Tuple,
+    Union,
+)
 
 import numpy as np
 import qcportal as ptl
@@ -35,6 +47,14 @@
 )
 from openff.qcsubmit.utils.smirnoff import split_openff_molecule
 
+if TYPE_CHECKING:
+    DictStrAny = Dict[str, Any]
+    IntStr = Union[int, str]
+    AbstractSetIntStr = AbstractSet[IntStr]
+    DictIntStrAny = Dict[IntStr, Any]
+    MappingIntStrAny = Mapping[IntStr, Any]
+
+
 if TYPE_CHECKING:
     from pydantic import AbstractSetIntStr
 
@@ -766,14 +786,14 @@ class Metadata(DatasetConfig):
         None,
         description="The name that will be given to the collection once it is put into QCArchive, this is updated when attached to a dataset.",
     )
-    short_description: Optional[constr(min_length=8, regex="[a-zA-Z]")] = Field(
+    short_description: Optional[constr(min_length=8, regex="[a-zA-Z]")] = Field(  # noqa
         None, description="A short informative description of the dataset."
     )
     long_description_url: Optional[HttpUrl] = Field(
         None,
         description="The url which links to more information about the submission normally a github repo with scripts showing how the dataset was created.",
     )
-    long_description: Optional[constr(min_length=8, regex="[a-zA-Z]")] = Field(
+    long_description: Optional[constr(min_length=8, regex="[a-zA-Z]")] = Field(  # noqa
         None,
         description="A long description of the purpose of the dataset and the molecules within.",
     )

openff/qcsubmit/datasets/datasets.py

@@ -74,15 +74,15 @@ class _BaseDataset(abc.ABC, CommonBase):
         ...,
         description="The name of the dataset, this will be the name given to the collection in QCArchive.",
     )
-    dataset_tagline: constr(min_length=8, regex="[a-zA-Z]") = Field(
+    dataset_tagline: constr(min_length=8, regex="[a-zA-Z]") = Field(  # noqa
         ...,
         description="The tagline should be a short description of the dataset which will be displayed by the QCArchive client when the collections are listed.",
     )
     type: Literal["_BaseDataset"] = Field(
         "_BaseDataset",
         description="The dataset type corresponds to the type of collection that will be made in QCArchive.",
     )
-    description: constr(min_length=8, regex="[a-zA-Z]") = Field(
+    description: constr(min_length=8, regex="[a-zA-Z]") = Field(  # noqa
         ...,
         description="A long description of the datasets purpose and details about the molecules within.",
     )

openff/qcsubmit/tests/test_submissions.py

@@ -783,8 +783,8 @@ def test_optimization_submissions(fractal_compute_server, specification):
             # if we used psi4 make sure the properties were captured
             if program == "psi4":
                 result = record.get_trajectory()[0]
-                assert "CURRENT DIPOLE X" in result.extras["qcvars"].keys()
-                assert "SCF QUADRUPOLE XX" in result.extras["qcvars"].keys()
+                assert "SCF DIPOLE" in result.extras["qcvars"].keys()
+                assert "SCF QUADRUPOLE" in result.extras["qcvars"].keys()
 
 
 def test_optimization_submissions_with_pcm(fractal_compute_server):

openff/qcsubmit/tests/utils/test_smirnoff.py

@@ -1,6 +1,5 @@
 import networkx as nx
 import numpy
-import pytest
 
 from openff.qcsubmit.utils.smirnoff import (
     combine_openff_molecules,

setup.cfg

@@ -20,6 +20,9 @@ exclude_lines =
 max-line-length = 88
 ignore = E203, E266, E501, W503
 select = B,C,E,F,W,T4,B9
+per-file-ignores =
+    openff/qcsubmit/datasets/dataset_utils.py:W605
+    openff/qcsubmit/datasets/datasets.py:W605
 
 [isort]
 multi_line_output=3