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rollback and update pre-commit config (#55)
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* Revert "ensure plotly customdata is JSON serializeable (#53)"

This reverts commit 7860e31.

* update pre-commit
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@PythonFZ
PythonFZ authored Feb 14, 2025
1 parent 7860e31 commit 834b6f3
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Showing 8 changed files with 23 additions and 55 deletions.
2 changes: 1 addition & 1 deletion mlipx/nodes/adsorption.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,7 @@ def compare(cls, *nodes: "RelaxAdsorptionConfigs") -> ComparisonResults:
name=node.name.replace(f"_{cls.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
),
mode="lines+markers",
)
)
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12 changes: 3 additions & 9 deletions mlipx/nodes/diatomics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -126,9 +126,7 @@ def figures(self) -> dict:
offset += self.n_points

fig.update_traces(
customdata=np.stack(
[np.arange(self.n_points) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(self.n_points) + offset], axis=1),
)
plots[f"{element}-{element} bond"] = fig
return plots
Expand Down Expand Up @@ -175,9 +173,7 @@ def compare(cls, *nodes: "HomonuclearDiatomics") -> ComparisonResults:
break
offset += node.n_points
fig.update_traces(
customdata=np.stack(
[np.arange(node.n_points) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(node.n_points) + offset], axis=1),
)
fig.update_layout(
plot_bgcolor="rgba(0, 0, 0, 0)",
Expand Down Expand Up @@ -231,9 +227,7 @@ def compare(cls, *nodes: "HomonuclearDiatomics") -> ComparisonResults:
break
offset += node.n_points
fig.update_traces(
customdata=np.stack(
[np.arange(node.n_points) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(node.n_points) + offset], axis=1),
)
fig.update_layout(
plot_bgcolor="rgba(0, 0, 0, 0)",
Expand Down
14 changes: 4 additions & 10 deletions mlipx/nodes/energy_volume.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,17 +81,13 @@ def figures(self) -> dict[str, go.Figure]:
"""Plot the energy-volume curve."""
fig = px.scatter(self.results, x="scale", y="energy", color="scale")
fig.update_layout(title="Energy-Volume Curve")
fig.update_traces(
customdata=np.stack([np.arange(self.n_points)], axis=1).tolist()
)
fig.update_traces(customdata=np.stack([np.arange(self.n_points)], axis=1))
fig.update_xaxes(title_text="cell vector scale")
fig.update_yaxes(title_text="Energy / eV")

ffig = px.scatter(self.results, x="scale", y="fmax", color="scale")
ffig.update_layout(title="Energy-Volume Curve (fmax)")
ffig.update_traces(
customdata=np.stack([np.arange(self.n_points)], axis=1).tolist()
)
ffig.update_traces(customdata=np.stack([np.arange(self.n_points)], axis=1))
ffig.update_xaxes(title_text="cell vector scale")
ffig.update_yaxes(title_text="Maximum Force / eV/Å")

Expand All @@ -110,9 +106,7 @@ def compare(*nodes: "EnergyVolumeCurve") -> ComparisonResults:
name=node.name.replace("_EnergyVolumeCurve", ""),
)
)
fig.update_traces(
customdata=np.stack([np.arange(node.n_points)], axis=1).tolist()
)
fig.update_traces(customdata=np.stack([np.arange(node.n_points)], axis=1))

# TODO: remove all info from the frames?
# What about forces / energies? Update the key?
Expand All @@ -137,7 +131,7 @@ def compare(*nodes: "EnergyVolumeCurve") -> ComparisonResults:
)
)
fig_adjust.update_traces(
customdata=np.stack([np.arange(node.n_points)], axis=1).tolist()
customdata=np.stack([np.arange(node.n_points)], axis=1)
)

fig_adjust.update_layout(title="Adjusted Energy-Volume Curve Comparison")
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6 changes: 2 additions & 4 deletions mlipx/nodes/evaluate_calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,7 @@ def get_figure(key: str, nodes: list["EvaluateCalculatorResults"]) -> go.Figure:
name=node.name.replace(f"_{node.__class__.__name__}", ""),
)
)
fig.update_traces(
customdata=np.stack([np.arange(len(node.plots.index))], axis=1).tolist()
)
fig.update_traces(customdata=np.stack([np.arange(len(node.plots.index))], axis=1))
fig.update_layout(
title=key,
plot_bgcolor="rgba(0, 0, 0, 0)",
Expand Down Expand Up @@ -117,7 +115,7 @@ def figures(self) -> dict:
title=key,
)
fig.update_traces(
customdata=np.stack([np.arange(len(self.plots))], axis=1).tolist(),
customdata=np.stack([np.arange(len(self.plots))], axis=1),
)
plots[key] = fig
return plots
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10 changes: 3 additions & 7 deletions mlipx/nodes/molecular_dynamics.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def figures(self) -> dict[str, go.Figure]:
title=key,
)
fig.update_traces(
customdata=np.stack([np.arange(len(self.plots))], axis=1).tolist(),
customdata=np.stack([np.arange(len(self.plots))], axis=1),
)
plots[key] = fig
return plots
Expand All @@ -150,9 +150,7 @@ def compare(*nodes: "MolecularDynamics") -> ComparisonResults:
y=energies,
mode="lines+markers",
name=node.name.replace(f"_{node.__class__.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
offset += len(energies)
Expand Down Expand Up @@ -193,9 +191,7 @@ def compare(*nodes: "MolecularDynamics") -> ComparisonResults:
y=energies,
mode="lines+markers",
name=node.name.replace(f"_{node.__class__.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
offset += len(energies)
Expand Down
16 changes: 4 additions & 12 deletions mlipx/nodes/nebs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -162,9 +162,7 @@ def frames(self) -> list[ase.Atoms]:
def figures(self) -> dict[str, go.Figure]:
fig = px.scatter(self.results, x="data_id", y="potential_energy")
fig.update_layout(title="NEB_path")
fig.update_traces(
customdata=np.stack([np.arange(len(self.results))], axis=1).tolist()
)
fig.update_traces(customdata=np.stack([np.arange(len(self.results))], axis=1))
return {"NEB_path": fig}

@property
Expand All @@ -185,9 +183,7 @@ def traj_plots(self) -> dict[str, go.Figure]:
y=energies,
mode="lines+markers",
name=f"{iteration}",
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
figure.update_layout(
Expand All @@ -210,9 +206,7 @@ def compare(*nodes: "NEBs") -> ComparisonResults:
y=energies,
mode="lines+markers",
name=node.name.replace(f"_{node.__class__.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
offset += len(energies)
Expand Down Expand Up @@ -250,9 +244,7 @@ def compare(*nodes: "NEBs") -> ComparisonResults:
y=energies,
mode="lines+markers",
name=node.name.replace(f"_{node.__class__.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
offset += len(energies)
Expand Down
12 changes: 4 additions & 8 deletions mlipx/nodes/structure_optimization.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ def figures(self) -> dict[str, go.Figure]:
x=list(range(len(energies))),
y=energies,
mode="lines+markers",
customdata=np.stack([np.arange(len(energies))], axis=1).tolist(),
customdata=np.stack([np.arange(len(energies))], axis=1),
)
)

Expand All @@ -102,7 +102,7 @@ def figures(self) -> dict[str, go.Figure]:
x=self.plots.index,
y=self.plots["fmax"],
mode="lines+markers",
customdata=np.stack([np.arange(len(energies))], axis=1).tolist(),
customdata=np.stack([np.arange(len(energies))], axis=1),
)
)

Expand All @@ -126,9 +126,7 @@ def compare(*nodes: "StructureOptimization") -> ComparisonResults:
y=energies,
mode="lines+markers",
name=node.name.replace(f"_{node.__class__.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
offset += len(energies)
Expand Down Expand Up @@ -166,9 +164,7 @@ def compare(*nodes: "StructureOptimization") -> ComparisonResults:
y=energies,
mode="lines+markers",
name=node.name.replace(f"_{node.__class__.__name__}", ""),
customdata=np.stack(
[np.arange(len(energies)) + offset], axis=1
).tolist(),
customdata=np.stack([np.arange(len(energies)) + offset], axis=1),
)
)
offset += len(energies)
Expand Down
6 changes: 2 additions & 4 deletions mlipx/nodes/vibrational_analysis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -286,9 +286,7 @@ def figures(self) -> dict[str, go.Figure]:
xaxis_title="Frame",
yaxis_title="ddG (eV)",
)
fig.update_traces(
customdata=np.stack([np.arange(len(self.results))], axis=-1).tolist()
)
fig.update_traces(customdata=np.stack([np.arange(len(self.results))], axis=-1))
return {"Gibbs": fig}

@staticmethod
Expand All @@ -305,7 +303,7 @@ def compare(*nodes: "VibrationalAnalysis") -> ComparisonResults:
name=node.name,
customdata=np.stack(
[np.arange(len(node.results["ddG"])) + offset], axis=1
).tolist(),
),
)
)
offset += len(node.results["ddG"])
Expand Down

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