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make mypy happy #194

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merged 2 commits into from
Oct 17, 2024
Merged

make mypy happy #194

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37d41a0
make mypy happy
keiyamamo Oct 15, 2024
319f126
add --break-system-packages when installing pip
keiyamamo Oct 15, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/build_docs.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ jobs:

- name: Upgrade pip and setuptools
run: |
python3 -m pip install pip setuptools --upgrade
python3 -m pip install --break-system-packages pip setuptools --upgrade

# See: https://github.com/marketplace/actions/setup-miniconda
- name: Setup Mambaforge
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5 changes: 5 additions & 0 deletions src/vasp/automatedPostprocessing/postprocessing_h5py/create_hi_pass_viz.py
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Expand Up @@ -180,6 +180,7 @@ def create_hi_pass_viz(formatted_data_folder: Path, output_folder: Path, mesh_pa
topo_array[...] = topo_array_fsi

if quantity in {"d", "v", "p"} and amplitude:
assert vector_data_amplitude is not None
geo_array = vector_data_amplitude.create_dataset("Mesh/0/mesh/geometry", (n_nodes_fsi, 3))
geo_array[...] = coord_array_fsi
topo_array = vector_data_amplitude.create_dataset("Mesh/0/mesh/topology", (n_elements_fsi, 4), dtype="i")
Expand Down Expand Up @@ -235,6 +236,7 @@ def create_hi_pass_viz(formatted_data_folder: Path, output_folder: Path, mesh_pa
att_type = "Scalar"

if amplitude:
assert vector_data_amplitude is not None
v_array_amplitude = vector_data_amplitude.create_dataset(array_name, (n_nodes_fsi, 1))
v_array_amplitude[:, 0] = components_data_amplitude[0][:, idx]
rms_magnitude[:, idx] = components_data_amplitude[0][:, idx]
Expand Down Expand Up @@ -263,6 +265,7 @@ def create_hi_pass_viz(formatted_data_folder: Path, output_folder: Path, mesh_pa
att_type = "Tensor"

if amplitude:
assert vector_data_amplitude is not None
array_name = f"{viz_type_amplitude}/{viz_type_amplitude}_{idx}"
if idx == 0:
assert dof_info is not None
Expand Down Expand Up @@ -310,6 +313,7 @@ def create_hi_pass_viz(formatted_data_folder: Path, output_folder: Path, mesh_pa

array_name = f"{viz_type_magnitude}/{viz_type_magnitude}_{idx}"
assert dof_info_amplitude is not None
assert vector_data_mps is not None
if idx == 0:
for name, data in dof_info_amplitude.items():
dof_array = vector_data_mps.create_dataset(f"{array_name}/{name}", data=data)
Expand All @@ -326,6 +330,7 @@ def create_hi_pass_viz(formatted_data_folder: Path, output_folder: Path, mesh_pa
att_type = "Vector"

if amplitude:
assert vector_data_amplitude is not None
v_array_amplitude = vector_data_amplitude.create_dataset(array_name, (n_nodes_fsi, 3))
v_array_amplitude[:, 0] = components_data_amplitude[1][:, idx]
v_array_amplitude[:, 1] = components_data_amplitude[2][:, idx]
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1 change: 1 addition & 0 deletions src/vasp/automatedPostprocessing/postprocessing_h5py/spectrograms.py
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Expand Up @@ -460,6 +460,7 @@ def get_spectrogram(dfNearest: pd.DataFrame, fsamp: float, nWindow: int, overlap
bins = np.linspace(start_t, end_t, 100)
Pxx_mean = interp_spline(freqs, bins)

assert Pxx_mean is not None, "Pxx_mean is None"
Pxx_mean[Pxx_mean < 0] = 1e-16

return Pxx_mean, freqs, bins
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