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Class_format #17

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merged 35 commits into from
Jul 25, 2024
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e5a4da9
Class for MRCC inputs
benshi97 Jun 9, 2024
8dd8cc5
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
3de98c0
Make a class for generating orca inputs
benshi97 Jun 9, 2024
449abe3
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
41dd029
Class for CreateSKZCAMClusters
benshi97 Jun 9, 2024
46367af
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
b0af380
Better variable definitions
benshi97 Jun 9, 2024
a00901e
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
ce0e106
Clean up docstrings
Andrew-S-Rosen Jun 9, 2024
7436ea0
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
115da6f
Fix conftest
Andrew-S-Rosen Jun 9, 2024
96f0365
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
e063664
Fix docs
Andrew-S-Rosen Jun 9, 2024
92708e5
Merge branch 'class_format' of github.com:benshi97/quacc into class_f…
Andrew-S-Rosen Jun 9, 2024
5625900
small cleanup
Andrew-S-Rosen Jun 9, 2024
3bee19c
pre-commit auto-fixes
pre-commit-ci[bot] Jun 9, 2024
0c8e03a
Remove stray comment
Andrew-S-Rosen Jun 9, 2024
db5cd04
Fix docstring
benshi97 Jun 10, 2024
c784ebd
pre-commit auto-fixes
pre-commit-ci[bot] Jun 10, 2024
a94c5ee
Order functions better
benshi97 Jun 10, 2024
0e9eecb
Merge branch 'class_format' of github.com:benshi97/quacc into class_f…
benshi97 Jun 10, 2024
9de94f9
pre-commit auto-fixes
pre-commit-ci[bot] Jun 10, 2024
ec2c53f
Update conftest.py
Andrew-S-Rosen Jun 10, 2024
ac07716
Fix unit tests
benshi97 Jun 11, 2024
d30569b
pre-commit auto-fixes
pre-commit-ci[bot] Jun 11, 2024
a228b25
Add attribute descriptions.
benshi97 Jun 11, 2024
375b5d3
Merge branch 'class_format' of github.com:benshi97/quacc into class_f…
benshi97 Jun 11, 2024
ed3383a
pre-commit auto-fixes
pre-commit-ci[bot] Jun 11, 2024
d285d20
Merge branch 'skzcam' into class_format
Andrew-S-Rosen Jun 20, 2024
2aa9ead
Merge branch 'main' into class_format
Andrew-S-Rosen Jun 29, 2024
14dda7e
Revert "Merge branch 'main' into class_format"
Andrew-S-Rosen Jun 29, 2024
5630cee
Update test_mrcc.py
Andrew-S-Rosen Jun 29, 2024
fdc46af
Merge branch 'skzcam' into class_format
Andrew-S-Rosen Jul 1, 2024
65619fb
Fix hinting
Andrew-S-Rosen Jul 1, 2024
760b52c
pre-commit auto-fixes
pre-commit-ci[bot] Jul 1, 2024
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2,403 changes: 1,161 additions & 1,242 deletions src/quacc/atoms/skzcam.py

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16 changes: 6 additions & 10 deletions tests/core/atoms/conftest.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,22 +9,18 @@
FILE_DIR = Path(__file__).parent


def mock_generate_chemshell_cluster(
slab, slab_center_idx, atom_oxi_states, filepath, **kwargs
):
def mock_run_chemshell(slab, slab_center_idx, atom_oxi_states, filepath, **kwargs):
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with (
gzip.open(
Path(FILE_DIR, "skzcam_files", "REF_ChemShell_cluster.xyz.gz"), "rb"
Path(FILE_DIR, "skzcam_files", "REF_ChemShell_Cluster.xyz.gz"), "rb"
) as f_in,
Path(filepath, "ChemShell_cluster.xyz").open(mode="wb") as f_out,
Path(filepath, "ChemShell_Cluster.xyz").open(mode="wb") as f_out,
):
shutil.copyfileobj(f_in, f_out)


@pytest.fixture(autouse=True)
def patch_generate_chemshell_cluster(monkeypatch):
from quacc.atoms import skzcam
def patch_run_chemshell(monkeypatch):
from quacc.atoms.skzcam import CreateSKZCAMClusters

monkeypatch.setattr(
skzcam, "generate_chemshell_cluster", mock_generate_chemshell_cluster
)
monkeypatch.setattr(CreateSKZCAMClusters, "run_chemshell", mock_run_chemshell)
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