Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module #3237

janosh · 2023-08-13T19:49:56Z

Closes #3138.

pymatgen plotting methods using the matplotlib backend return the matplotlib.pyplot module (plt), rather than an object related to the plot itself, such as the Figure or Axes. This is suboptimal API design and inconsistent with the plotly backend which returns go.Figure.

This PR changes all plotting methods to return a plt.Axes object (same as pymatviz) instead of plt.

Reasons:

More Intuitive as Axes actually contains the plot attributes (lines, legend, labels, etc.), and is more in line with what users may expect and what they typically interact with when customizing plots.
Consistency with pymatviz and pymatgen's own plotly backend.

E AttributeError: 'Axes' object has no attribute 'subplot' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:1082

E AttributeError: 'Axes' object has no attribute 'ylim' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:3834

E AttributeError: 'Axes' object has no attribute 'gca' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:360:

E AttributeError: 'Axes' object has no attribute 'ylim' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:3838: AttributeError

E AttributeError: 'Axes' object has no attribute 'xlim' pymatgen/electronic_structure/plotter.py:3836: AttributeError

E AttributeError: 'Axes' object has no attribute 'gca' /home/runner/work/pymatgen/pymatgen/pymatgen/phonon/plotter.py:266: AttributeError

E AttributeError: 'Axes' object has no attribute 'setp' pymatgen/electronic_structure/plotter.py:3875: AttributeError

…t_range_map and get_ir_spectra

…expect plt.axes instead of plt

… downstream repercussions

def test_plot(self): # Disabling latex for testing. from matplotlib import axes, rc rc("text", usetex=False) self.plotter.add_dos("Total", self.dos) self.plotter.get_plot(units="mev") self.plotter_nostack.add_dos("Total", self.dos) plt = self.plotter_nostack.get_plot(units="mev") > ax = plt.gca() also attempt fix get_elt_projected_plots

> assert plt.ylim() == (-4.0, 7.6348), "wrong ylim" and > ax.set_title(ax.get_title(), size=width * 4) E AttributeError: 'numpy.ndarray' object has no attribute 'set_title'

fraricci · 2023-11-02T17:23:15Z

If I can chime in here, I noticed a bug potentially introduced by this pull request.
As mentioned here, there is a "ax =" missing here

janosh · 2023-11-02T19:34:20Z

@fraricci Thanks for reporting and troubleshooting!

This reverts commit a8d04f9.

* remove unused read_cube import * tweak test.yml comments * try to install BoltzTraP * fix decompress command * make installation script modular * try to modify PATH, test split 4 * fix boltztrap unit test * use rtol * properly skip unit test * fix fig.xticks to ax migration in #3237 * ax.gca -> plg.gca() * properly use ScalarFormatter * NEED CONFIRM: fix number of lines * NEED CONFIRM: fix unit test values * try to install open babel * NEED CONFIRM: include fdint * Revert "NEED CONFIRM: include fdint" This reverts commit 6b19836. * skip tests if no fdint * try to install Vampire * make vampire executable * relocate attribute to class docstring * try to use absolute path in PATH * use VAMPEXE * mark vampire test for fix and skip for now * restore conda openbabel install * use openbabel-wheel instead * make download and decompress less verbose * make module level var all capital * re-enable matgl tests * add TODO tag for skipped unit test * bump matgl version * bump matgl in optional * pin torch version in CI * add reference url * clarify comment * remove unused guarded matgl import * relocate import * update requirements.txt * bump openbabel version * bump openbabel-wheel to latest release 19 * remove matplotlib != 3.9.1 pin as it has been yanked * remove linux only pin for openbabel-wheel * add more comment about bolztrap2 * skip openbabel for windows for now * add TODO tag * make module var all cap * rename non test function to avoid test_xxx pattern * install tblite thru conda-forge * sort conda forge pack order alphabetically * fix io.qchem test dir path * add separate dir var for new qchem files * TO FIX: enable qchem test * I tried but failed, need someone smarter than me to fix this * remove non-win pin for openbabel-wheel * skip failing openbabel tests for Windows * skip left out tests for openbabel on win * uncomment hiphive * use numpy recommended 2.0.0rc1 * bumpy build sys numpy to 2.1.0 * fall back to numpy 2.0.1 as 2.1.0 don't support python39 * mark test_zsl as to be fixed in this PR * use float array as per fast_norm require * reverse numba version bump * drop upgrade arg for pip install torch * instead of hinting, just handle * re-raise from previous error * make ubuntu dep install inline * fix test skip and make module var all cap * add TODO tags * renames * Revert "properly use ScalarFormatter" This reverts commit e2ff5fa. * Revert "ax.gca -> plg.gca()" This reverts commit 1d104cb. * Revert "fix fig.xticks to ax migration in #3237" This reverts commit a8d04f9. * Revert "NEED CONFIRM: fix number of lines" This reverts commit eb7978d. * Revert "NEED CONFIRM: fix unit test values" This reverts commit f6a3fc7. * ruff fix * skip entire TestBoltztrapPlotter * use platform.system() == "Windows" over os.name == "nt" * use platform.system() == "Windows" over sys.platform == "win32" --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

janosh added 2 commits August 13, 2023 12:39

return plt.Axes instead of plt from plot methods

f065118

VoltageProfilePlotter.get_plot and get_chgint_plot

187113c

janosh added data viz PRs and issues about pymatgen plotting functionality breaking Breaking change api Application programming interface ux User experience labels Aug 13, 2023

janosh added 19 commits August 13, 2023 13:12

fix > plt.subplot(220 + count)

1092642

E AttributeError: 'Axes' object has no attribute 'subplot' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:1082

fix > ylim = plt.ylim()

3e33ed5

E AttributeError: 'Axes' object has no attribute 'ylim' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:3834

fix > plt.gca().set_xticks(uniq_d)

dd920cd

E AttributeError: 'Axes' object has no attribute 'gca' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:360:

fix > ylim = plt.ylim()

5d1db50

E AttributeError: 'Axes' object has no attribute 'ylim' /home/runner/work/pymatgen/pymatgen/pymatgen/electronic_structure/plotter.py:3838: AttributeError

fix mypy and add type hints to RelaxationAnalyzer

3c8c3b5

fix > ax.xlim((min(relevanty), max(relevanty)))

cfde8d8

E AttributeError: 'Axes' object has no attribute 'xlim' pymatgen/electronic_structure/plotter.py:3836: AttributeError

fix > plt.gca().set_xticks(uniq_d)

7d2e696

E AttributeError: 'Axes' object has no attribute 'gca' /home/runner/work/pymatgen/pymatgen/pymatgen/phonon/plotter.py:266: AttributeError

don't use get_plot return value, use imported plt module directly

470e563

improve plot_compare_gs error message on incompatible plotters

f5ecd9a

update SpectrumPlotter.get_plot and pretty_polyfit_plot

530e68a

fix > ax.setp(legend_text, fontsize=30)

bfdc1d2

E AttributeError: 'Axes' object has no attribute 'setp' pymatgen/electronic_structure/plotter.py:3875: AttributeError

return plt.axes instead of plt in SurfaceEnergyPlotter.surface_chempo…

755f56b

…t_range_map and get_ir_spectra

fix PhononDosPlotter.get_plot()

7481a18

refactor tests

545f539

update test_gruneisen.py and electronic_structure/test_plotter.py to …

7eb286e

…expect plt.axes instead of plt

fix SpectrumPlotter.get_plot and DosPlotter.get_plot

0f352bf

remove redundant os.path.join(".", ...) in pymatgen/io/feff/sets.py

b43d479

replace all plt = pretty_plot(...) with ax = pretty_plot(...) and fix…

8af131e

… downstream repercussions

add missing set_ prefix to Axes methods

66b45a7

janosh changed the title ~~Plot methods return plt.Axes object, not plt module~~ Breaking: Have plot methods return plt.Axes object, not matplotlib module Aug 17, 2023

janosh added 4 commits August 17, 2023 14:27

update return type doc strings and type hints

de9beb4

pre-commit autoupdate && ruff . --fix

b0d39f3

rename all subplot vars to ax

ed8e09c

janosh added 2 commits August 17, 2023 15:18

fix AttributeError: 'Axes' object has no attribute 'ylim'

36f9c90

> assert plt.ylim() == (-4.0, 7.6348), "wrong ylim" and > ax.set_title(ax.get_title(), size=width * 4) E AttributeError: 'numpy.ndarray' object has no attribute 'set_title'

fix TestBSPlotter.test_get_plot()

3ee84ea

janosh merged commit 5abfb63 into master Aug 17, 2023

janosh deleted the return-plt-axes-not-plt branch August 17, 2023 22:35

janosh mentioned this pull request Nov 2, 2023

Bug in BSPlotterProjected.get_elt_projected_plots() #3450

Closed

janosh mentioned this pull request Apr 12, 2024

Breaking: all plot methods return plt.Axes #3749

Merged

DanielYang59 added a commit to DanielYang59/pymatgen that referenced this pull request Aug 9, 2024

fix fig.xticks to ax migration in materialsproject#3237

a8d04f9

DanielYang59 mentioned this pull request Aug 9, 2024

Install optional boltztrap, vampire and openbabel in CI #3985

Merged

7 tasks

DanielYang59 added a commit to DanielYang59/pymatgen that referenced this pull request Sep 6, 2024

Revert "fix fig.xticks to ax migration in materialsproject#3237"

49bdd5f

This reverts commit a8d04f9.

DanielYang59 mentioned this pull request Sep 6, 2024

[BUG] Entire BoltztrapPlotter is broken #4045

Open

DanielYang59 mentioned this pull request Oct 14, 2024

pmg plot --dos ... errs in matplotlib call #4108

Closed

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Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module #3237

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Breaking: Have plot methods return `plt.Axes` object, not `matplotlib` module #3237

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