Prepare initial pre-release (#54)

* add links between sub-libraries

* bump version

* use accessor in plot_forest docstring

* bump version and configure publishing

.github/workflows/publish.yml

@@ -2,16 +2,19 @@ name: Publish library
 
 on:
   push:
-    branches:
-      - main
     tags:
       # Don't try to be smart about PEP 440 compliance,
       # see https://www.python.org/dev/peps/pep-0440/#appendix-b-parsing-version-strings-with-regular-expressions
       - v*
 
 jobs:
   publish:
+    environment:
+      name: publish
+      url: https://pypi.org/p/arviz-plots
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -25,6 +28,3 @@ jobs:
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}

.pylintrc

@@ -66,6 +66,7 @@ disable=missing-docstring,
         not-an-iterable,
         no-member,
         import-error,
+        possibly-used-before-assignment,
         fixme
 
 

docs/source/_static/custom.css

@@ -0,0 +1,9 @@
+html[data-theme="light"] {
+  --pst-color-primary: rgb(11 117 145);
+  --pst-color-secondary: rgb(238 144 64);
+}
+
+html[data-theme="dark"] {
+  --pst-color-primary: rgb(0 192 191);
+  --pst-color-secondary: rgb(238 144 64);
+}

docs/source/_templates/name.html

@@ -0,0 +1,5 @@
+<div class="sd-d-flex-row sd-align-major-spaced sd-align-minor-center">
+  <a href="https://arviz-base.readthedocs.io"><div class="sd-fs-6 sd-font-weight-lighter sd-text-muted">BASE</div></a>
+  <a href="https://arviz-stats.readthedocs.io"><div class="sd-fs-6 sd-font-weight-lighter sd-text-muted">STATS</div></a>
+  <a href="{{ pathto(root_doc) }}"><div class="sd-fs-3 sd-font-weight-bold sd-text-primary">PLOTS</div></a>
+</div>

docs/source/conf.py

@@ -124,4 +124,15 @@
         "image_dark": "_static/ArviZ_white.png",
     }
 }
+html_favicon = "_static/favicon.ico"
 html_static_path = ["_static"]
+html_css_files = ["custom.css"]
+html_sidebars = {
+    "**": [
+        "navbar-logo.html",
+        "name.html",
+        "icon-links.html",
+        "search-button-field.html",
+        "sbt-sidebar-nav.html",
+    ]
+}

pyproject.toml

@@ -26,8 +26,8 @@ classifiers = [
 ]
 dynamic = ["version", "description"]
 dependencies = [
-  "arviz-base",
-  "arviz-stats @ git+https://github.com/arviz-devs/arviz-stats",
+  "arviz-base==0.2",
+  "arviz-stats[xarray]==0.2",
 ]
 
 [tool.flit.module]

src/arviz_plots/_version.py

@@ -1,2 +1,2 @@
 """Base ArviZ version."""
-__version__ = "0.1.0"
+__version__ = "0.2.0"

src/arviz_plots/plots/distplot.py

@@ -66,7 +66,7 @@ def plot_dist(
         How to represent the marginal density.
         Defaults to ``rcParams["plot.density_kind"]``
     point_estimate : {"mean", "median", "mode"}, optional
-        Which point estimate to plot. Defaults to ``rcParams["plot.point_estimate"]``
+        Which point estimate to plot. Defaults to rcParam :data:`stats.point_estimate`
     ci_kind : {"eti", "hdi"}, optional
         Which credible interval to use. Defaults to ``rcParams["stats.ci_kind"]``
     ci_prob : float, optional
@@ -173,7 +173,7 @@ def plot_dist(
     if ci_kind is None:
         ci_kind = rcParams["stats.ci_kind"] if "stats.ci_kind" in rcParams else "eti"
     if point_estimate is None:
-        point_estimate = rcParams["plot.point_estimate"]
+        point_estimate = rcParams["stats.point_estimate"]
     if kind is None:
         kind = rcParams["plot.density_kind"]
     if plot_kwargs is None:

src/arviz_plots/plots/forestplot.py

@@ -63,7 +63,7 @@ def plot_forest(
         Whether to plot intervals for each chain or not. Ignored when the "chain" dimension
         is not present.
     point_estimate : {"mean", "median", "mode"}, optional
-        Which point estimate to plot. Defaults to ``rcParams["plot.point_estimate"]``
+        Which point estimate to plot. Defaults to rcParam :data:`stats.point_estimate`
     ci_kind : {"eti", "hdi"}, optional
         Which credible interval to use. Defaults to ``rcParams["stats.ci_kind"]``
     ci_probs : (float, float), optional
@@ -187,14 +187,14 @@ def plot_forest(
         :context: close-figs
 
         >>> from arviz_plots import visuals
-        >>> from arviz_stats.base import ess
+        >>> import arviz_stats  # make accessor available
         >>>
         >>> c_aux = centered["posterior"].expand_dims(
         >>>     column=3
         >>> ).assign_coords(column=["labels", "forest", "ess"])
         >>> pc = plot_forest(c_aux, combined=True)
         >>> pc.map(
-        >>>     visuals.scatter_x, "ess", data=ess(centered),
+        >>>     visuals.scatter_x, "ess", data=centered.azstats.ess().ds,
         >>>     coords={"column": "ess"}, color="C0"
         >>> )
 
@@ -217,7 +217,7 @@ def plot_forest(
     if ci_kind is None:
         ci_kind = rcParams["stats.ci_kind"] if "stats.ci_kind" in rcParams else "eti"
     if point_estimate is None:
-        point_estimate = rcParams["plot.point_estimate"]
+        point_estimate = rcParams["stats.point_estimate"]
     if plot_kwargs is None:
         plot_kwargs = {}
     if pc_kwargs is None:
@@ -328,7 +328,7 @@ def plot_forest(
                 np.linspace(-0.2, 0.2, distribution.sizes["model"]),
                 coords={"model": distribution.model},
             )
-            chain_lim = 0.4 * (model_spacing[1] - model_spacing[0])
+            chain_lim = 0.4 * (model_spacing[1] - model_spacing[0]).item()
             chain_spacing = xr.DataArray(
                 np.linspace(-chain_lim, chain_lim, distribution.sizes["chain"]),
                 coords={"chain": distribution.chain},