Add more flexibility to `PhononDOSPlotter` and `PhononBSPlotter` #3700

ab5424 · 2024-03-22T10:44:35Z

Summary

Major changes:

feature 1: Add invert_axes to PhononDOSPlotter (similar to DOSPlotter)
feature 2: Compare to more than one other PhononBSPlotter

Checklist

Google format doc strings added. Check with ruff.
Type annotations included. Check with mypy.
Tests added for new features/fixes.
If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Summary by CodeRabbit

New Features
- Added an invert_axes parameter to various plotting methods for axis inversion, enhancing plot customization.
- Enhanced color handling and customization options for comparing multiple plots.
Refactor
- Renamed a parameter for clarity and adjusted plot dimensions based on new axis inversion feature.
Tests
- Updated plotting tests to reflect changes in plotting methods and configurations, including the use of matplotlib.pyplot.

janosh · 2024-03-22T10:51:03Z

pymatgen/phonon/plotter.py

@@ -590,7 +619,7 @@ def get_ticks(self) -> dict[str, list]:

    def plot_compare(
        self,
-        other_plotter: PhononBSPlotter,
+        other_plotter: PhononBSPlotter | Sequence[PhononBSPlotter],


how about we use dict[str, PhononBSPlotter] here so we can label other band structures? would be great to add a legend mapping colors to dict keys.

see pymatviz for what that might look like

There is also labels a few lines below, doesn't that do the same? I could refactor though.

yeah i think refactoring would make for a better API here. labels was only added 3 months in 9268942 ago so i think even a breaking change would be acceptable

I removed labels. I changed the logic so that no legend is shown if the Plotter is initialised without a label (i.e. if the "original" PhononBS has no label).

it's important to still support passing in single PhononBSPlotters. made some changes to that effect in
26fb878. also i think if there are multiple band structures, we should always show a legend

could you make sure we test both the dict and single PhononBSPlotter case?

I added a test for the single PhononBSPlottter case.

@janosh Is there a best way to add custom colours for the comparison? With PhononDOSPlotter, it is done via add_dos(), but here it is not obvious to me. Is it better to add the colour to the init or passing multiple colours to plot_compare?

definitely plot_compare. usually it's best for arguments to be as close to where they're used as possible

I added a colors variable to plot_compare().

…rd, change other_plotter type to PhononBSPlotter | dict[str, PhononBSPlotter]

…plot_compare

coderabbitai · 2024-03-26T07:40:40Z

Walkthrough

The recent update introduces an invert_axes parameter to various plotter methods within pymatgen's phonon module, enhancing flexibility in data visualization by allowing axis inversion. Additionally, it refines the plotter's functionality with clearer variable naming, dimension adjustments based on axis orientation, and improved color customization for comparative plots. The accompanying tests have been revised to reflect these changes, utilizing matplotlib.pyplot for a more streamlined approach to plotting.

Changes

Files	Changes
`.../phonon/plotter.py`	Added `invert_axes`, renamed `y` to `ys`, adjusted dimensions and logic for axis inversion, enhanced color handling.
`.../phonon/test_plotter.py`	Updated to use `matplotlib.pyplot`, modified plotter methods and configurations, added new instances for testing.

🐰✨🎨
In the realm of plots and lines, a change unfolds,
Axes invert, colors bold, a story told.
With invert_axes we twist and turn,
Through tests and tales, we live and learn.
Here's to the plots, now more versatile,
Crafted by code, with a rabbit's smile.
🌟📊🐇

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janosh

thanks a lot @ab5424, nice work!

coderabbitai

Review Status

Actionable comments generated: 0

Configuration used: CodeRabbit UI

Commits

Files that changed from the base of the PR and between b1e5023 and 4ae33eb.

Files selected for processing (2)

pymatgen/phonon/plotter.py (10 hunks)
tests/phonon/test_plotter.py (4 hunks)

Additional comments: 9

tests/phonon/test_plotter.py (9)

6-6: Consider using a more specific import for matplotlib.pyplot if only a few functions are used, to improve code readability and potentially reduce import overhead.

13-13: Disabling LaTeX rendering in matplotlib globally might affect other tests if they run in the same environment. Consider using a fixture to ensure this setting is only applied to the tests that require it.

20-22: Creating multiple instances of PhononDosPlotter with different configurations in the setUp method is a good practice for testing various scenarios. Ensure that each instance is adequately tested in separate test methods to cover all configurations.

34-34: Using a set comparison to assert the keys in the dictionary is a robust way to ensure that all expected elements are present, regardless of order. Good use of Python's set operations for testing.

41-43: Asserting the type of the returned object and the labels on the axes is a good practice to ensure the plotter's functionality. Consider also adding assertions for the plot data to ensure the correctness of the plotted values.

46-49: Testing the invert_axes feature by asserting the swapped labels is a good approach. Additionally, consider verifying that the axes' limits are correctly inverted to ensure the feature works as expected.

71-74: Asserting the type of the returned object and the labels on the axes for the PhononBSPlotter is consistent with the tests for PhononDosPlotter. This consistency in testing approach is commendable.

89-101: Testing the plot_compare method with different scenarios and asserting the legend labels and colors is thorough. It ensures that the comparison feature works correctly for multiple cases. Consider adding a test to verify the handling of incompatible band structures if not already covered.

111-120: Testing various thermodynamic properties plotting functions in ThermoPlotter and asserting the type of the returned object is a good practice. It would be beneficial to also verify the correctness of the plotted data, possibly by checking specific values at known points.

janosh · 2024-03-26T07:50:44Z

@ab5424 actually, maybe these two CodeRabbit comments are worth addressing. would you be able to add these checks to tests/phonon/test_plotter.py

46-49: Testing the invert_axes feature by asserting the swapped labels is a good approach. Additionally, consider verifying that the axes' limits are correctly inverted to ensure the feature works as expected.

89-101: Testing the plot_compare method with different scenarios and asserting the legend labels and colors is thorough. It ensures that the comparison feature works correctly for multiple cases. Consider adding a test to verify the handling of incompatible band structures if not already covered.

coderabbitai

Review Status

Actionable comments generated: 0

Configuration used: CodeRabbit UI

Commits

Files that changed from the base of the PR and between 4ae33eb and 966eefd.

Files selected for processing (2)

pymatgen/phonon/plotter.py (10 hunks)
tests/phonon/test_plotter.py (4 hunks)

Files skipped from review as they are similar to previous changes (2)

pymatgen/phonon/plotter.py
tests/phonon/test_plotter.py

ab5424 · 2024-03-26T10:46:51Z

@janosh I changed the code according to the suggestions. Interestingly, I found that I was able to get the NaCl/STO comparison though the checking block because the distances lists had the same length (but not the same shape so there was an IndexError on line 691). I changed it so that the shape must be the same.

ab5424 added 5 commits March 20, 2024 18:44

Add invert_axes to PhononDosPlotter

98d1de4

Add tests for invert_axes in PhononDosPlotter

0b87ce2

Add kwargs to PhononDOSPlotter

ab0d5ae

Compare more than two PhononBSPlotters

f3392b3

Add tests to compare more than two PhononBSPlotters

43398c2

ab5424 requested review from shyuep, janosh and mkhorton as code owners March 22, 2024 10:44

Merge branch 'master' into phonon-dos-interted

a3ce5f2

janosh reviewed Mar 22, 2024

View reviewed changes

ab5424 and others added 8 commits March 22, 2024 12:02

Fix docstring

d971df2

Use dicts with labels as keys in plot_compare instead of separate labels

2399ad0

always show legend, default self label to 'self' via self_label keywo…

26fb878

…rd, change other_plotter type to PhononBSPlotter | dict[str, PhononBSPlotter]

Test single Plotter in plot_compare

2788441

Use label from Plotter initialisation if single Plotter is passed to …

e2f19bd

…plot_compare

Fix Test

938c085

Add colors to plot_compare in PhononBSPlotter

c44cb50

refactor code and tests

4ae33eb

janosh added enhancement A new feature or improvement to an existing one data viz PRs and issues about pymatgen plotting functionality phonon Lattice vibrations labels Mar 26, 2024

janosh approved these changes Mar 26, 2024

View reviewed changes

janosh enabled auto-merge (squash) March 26, 2024 07:41

coderabbitai bot reviewed Mar 26, 2024

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janosh disabled auto-merge March 26, 2024 07:49

ab5424 added 2 commits March 26, 2024 11:35

Compare shape of distances array for plot_compare()

a20a232

Extend tests

966eefd

coderabbitai bot reviewed Mar 26, 2024

View reviewed changes

janosh merged commit 77429a6 into materialsproject:master Mar 26, 2024
21 of 22 checks passed

ab5424 deleted the phonon-dos-interted branch March 26, 2024 11:30

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Add more flexibility to `PhononDOSPlotter` and `PhononBSPlotter` #3700

Add more flexibility to `PhononDOSPlotter` and `PhononBSPlotter` #3700

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Add more flexibility to PhononDOSPlotter and PhononBSPlotter #3700

Add more flexibility to PhononDOSPlotter and PhononBSPlotter #3700

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ab5424 commented Mar 22, 2024 • edited by coderabbitai bot Loading

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ab5424 commented Mar 26, 2024

Add more flexibility to `PhononDOSPlotter` and `PhononBSPlotter` #3700

Add more flexibility to `PhononDOSPlotter` and `PhononBSPlotter` #3700

ab5424 commented Mar 22, 2024 •

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