Add separated prior and likelihood groups #117
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## main #117 +/- ##
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PiyushPanwarFST
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Mar 1, 2025
improve plot_posterior and add tests for it add minimal docstrings add init to test folder update plot_posterior add some docs add docs and implement some feedback improve api docs ignore mystnb warning add plot_trace (arviz-devs#1) * add trace plot * use convert_to_datatree in tests * fix linters * Add to draft API docs --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> rename plot_posterior and small improvements fix test rename source file add style add styles update intro plotcollection update intro plotcollection add ecdf to distplot draft trace_dens draft trace_dens draft Update src/arviz_plots/plots/tracedensplot.py Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Update src/arviz_plots/plots/tracedensplot.py Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Update src/arviz_plots/plots/utils.py Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Update src/arviz_plots/plots/utils.py Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> fix missing argument try fixing docs fix docs Issue was due to wrong handling of try except. To avoid depending on matplotlib, it is imported within a try except to register the colormaps and styles, but then it is deleted from the namespace which was happening outside the try except and so arviz_plots failed to import on envs without matplotlib rename dens -> dist update api index Add legend method to PlotCollection and improve docs (arviz-devs#32) * start work on legend and improve docs * add anchor placeholder * work on docs * add backend functions to docs and improve plot_collection docs * add missing files * extend api docs * first attempt at bokeh legend * make no-duplication of backend api docs work * run pre-commit * fix and docs on generate_aes_dt * doc improvements * some doc extensions * improve plot_dist docs * fix bokeh legend generation * add warning to legend method Add plot_forest and tests (arviz-devs#34) * some improvements to PlotCollection * add classmethod tests * add more tests * add divergences to plot_trace * extend tests * add divergence data to test_plots * add plot_forest draft For everything to work, the following features were added to: * support for "__variable__" in aesthetics * default values for common aesthetics * support for dict of datatree input -> multiple models aligned within the same plot * add labels to plot_forest still some backend elements missing for bokeh * further improvements to plot_forest * invert y aes to preserve order top-down * improvements to aes_map defaults and shading * attempt support for InferenceData inputs * plot_dist support for multiple models and docs * update dependencies * add more tests * raise error on wrong use of combined * better support for aesthetics in labels elements Add neutral element concept to aes generation (arviz-devs#35) * First try at neutral element * Fix syntax * Try fixing syntax and improve readability * Fix shade aes default * update and extend tests * update aes_dt to aes_dict conversion * run tests with coverage on CI Fixes and improvements to plot_trace_dist (arviz-devs#36) * very rough draft to fix aesthetic mapping defaults * fix plot_trace_dist and add tests * use neutral element for combined elements * add example to plot_trace Extend and rerun tutorials (arviz-devs#38) * add xlabel to plot_trace * rerun plots_intro notebook * update leftover arviz-base references * write use plotcollection notebook and some improvements * fix scale_fig_size defaults * switch docs theme, default to light version PlotCollection coords attribute for better composability (arviz-devs#39) * prepare reuse of plotting functions * call plot_trace within plot_trace_dist * use plot_dist in plot_trace_dist * add contributing section to docs * fix doc warnings * fix dark-light issue with backend logos * write new_plot docs * improve neutral element behaviour and docs * fix a couple cross-references add none backend and hypothesis tests (arviz-devs#41) * add none backend and hypothesis tests * add more tests with hypothesis and scheduled actions * fix hypothesis yaml syntax * use unset as default for none backend so keys are filtered * add branch reference to issue add codecov token (arviz-devs#42) change action to create issue/comment (arviz-devs#44) fix hypothesis action (arviz-devs#46) * add condition to run if testing failed * try fixing branch name * try adding a more specific link to action logs * switch pytest-store_date command order Prepare initial pre-release (arviz-devs#54) * add links between sub-libraries * bump version * use accessor in plot_forest docstring * bump version and configure publishing Fix issue in plot_dist_trace (arviz-devs#64) don't try to rename artists if they haven't been drawn Adding Ridgeplot to Arviz-Plots (arviz-devs#57) * First commit for adding ridgeplot * Updated `plot_ridge` with 'face' and 'edge' artists now and updated visual elements `line_xy` and `fill_between_y` * Modified density calculation pre-check in plot_ridge and modified visual element functions * Added hypothesis tests for plot_ridge * Added ridge_height as a top level arg and other modifications * final changes --------- Co-authored-by: Oriol (ProDesk) <oriol.abril.pla@gmail.com> Removed unused 'extra_data' arg (arviz-devs#73) Add plotly backend and gallery prototype (arviz-devs#61) * plotly backend proof of concept * be more consistend with kwarg handling and defaults * restructure backend dependencies and install process * fix typo in bokeh's remove_ticks * complete plotly backend * gallery prototype * extend docs and tests * add plotly equivalences to glossary * more sensible defaults and kwarg handling * automate gallery generation via sphinx extension * figsize and gallery related fixes * full fledged gallery * remove unused references * update gallery generator * initial plotly support for styles * fix gallery generator processing add pp-obs comparison with plot_forest example (arviz-devs#74) * add pp-obs comparison with plot_forest example * improve example expand style functionality (arviz-devs#75) * expand style functionality * add feedback * Apply suggestions from code review Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Improve backend documentation and get plot_forest to follow best practices (arviz-devs#78) * start working on best practices and backend docs * use none backend as documentation base * add images for plotly and none * adapt minigallery directive * use none backend instead of arviz_plots.backend * gallery references and plot sizing improvements * fix typo * pylint * wait until using sphinx 8 * pseudo fix for empty minigallery * modify slightly auto sizing * Apply suggestions from code review Co-authored-by: Osvaldo A Martin <aloctavodia@gmail.com> * add see also --------- Co-authored-by: Osvaldo A Martin <aloctavodia@gmail.com> Histogram support addition to distplot.py (arviz-devs#47) * WIP histogram addition to distplot.py * Added histogram computing if kind='hist' * reformatted histogram dataarrays into a dataset * Modified histogram dataset plot_axis coords to 'x' and 'y' and added visual element function, backend interface and matplotlib backend function for plotting histogram * Allowing xarray_einstats.histogram() function to determine default number of bins * Modified histogram data restructuring function to include bin edge data and modified docstrings for hist backend interface * added plot_dist test parametrizations for kind=kde, hist, ecdf, adjusted hypothesis time limit to 2 seconds and modified backend hist plotting function * added width to histogram plotting, removed print statements from previous commits and updated restructure_hist_data() docstring * switched histogram computation to arviz stats, modified plot_hist visual element slightly for new returned hist density data structure * added 'density=True' to normalize histogram heights and removed axis by default for histograms * added Bokeh backend for hist visual element and removed ecdf parametrization from test_plot_dist_models * updated docstring, added 'alpha' argument to the 'hist' backend plotting functions, renamed 'plot_hist' to 'hist', modified `remove_axis` logic slightly and set density=True as default in stats_kwargs * Added 'hist' to visuals.rst * deactivate tests for hist kind and multiple models It needs a fix in arviz-stats to work * removed restructure_dist and glyph default artist kwarg in bokeh * updated hist backend interface and matplotlib hist backend function with updates fromrootogram plot * plotly hist and plot_dist improvements --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Add plot_compare (arviz-devs#77) * add plot_compare * directly use plot_backend * add new kwargs * use fill_between_y * docs * remove commented code * use plot_kwargs * use plotcollection * use plotcollection * alow disabling elements * pass pc_kwargs to plotcollection * try to fix example in gallery * add missing import * Update gallery_generator.py * Improve show method for plotcollection * fix 1x1 grid generation in plotly * fix plotly 1x1 plots * add basic test * fix tests * isort * remove redundant array conversion --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> rework styles (arviz-devs#88) * rework color palletes * update plotly clean template fix link to github (arviz-devs#91) Add ESS Plot (arviz-devs#58) * First commit for essplot and scatter_xy visual element * update for ess plot and addition of 'x' aesthetic for 'model' dim * addition of quantile plot and updated x aesthetic mapping * Added rugplot to essplot * updates to essplot * fixed default value for arg 'extra_methods' * modified scatter_xy visual element to take into account _process_da_x_y update * Added color/linestyles aesthetics and simplified min_ess plotting * Added annotate_xy visual element, applied to essplot for extra_methods * visual element vertical alignment logic modification and arviz-stats compute_ranks addition attempt * added docs for essplot * tests for essplot * added scatter_xy to visuals.rst * added rug=True to example gallery plot_ess_local * fixes for rugplot issue and hypothesis test failures * shifted mean_ess, sd_ess computing to before plot_kwargs check+artist plotting logic and modified hypothesis tests * Updated plot_ess and tests * updated .toml file for arviz-stats dependency * Modified figsize to more of a plot_forest approach, fixed order of plots in plots.rst and expanded max limit for test methods in testplots.py in .pylintrc * Updated plot_ess docstring * Switched from .grid to .wrap, removed unused figsize coeffs, disabled pylint warning on testplots.py * final fixes now only waiting for us to figure out behaviour and scope in arviz-stats and xarray-einstats * update pyproject requirements * pylint --------- Co-authored-by: Oriol (ProDesk) <oriol.abril.pla@gmail.com> fix warning (arviz-devs#99) Adding Plot ESS Evolution (arviz-devs#71) * Initial ess evolution plot updated plot_ess_evolution including a common ess_dataset computing func added mean and sd annotations like essplot docs and example gallery for plot_ess_evolution updated verticalalign logic for mean/sd and correct (although overlaid and not flattened yet) rug is now displayed removed rug plot added tests updated scatter_xy func to plot_ess version fixed docstring altered store_artist for xlabel, ylabel and modified hypothesis tests shifted mean_ess, sd_edd computing to before plot_kwargs check+artist plotting logic updated docstring, added figsizing and set vertical_align for mean and sd text kwargs as setdefault removed 'rankdata' branch of arviz-stats from dependencies docstring typo fix gallery-generator updated for documentation building * remove visual duplicated when rebasing --------- Co-authored-by: Oriol (ProDesk) <oriol.abril.pla@gmail.com> Add plot_psense_dist (arviz-devs#93) * Add plot_psense_dist * Update src/arviz_plots/plots/psensedistplot.py Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * Update src/arviz_plots/plots/psensedistplot.py Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * concat da and simplify logic * set sample_dims to sample * refactor * minor fixes and update pyproject to install from GH * support sample_dims argument and all backends * add minigallery to docstring * tweak example * ensure pointinterval only plot does not have yticks * add initial test for psense plot * add test and example * fix test * fix docstring * rename __group__ --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> pin datatree and prepare release (arviz-devs#103) * pin datatree and prepare release * update naming for hist_dim to match arviz-stats install arviz-base/stats from github (arviz-devs#104) move out new_ds to arviz-stats (arviz-devs#102) Bump codecov/codecov-action from 4 to 5 (arviz-devs#107) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> update version, dependencies and CI (arviz-devs#110) * update version, dependencies and CI * skip 3.13 until numba release * update rtd env * ignore line too long in gallery template string Use DataTree class from xarray (arviz-devs#111) * start work for xarray datatree compatibility * use datatree from xarray * fix docs * remove unused import Update pyproject.toml (arviz-devs#113) Add energy plot (arviz-devs#108) * add energy plot * remove __variable__, add example * hardcode sampler_dims * use legend only with matplotlib Add plot for distribution of convergence diagnostics (arviz-devs#105) * Add plot for distribution of convergence diagnostics * add ref_line and methods for r-hat * fix docstring * rename, add example * update gallery example * use rhat instead of rhat_rank * update sphinx.configuration key * update sphinx.configuration key * add vline/hline. Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> * fix test * fix docstring * fix docstring --------- Co-authored-by: Oriol Abril-Pla <oriol.abril.pla@gmail.com> Add separated prior and likelihood groups (arviz-devs#117) * Add separated prior and likelihood groups * upper bound for plotly Add psense_quantities plot (arviz-devs#119) * add psense_quantities plot * remove comment * fix conflicting dimension * update docts * fix color * fix ls * split quantities * fix docstring rename arviz-clean to arviz-variat (arviz-devs#120) rename arviz-clean to arviz-variat add cetrino and vibrant styles to plotly (arviz-devs#121) psense: fix facetting and add xlabel (arviz-devs#123) * fix facetting * add x-label Add summary dictionary arguments (arviz-devs#125) * add summary dictionary arguments * fix spelling plotly: change format of title update in backend (arviz-devs#124) * plotly: change format of title update in backend * update the pyproject.toml file to restrict lower bound of plotly version to 6 Update glossary.md (arviz-devs#126) Add PAV-adjusted calibration plot (arviz-devs#127) * draft pava ppc * add pava-adjusted calibration plot * use dt * fix var name upper bound plotly (arviz-devs#128) use isotonic function that work with datatrees (arviz-devs#131) add reference, fix xlabel (arviz-devs#132) Fix bug when setting some plot_kwargs to false (arviz-devs#134) * fix bug setting when setting some plot_kwargs to false * remove references Add citations (arviz-devs#135) * add citations * reformat citations * fix indentation * fix links * add reference file use <6 version of plotly for documentation and use latest for other purposes (arviz-devs#136) * temporary fix for plotly-plot-rendering-on-webpage * include plotly also in readthedocs fix see algo pava gallery (arviz-devs#137) Add plot_ppc_dist (arviz-devs#138) * add plot_ppc_dist * remove comments * add test and small fixes * fix typo Add warning message for discrete data (arviz-devs#139) * add warning message for discrete data * do not fail on warnings rename plot_pava and minor fixes (arviz-devs#140) fix excesive margins (arviz-devs#141) add arviz-style for bokeh (arviz-devs#122) * add arviz-styles for bokeh * add arviz-styles for bokeh * Update arviz-variat.yml * add more styles Add rootogram (arviz-devs#142) fix examples (arviz-devs#144) Reorganize categories in the gallery (arviz-devs#145) * reorganize categories gallery * update condig * rename remove plots from titles (arviz-devs#146) * remove plots from titles * more renaming * more renaming consistence data_pairs, remove markers pava (arviz-devs#152) added functionality of step histogram for all three backends (arviz-devs#147) * added functionality of step histogram for all three backends * changed user preference format for step histograms * clean * little modifications to make it compatible with cleaned code and to have consistent edgecolor * added test for plot_dist with step value as true * minor fixes: step hist test is not required for 'none' backend --------- Co-authored-by: aloctavodia <aloctavodia@gmail.com> use continuous outcome for plot_ppc_dist example (arviz-devs#154) add grid visual (arviz-devs#155) all test cases are passed ruff changes seperating plotting functionality of bayes_factor testing get_plotting funcitonality new implementation of arviz-plot Update bfplot.py it should be something like this. Please, check that it works properly, add docstrings and improve when necessary Improved the plot_bf() function, applied fixes, and added additional assert for test cases Fixed the check for ref_val Added a docstring for plot_bf() Change the backend from matplotlib to none Added a legend to componenet_groups Added few more asserts in test cases Did some other minor fixing and refractoring Signed-off-by: PiyushPanwarFST <piyush2002panwar@gmail.com> Enhance plot_bf() Visualization & Documentation, Fix Linter Issues Adjusted and re-centered BF values for better graph representation. Added plot_bf() function to the documentation. Resolved pylint linter errors in code. Signed-off-by: PiyushPanwarFST <piyush2002panwar@gmail.com> deleting some files and modifying some files
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📚 Documentation preview 📚: https://arviz-plots--117.org.readthedocs.build/en/117/