Unverified Commit 1522492b authored by Oriol Abril's avatar Oriol Abril Committed by GitHub

get docs for stats and plots to link to ArviZ (#3927)

* get docs for stats and plots to link to ArviZ

* update release notes
parent 9e8a20dc
...@@ -16,6 +16,7 @@ ...@@ -16,6 +16,7 @@
- `pm.LKJCholeskyCov` now automatically computes and returns the unpacked Cholesky decomposition, the correlations and the standard deviations of the covariance matrix (see [#3881](https://github.com/pymc-devs/pymc3/pull/3881)). - `pm.LKJCholeskyCov` now automatically computes and returns the unpacked Cholesky decomposition, the correlations and the standard deviations of the covariance matrix (see [#3881](https://github.com/pymc-devs/pymc3/pull/3881)).
- `pm.Data` container can now be used for index variables, i.e with integer data and not only floats (issue [#3813](https://github.com/pymc-devs/pymc3/issues/3813), fixed by [#3925](https://github.com/pymc-devs/pymc3/pull/3925)). - `pm.Data` container can now be used for index variables, i.e with integer data and not only floats (issue [#3813](https://github.com/pymc-devs/pymc3/issues/3813), fixed by [#3925](https://github.com/pymc-devs/pymc3/pull/3925)).
- `pm.Data` container can now be used as input for other random variables (issue [#3842](https://github.com/pymc-devs/pymc3/issues/3842), fixed by [#3925](https://github.com/pymc-devs/pymc3/pull/3925)). - `pm.Data` container can now be used as input for other random variables (issue [#3842](https://github.com/pymc-devs/pymc3/issues/3842), fixed by [#3925](https://github.com/pymc-devs/pymc3/pull/3925)).
- Plots and Stats API sections now link to ArviZ documentation [#3927](https://github.com/pymc-devs/pymc3/pull/3927)
### Maintenance ### Maintenance
- Tuning results no longer leak into sequentially sampled `Metropolis` chains (see #3733 and #3796). - Tuning results no longer leak into sequentially sampled `Metropolis` chains (see #3733 and #3796).
......
...@@ -3,7 +3,20 @@ Plots ...@@ -3,7 +3,20 @@ Plots
***** *****
.. currentmodule:: pymc3.plots .. currentmodule:: pymc3.plots
Plots are delegated to the
`ArviZ <https://arviz-devs.github.io/arviz/index.html>`_.
library, a general purpose library for
"exploratory analysis of Bayesian models."
For plots, ``pymc3.<function>`` are now aliases
for ArviZ functions. Thus, the links below will redirect you to
ArviZ docs:
.. automodule:: pymc3.plots - :func:`pymc3.traceplot <arviz:arviz.plot_trace>`
:members: traceplot, plot_posterior, forestplot, compareplot, autocorrplot, - :func:`pymc3.plot_posterior <arviz:arviz.plot_posterior>`
energyplot, kdeplot, densityplot, pairplot - :func:`pymc3.forestplot <arviz:arviz.plot_forest>`
- :func:`pymc3.compareplot <arviz:arviz.plot_compare>`
- :func:`pymc3.autocorrplot <arviz:arviz.plot_autocorr>`
- :func:`pymc3.energyplot <arviz:arviz.plot_energy>`
- :func:`pymc3.kdeplot <arviz:arviz.plot_kde>`
- :func:`pymc3.densityplot <arviz:arviz.plot_density>`
- :func:`pymc3.pairplot <arviz:arviz.plot_pair>`
***** *****
Stats Stats
***** *****
Statistics and diagnostics are delegated to the
`ArviZ <https://arviz-devs.github.io/arviz/index.html>`_.
library, a general purpose library for
"exploratory analysis of Bayesian models."
For statistics and diagnostics, ``pymc3.<function>`` are now aliases
for ArviZ functions. Thus, the links below will redirect you to
ArviZ docs:
.. currentmodule:: pymc3.stats .. currentmodule:: pymc3.stats
.. automodule:: pymc3.stats
:members: - :func:`pymc3.bfmi <arviz:arviz.bfmi>`
- :func:`pymc3.compare <arviz:arviz.compare>`
- :func:`pymc3.ess <arviz:arviz.ess>`
- :data:`pymc3.geweke <arviz:arviz.geweke>`
- :func:`pymc3.hpd <arviz:arviz.hpd>`
- :func:`pymc3.loo <arviz:arviz.loo>`
- :func:`pymc3.mcse <arviz:arviz.mcse>`
- :func:`pymc3.r2_score <arviz:arviz.r2_score>`
- :func:`pymc3.rhat <arviz:arviz.rhat>`
- :func:`pymc3.summary <arviz:arviz.summary>`
- :func:`pymc3.waic <arviz:arviz.waic>`
...@@ -37,6 +37,7 @@ extensions = [ ...@@ -37,6 +37,7 @@ extensions = [
"sphinx.ext.autodoc", "sphinx.ext.autodoc",
"sphinx.ext.autosummary", "sphinx.ext.autosummary",
"sphinx.ext.mathjax", "sphinx.ext.mathjax",
"sphinx.ext.intersphinx",
"nbsphinx", "nbsphinx",
"numpydoc", "numpydoc",
"IPython.sphinxext.ipython_console_highlighting", "IPython.sphinxext.ipython_console_highlighting",
...@@ -130,6 +131,11 @@ pygments_style = "friendly" ...@@ -130,6 +131,11 @@ pygments_style = "friendly"
# If true, `todo` and `todoList` produce output, else they produce nothing. # If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False todo_include_todos = False
# intersphinx configuration to ease linking arviz docs
intersphinx_mapping = {
"arviz": ("https://arviz-devs.github.io/arviz/", None),
}
# -- Options for HTML output ---------------------------------------------- # -- Options for HTML output ----------------------------------------------
......
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