changelog.md

Changelog

All notable changes to this project will be documented in this file. Dates are displayed in UTC.

v0.8.2

11 May 2024

• Add pymatviz/enums.py for SSOT on dataframe column and dict key names #143
• Add keyword hide_f_block: bool = None (La and Ac series) to ptable plotters #140
• Remove text background and fix z-order in structure_viz #139
• Refactor ptable plotters and add ptable_heatmap with diagonally-split tiles #131
• Migrate to flat eslint config file #137
• Copy color options for element types from ptable_plots to ptable_hists #129
• MACE-MP pair repulsion curves #127
• Add validate_fig decorator utility #126
• add_best_fit_line() power-up #125
• plot_phonon_bands() add kwargs branch_mode: "union" | "intersection" = "union" and branches: Sequence[str] = () #124
• breaking: rename fmt_spec keyword to fmt in si_fmt() for code base consistency 4d3091e
• add decimal_threshold: float = 0.01 to si_fmt() 6ecf68a
• fix docs build error and address bullet point 3 in #138 492cd53
• update bibtex citation author list aa132d9

v0.8.1

11 February 2024

• Breaking: rename custom plotly template pymatviz_(black->dark) #123
• Add ptable_scatter #122
• Minor format tweaks #120
• Add pytest fixtures df_(float|mixed) to replace deleted pd._testing.make(Mixed)DataFrame() #121
• add_ecdf_line() utility for plotting empirical cumulative distribution functions #117
• Spacegroup hist plotly #116
• Add plot_phonon_bands_and_dos() #115
• Add show_values: bool = True to ptable_heatmap_plotly() and last_peak_anno: str to plot_phonon_dos() #114
• Add plot_phonon_dos() for interactive plotly DOS plots #113
• _generate_assets.py add code for assets/(phonon-bands-and-dos-dft|phonon-bands-dft|phonon-dos-dft).svg 93f72dc
• ruff enable PD901+PLW2901 and fix violations 36f4771
• breaking: absorb keywords sort and density_bins into hist_density_kwargs 64da6b2
• breaking: rename elements_hist to hist_elemental_prevalence in pymatviz/histograms.py ebd067a
• gray-shade negative frequencies in phonon bands and bands+DOS plots 882a6ca
• breaking: remove residual_hist() from pymatviz/histograms.py 7780f68
• mv dataset_exploration examples 8bfa4b8

v0.8.0

15 December 2023

• Add plot_band_structure in new pymatviz/bandstructure.py module #112
• Add hist_kwds arg to ptable_hists to customize histograms #111
• Define custom pymatviz plotly templates #110
• Support matplotlib Axes and Figure in add_identity_line #109
• Tweaks #108
• Add function ptable_hists #100
• ptable_heatmap_plotly support 1s, 0s and negative values with log=True #107
• ptable_heatmap add keywords cbar_range and cbar_kwargs #105
• Add class TqdmDownload #104
• Breaking: rename get_crystal_sys to crystal_sys_from_spg_num #103
• Support semi-log + log-log plots in add_identity_line #102
• plot_structure_2d add special site_labels: "symbol" | "species" #101
• ptable_heatmap_ratio allow disabling not_in_numerator, not_in_denominator, not_in_numerator c4bc03d
• fix add_identity_line for log-scaled matplotlib Axes: TypeError: 'slope' cannot be used with non-linear scales ead0ce9
• add and test si_fmt_int in pymatviz/utils.py fc40cd7

v0.7.3

4 November 2023

• Add styled_html_tag() in utils.py #99
• Add si_fmt() for formatting large numbers in human-readable format #98

v0.7.2

30 October 2023

• Fix and rename df_to_(svelte->html)_table #97
• Add keyword default_styles: bool = True to df_to_pdf #96

v0.7.1

22 October 2023

• Periodic table UX improvements #95
• annotate_bars add keyword adjust_test_pos: bool = False #94
• Add df_to_svelte_table #93
• fix invalid count_mode ValueError err msg ae77997

v0.7.0

9 October 2023

• Bump minimum Python version to 3.9 #92
• Split pymatviz/io.py out from pymatviz/utils.py and add df_to_pdf() export function #91
• Add KDE support to bin_df_cols utility function #90
• Add patch_dict() utility #88
• Breaking: rename ptable_heatmap and annotate_metrics float precision kwargs to fmt #87
• Rename ptable_heatmap(_plotly) 1st arg: elem_values->values #86

v0.6.3

24 July 2023

• Fix "Loading [MathJax]/extensions/MathMenu.js" in Plotly figures exported to PDF #83
• Tiny doc update in ptable.py #82
• Better type errors #80
• ruff enable more rule sets #79
• Disable save_fig() in CI #78
• adhere to PEP 484 (no implicit optional) 8e50218
• fix ruff TCH002,TCH003 d60276b
• add ptable_heatmap_plotly kwarg label_map: dict[str, str] | False | None = None ef40171
• migrate site to eslint-plugin-svelte 91d7909

v0.6.2

29 April 2023

• Per-module doc pages #77
• Refactor make_docs.py #76
• DRY workflows #74
• More flexible annotate_metrics util #73

v0.6.1

21 March 2023

• Add kwarg axis: bool | str = "off" to plot_structure_2d() #72
• Add ptable_heatmap cbar_precision kwarg #70
• add changelog.md via auto-changelog 05da617
• add half-baked /plots and /notebook pages ed171ec
• add svelte-zoo PrevNext to notebooks pages 05368c0
• add new option 'occurrence' for CountMode = element_composition|fractional_composition|reduced_composition bf1604a
• refactor ptable_heatmap()'s tick_fmt() and add test for cbar_precision kwarg 3427e1f
• plot_structure_2d() in site /api docs fcf75de

v0.6.0

21 February 2023

• Pyproject #69

v0.5.3

20 February 2023

• Pyproject #69
• Add Ruff pre-commit hook #68
• scatter_density() use x, y args as axis labels if strings 0f2386a
• fix util save_and_compress_svg() and update plot_structure_2d() assets e0020aa
• use redirect in layout.ts instead of ugly DOM href surgery to forward readme links to GH repo 7da3c0c
• rename add_mae_r2_box() to annotate_mae_r2() c550332

v0.5.2

13 January 2023

• pre-commit autoupdate #65
• Deploy demo site to GitHub pages #64
• Configure devcontainer for running notebooks in Codespace #63
• Customizable parity stats #61
• Support dataframes in true_pred_hist() #60
• Support dataframes in relevance and uncertainty plots #59
• Allow passing in dataframes and x, y as column names in parity plots #58
• plot_structure_2d() doc str add "multiple structures in single figure example" #57
• update examples/mp_bimodal_e_form.ipynb with MP r2SCAN beta release formation energies 396bdf4
• add save_fig() to pymatviz/utils.py covered by test_save_fig() bcb8a06
• add assets/make_api_docs.py 1b05792
• Revert "Python 3.7 support (#55)" 4335001
• remove google colab compat notices from example notebooks e7cc488
• tweak docs CSS, add site footer 6319379
• type test functions, update commit hooks incl. mypy, setup.cfg set implicit_optional=true which defaults to false in newer mypys 9303f7d
• add docformatter pre-commit hook 25d700c
• add citation.cff 531133c
• residual_hist() remove args y_true, y_pred, now takes y_res directly 5c8ccbe

v0.5.1

8 October 2022

• Python 3.7 support #55
• move plot_defaults.py into pymatviz pkg #23973
• add kwarg y_max_headroom=float to annotate_bars() d613d99

v0.5.0

21 September 2022

• Support log-scaled heat maps in ptable_heatmap_plotly() #53
• Improve tests for parity.py and relevance.py #51
• Fix plot_structure_2d() show_bonds for disordered structures #50
• Dataset exploration #49
• Add examples/mp_bimodal_e_form.ipynb #47
• Add unary ptable heatmap plot to examples/mprester_ptable.ipynb #46
• fix: add .py to readme link #45
• add test_ptable_heatmap_plotly_kwarg_combos #44
• Fix windows CI #43
• rm data/ex-ensemble-roost.csv, generate random regression data to plot example assets with numpy instead 11a47d3
• breaking: rename {elements=>ptable}.py 1a87845
• merge pymatviz/{quantile,ranking}.py into new pymatviz/uncertainty.py c4e0872
• add examples/mprester_ptable.ipynb 04bf077
• cleaner plt.Axes and go.Figure imports d21e6b4
• add JupyterDash example to mprester_ptable.ipynb c4381d3
• remove save_reference_img() from conftest.py 73fd600
• rename cum_{res,err} to cumulative_{residual,error} 5d52181
• add readme table with links to open notebooks in GH, Colab, Binder 13df583
• add standardize_struct kwarg to plot_structure_2d() 21d1264
• add pre-commit hook https://github.com/jendrikseipp/vulture 9dfb806

v0.4.4

9 July 2022

• Add kwarg show_bonds to plot_structure_2d() #41
• Add kwarg exclude_elements: Sequence[str] to ptable_heatmap() #40
• fix broken readme image ![matbench-phonons-structures-2d] 17742d1
• fix flaky CI error from matminer load_dataset() 0c0c043
• fix plot_structure_2d() for pymatgen structures with oxidation states b61f4c0
• plotly add_identity_line() use fig.full_figure_for_development() to get x/y-range 8ddf049
• move codespell and pydocstyle commit hook args to setup.cfg 7338173
• [pre-commit.ci] pre-commit autoupdate a0b5195

v0.4.3

2 June 2022

• Fix GH not showing interactive Plotly figures in Jupyter #39
• Add new plotly function sankey_from_2_df_cols() #37
• note relation to ase.visualize.plot.plot_atoms() in plot_structure_2d() doc string f4c9fb7
• corrections to element property data in pymatviz/elements.csv (thanks @robertwb) + origin link 444f9ba
• fix add_identity_line() if plotly trace data contains NaNs c31ac55

v0.4.2

16 May 2022

• Improve ptable_heatmap_plotly() colorscale kwarg #35
• [pre-commit.ci] pre-commit autoupdate #34
• Accept pmg structures as input for spacegroup_(hist|sunburst) #33
• Fix spacegroup_hist() crystal system counts #32
• Expand testing of keyword arguments #31
• generate_assets.py refactor save_and_compress_svg() a47b811
• add add_identity_line() in tests/test_utils.py faa6a52
• readme remove ml-matrics to pymatviz migration cmd 0d123d4

v0.4.1

20 March 2022

• Support space groups symbols as input to spacegroup_hist() #30
• Support space groups symbols as input to spacegroup_sunburst() #28
• Add some Juypter notebooks with usage examples #25
• rm local structures data/structures/mp-*.yml, use matbench phonon structures instead 7ee4105
• GH action bump setup-python to v3 9f21079
• incl jupyter notebooks in ml-matrics to pymatviz migration cmd 619075f
• readme clarify not being associated with pymatgen 64c95fb
• fix plt.tight_layout() throwing AttributeError on density_hexbin plots (matplotlib/matplotlib#22576) e5599a6
• compress new SVG assets fe88271

v0.4.0

1 March 2022

• Rename package to pymatviz (formerly ml-matrics) #23

v0.3.0

28 February 2022

• Add plot_structure_2d() in new module ml_matrics/struct_vis.py #20
• git mv data/{mp-n_elements<2,mp-elements}.csv (closes #19) #19
• support atomic numbers in count_elements(), only element symbols before, add kwarg text_color in ptable_heatmap ada57cc
• add kwargs {pre,suf}fix in add_mae_r2_box(), use pip cache in **publish.yml** 6f64c3b
• better handling of atomic numbers in count_elements() when outside range [1, 118] e46b2c4
• python-requires>=3.8 e0560af

v0.2.6

6 February 2022

• add test for count_elements 4060d4e
• use future import for py 3.10 type annotations ae5aa96
• fix get_crystal_sys raise ValueError on non-positive space group numbers 9a535f7
• add .github/workflows/publish.yml 7ce1c55
• use actions/setup-{python,node} auto caching 613706c
• drop py3.7 support, update pre-commit hooks 93c3eeb
• gha test.yml add pytest-cov 16c92ab
• readme remove asset compression note, rename scripts 41d5b6c

v0.2.5

26 November 2021

• add ptable_heatmap_plotly() (closes #16) #16
• delete metrics.py module + tests as they're better placed in CompRhys/aviary#13 6870f2d
• add new plotly fig spacegroup_sunburst 871c42a
• some tweaks to ptable_heatmap_plotly, delete unused softmax + one_hot utils 3e931f2

v0.2.4

2 November 2021

• ptable_heatmap add label precision kwarg, change text color to white on dark tiles, spacegroup_hist better label fontsizes, doc string improvements all around, pre-commit enforce all assets are SVGs d45511f

v0.2.3

18 October 2021

• refactor ptable_heatmap to plot arbitrary data, not just elemental prevalence, add element properties to elements.csv 57ceb4d
• ptable_heatmap add heat_labels kwarg for fraction, percent or None heat labels, make ptable_heatmap_ratio colors and legend customizable c3210bf

v0.2.2

14 October 2021

• add typing_extensions as py37 dep and dynamically import Literal e69face
• add codespell pre-commit hook + fix typos 58bfa75

v0.2.1

7 October 2021

• readme move ptable_heatmap() and spacegroup_hist() plots to top ac000a4
• spacegroup_hist() add crystal system counts 693307e
• [pre-commit.ci] pre-commit autoupdate d6227dd

v0.2.0

4 October 2021

• doc string improvements 6572d85
• rename ptable_elemental_prevalence -> ptable_heatmap, ptable_elemental_ratio -> ptable_heatmap_ratio f4c915d
• add pydocstyle pre-commit hook a379621
• err_decay() accept and return axes object 60c0ceb
• handle nan values in add_mae_r2_box be0acf1
• fix on.paths in CI workflows f9e9ba2

v0.1.9

26 August 2021

• remove ml_matrics.utils.add_identity, use plt.axline instead https://git.io/JERaj d30a29f

v0.1.8

25 August 2021

• [pre-commit.ci] pre-commit autoupdate #12
• use numpy.typing.NDArray for type hints c99062c
• add some more pre-commit-hooks dfb93e4

v0.1.7

3 July 2021

• fully type annotate all functions and fix mypy errors b5729e3

v0.1.6

2 July 2021

• fix ptable_elemental_prevalence cbar_max kwarg 9c92e7c

v0.1.5

12 May 2021

• [pre-commit.ci] pre-commit autoupdate #11
• ptable_elemental_prevalence change color map as black text on dark green (high prevalence) elements was unreadable 8bc17b5

v0.1.4

6 May 2021

• add count as label below element symbols in ptable_elemental_prevalence 1a8d077
• add format-ipy-cells pre-commit hook 7f83ce3
• [pre-commit.ci] pre-commit autoupdate 70a5695

v0.1.3

10 April 2021

• ptable_elemental_prevalence add cbar_max kwarg 829f762

v0.1.2

6 April 2021

• release as PyPI package 1ab0d29
• manually merge branch metrics. thx @CompRhys! 3ddb232
• rename repo mlmatrics -> ml-matrics b65f50f
• fix ptable_elemental_prevalence log scale colorbar 0913416
• readme use referenced links for raw.githubusercontent images cbd1033
• rename branch master -> main 50d73c6
• fix setup.cfg to not pollute top level namespace in site-packages with generic data folder 10c8589

v0.1.1

6 April 2021

• fix setup.cfg to not pollute top level namespace in site-packages with generic data folder 68a84b2
• [pre-commit.ci] pre-commit autoupdate 49caa7f

v0.1.0

5 April 2021

• concept names, publication plot params #2
• clean up cumulative plots, add better data source for example plots, rename density_scatter to parity #1
• add spacegroup_hist to histograms.py 41297ec
• add clf_metrics.py ce4f864
• initial commit 4a985c1
• add correlation.py with marchenko_pastur plot 2e6665c
• add more tests, especially for kwargs 600adbf
• add residual_vs_actual(), residual_hist() in new histograms.py, add readme glossary ed8393c
• release as PyPI package 511b5e3
• manually merge branch metrics. thx @CompRhys! c3c284d
• add bar values percent or count to hist_elemental_prevalence, more tests for elements.py + log_scale plots in readme 8d722f8
• rename repo mlmatrics -> ml-matrics d5b741c
• change ptable prevalence colors, log now uses base 10 494ac24
• add true_pred_hist to histograms.py 0ea0ef6
• add new plot ptable_elemental_ratio 6e91792
• add err_decay to parity.py, display MAE + R^2 on all parity plots 3999b60
• add type hints to parity.py ea94b0d
• feature: add regression basic metrics for ensembles 141f4d9
• fea: allow pre-computed elem_counts for ratio plot, allow cmap to be changed via kwarg 7ac598b
• fix ptable_elemental_prevalence log scale colorbar c9d085e
• add err_decay plots + plot function names to readme 9e994bb
• err_decay use analytic rand_mean rather than estimating from sample be2b834
• change ptable plots color bar to show log numbers when log_scale=True ed35532
• add doc strings for density_scatter, residual_vs_actual, revert dependence on numpy.typing for now 006fdff
• refactor using ax.set property batch setter 5a41284
• add marchenko-pastur example with significant eigenvalue db7e725
• readme add tip for how to depend on this package, regenerate requirements with pipreqs --force . cdae757
• fix spacegroup_hist bars having wrong face colors 6a9ee75
• add github action to compress SVGs on PR 2be7725
• appease linter 39a3b15
• speed up count_elements by removing for loop 1495701
• add doc strings to relevance.py f372631
• rename branch master -> main f56cf6e
• fix requirements typo 9653a82
• ptable_elemental_prevalence display original values above log-scale colorbar 665b05c
• fix qq_gaussian miscal_area 8239949