From c3678ec2b2a3398392362a5ff9df5cde00478c8d Mon Sep 17 00:00:00 2001
From: Hassan Kibirige <has2k1@gmail.com>
Date: Thu, 13 Jun 2024 22:21:06 +0300
Subject: [PATCH 1/2] Fix layers 3 & above overlapping the axis lines

fixes #798
---
 doc/changelog.qmd            |  4 ++++
 plotnine/themes/themeable.py | 14 ++++++++++++--
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/doc/changelog.qmd b/doc/changelog.qmd
index 1b6869cb3..11cde42a7 100644
--- a/doc/changelog.qmd
+++ b/doc/changelog.qmd
@@ -15,6 +15,10 @@ title: Changelog
 - [](:class:`~plotnine.geom_text`) has gained new aesthetics
   `fontvariant` and `fontstretch`.
 
+### Bug Fixes
+
+- Fix layers 3 and above not to overlap the axis lines if there are any
+  ({{< issue 798 >}}).
 
 ## v0.13.6
 (2024-05-09)
diff --git a/plotnine/themes/themeable.py b/plotnine/themes/themeable.py
index 92cf8d52b..f222a00cf 100644
--- a/plotnine/themes/themeable.py
+++ b/plotnine/themes/themeable.py
@@ -893,8 +893,13 @@ class axis_line_x(themeable):
 
     def apply_ax(self, ax: Axes):
         super().apply_ax(ax)
+        properties = self.properties
+        # MPL has a default zorder of 2.5 for spines
+        # so layers 3+ would be drawn on top of the spines
+        if "zorder" not in properties:
+            properties["zorder"] = 10000
         ax.spines["top"].set_visible(False)
-        ax.spines["bottom"].set(**self.properties)
+        ax.spines["bottom"].set(**properties)
 
     def blank_ax(self, ax: Axes):
         super().blank_ax(ax)
@@ -916,8 +921,13 @@ class axis_line_y(themeable):
 
     def apply_ax(self, ax: Axes):
         super().apply_ax(ax)
+        properties = self.properties
+        # MPL has a default zorder of 2.5 for spines
+        # so layers 3+ would be drawn on top of the spines
+        if "zorder" not in properties:
+            properties["zorder"] = 10000
         ax.spines["right"].set_visible(False)
-        ax.spines["left"].set(**self.properties)
+        ax.spines["left"].set(**properties)
 
     def blank_ax(self, ax: Axes):
         super().blank_ax(ax)

From a3d893f7c30e654ea5a249c83c77ea532f23380f Mon Sep 17 00:00:00 2001
From: Hassan Kibirige <has2k1@gmail.com>
Date: Wed, 12 Jun 2024 19:57:29 +0300
Subject: [PATCH 2/2] ENH: Read quarto fig-width, fig-height, fig-format

---
 doc/changelog.qmd   |  3 +++
 plotnine/options.py | 37 +++++++++++++++++++++++++++++++++++--
 2 files changed, 38 insertions(+), 2 deletions(-)

diff --git a/doc/changelog.qmd b/doc/changelog.qmd
index 11cde42a7..88198c4a4 100644
--- a/doc/changelog.qmd
+++ b/doc/changelog.qmd
@@ -10,6 +10,9 @@ title: Changelog
 - The `family`, `fontstyle` and `fontweight` parameters of
   [](:class:`~plotnine.geom_text`) are now aesthetics ({{< issue 790 >}}).
 
+- plotnine now responds to the `fig-width`, `fig-height` and `fig-format`
+  settings in the meta section of a quarto document.
+
 ### New Features
 
 - [](:class:`~plotnine.geom_text`) has gained new aesthetics
diff --git a/plotnine/options.py b/plotnine/options.py
index df7b1fd0f..bc39b7b8d 100644
--- a/plotnine/options.py
+++ b/plotnine/options.py
@@ -1,8 +1,9 @@
 from __future__ import annotations
 
-import typing
+import os
+from typing import TYPE_CHECKING
 
-if typing.TYPE_CHECKING:
+if TYPE_CHECKING:
     from typing import Any, Literal, Optional, Type
 
     from plotnine import theme
@@ -105,3 +106,35 @@ def set_option(name: str, value: Any) -> Any:
     old = d[name]
     d[name] = value
     return old
+
+
+# Quarto sets environment variables for the figure dpi, size and format
+# for the project or document.
+#
+# https://quarto.org/docs/computations/execution-options.html#figure-options
+#
+# If we are in quarto, we read those and make them the default values for
+# the options.
+# Note that, reading the variables and setting them in a context manager
+# cannot not work since the option values would be set after the original
+# defaults have been used by the theme.
+if "QUARTO_FIG_WIDTH" in os.environ:
+
+    def _set_options_from_quarto():
+        """
+        Set options from quarto
+        """
+        global dpi, figure_size, figure_format
+
+        dpi = int(os.environ["QUARTO_FIG_DPI"])
+        figure_size = (
+            float(os.environ["QUARTO_FIG_WIDTH"]),
+            float(os.environ["QUARTO_FIG_HEIGHT"]),
+        )
+
+        # quarto verifies the format
+        # If is retina, it doubles the original dpi and changes the
+        # format to png
+        figure_format = os.environ["QUARTO_FIG_FORMAT"]  # pyright: ignore
+
+    _set_options_from_quarto()