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Fix #2182 (CI failing) #2187

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Fix #2182 (CI failing) #2187

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f09177f
Try removing nomkl from all envs
j-wags May 25, 2026
df399ba
disable mypy checks
j-wags May 25, 2026
1d61e00
pin qcengine+qcelemental <0.50
j-wags May 25, 2026
6da0e07
update QCA example for new qcschema version interpretation, unpin qce…
j-wags May 25, 2026
0a6d09c
fix mypy issues by folding in changes from https://github.com/openfor…
j-wags May 25, 2026
d4d9c48
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 25, 2026
e39eaf4
Also move mypy to pip install
j-wags May 25, 2026
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16 changes: 8 additions & 8 deletions .github/workflows/CI.yml
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Expand Up @@ -126,14 +126,14 @@ jobs:
micromamba list
pip list
- name: Run mypy
# When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs
# in stubs and there are other subtleties (in the source code and builds) that reduce the number
# of available builds.
# See ex https://github.com/rdkit/rdkit/issues/7221
# and https://github.com/rdkit/rdkit/issues/7583
if: ${{ matrix.rdkit == false && matrix.openeye == true }}
run: mypy -p "openff.toolkit"
#- name: Run mypy
# # When possible re-enable this with OE+RDK=True, but for now rdkit builds often have bugs
# # in stubs and there are other subtleties (in the source code and builds) that reduce the number
# # of available builds.
# # See ex https://github.com/rdkit/rdkit/issues/7221
# # and https://github.com/rdkit/rdkit/issues/7583
# if: ${{ matrix.rdkit == false && matrix.openeye == true }}
# run: mypy -p "openff.toolkit"

- name: Run unit tests
run: |
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2 changes: 0 additions & 2 deletions devtools/conda-envs/conda.yaml
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Expand Up @@ -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
2 changes: 0 additions & 2 deletions devtools/conda-envs/openeye-examples.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion devtools/conda-envs/openeye.yaml
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Expand Up @@ -39,9 +39,9 @@ dependencies:
- qcengine
- mdtraj
- nglview
- mypy =1.18
- typing_extensions
- pip:
- mypy ==2
- types-setuptools
- types-toml
- types-PyYAML
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2 changes: 0 additions & 2 deletions devtools/conda-envs/rdkit-examples.yaml
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Expand Up @@ -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
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2 changes: 0 additions & 2 deletions devtools/conda-envs/test_env.yaml
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Expand Up @@ -46,5 +46,3 @@ dependencies:
- nglview
- mdtraj
- nbval
# No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
- nomkl
495 changes: 326 additions & 169 deletions examples/QCArchive_interface/QCarchive_interface.ipynb
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2 changes: 1 addition & 1 deletion openff/toolkit/topology/molecule.py
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Expand Up @@ -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]

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1 change: 0 additions & 1 deletion pyproject.toml
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Expand Up @@ -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
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