Fix #2182 (CI failing) (#2187)

* Try removing nomkl from all envs

* disable mypy checks

* pin qcengine+qcelemental <0.50

* update QCA example for new qcschema version interpretation, unpin qcengine and qcelemental

* fix mypy issues by folding in changes from #2181

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Also move mypy to pip install

* re enable mypy tests

* update releasehistory

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: j-wags

devtools/conda-envs/conda.yaml

@@ -12,5 +12,3 @@ dependencies:
   - numpy <2.3
   # https://github.com/openforcefield/openff-toolkit/issues/2150
   - xmltodict <=1.0.2
-  # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
-  - nomkl

devtools/conda-envs/openeye-examples.yaml

@@ -19,8 +19,6 @@ dependencies:
   - openff-units
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
-  # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
-  - nomkl
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0
   - typing_extensions

devtools/conda-envs/openeye.yaml

@@ -39,9 +39,9 @@ dependencies:
   - qcengine
   - mdtraj
   - nglview
-  - mypy =1.18
   - typing_extensions
   - pip:
+    - mypy ==2
     - types-setuptools
     - types-toml
     - types-PyYAML

devtools/conda-envs/rdkit-examples.yaml

@@ -18,8 +18,6 @@ dependencies:
   - openff-units
   - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
-  # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
-  - nomkl
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0
   - typing_extensions

devtools/conda-envs/test_env.yaml

@@ -46,5 +46,3 @@ dependencies:
   - nglview
   - mdtraj
   - nbval
-  # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
-  - nomkl

docs/releasehistory.md

@@ -19,6 +19,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 - [PR #2174](https://github.com/openforcefield/openff-toolkit/pull/2174): Drop support for Python 3.11
 
 ### Bugfixes
+- [PR #2187](https://github.com/openforcefield/openff-toolkit/pull/2187): Updated the QCArchive example notebook to be compliant with new validation behavior in QCEngine and QCElemental >=0.50. 
 
 ### New features
 

examples/QCArchive_interface/QCarchive_interface.ipynb

@@ -5654,7 +5654,7 @@ def _networkx_graph_to_hill_formula(graph: "nx.Graph[int]") -> str:
     if not isinstance(graph, nx.Graph):
         raise ValueError("The graph must be a NetworkX graph.")
 
-    atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)]
+    atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)]  # type: ignore[misc]
 
     return _atom_nums_to_hill_formula(atom_nums)  # type:ignore[arg-type]
 

openff/toolkit/topology/molecule.py

@@ -44,7 +44,6 @@ lint.isort.known-third-party = [ "openff.interchange", "openff.utilities", "open
 
 [tool.mypy]
 python_version = 3.12
-plugins = "numpy.typing.mypy_plugin"
 warn_unused_configs = true
 # would be nice to flip back to true
 warn_unused_ignores = false