Merge branch 'main' into sph_pixavproj

Author: nastasha-w

.github/workflows/bleeding-edge.yaml

@@ -40,7 +40,7 @@ jobs:
         # the '-dev' suffix allows to use pre-releases if no final release is available yet
         # this version should be upgraded as often as possible, typically once a year when
         # Cython, numpy and matplotlib are known to be compatible
-        python-version: '3.12-dev'
+        python-version: '3.13-dev'
 
     - name: Install dependencies
       # PyYAML needs to be installed in isolation for now, because of a known

.github/workflows/build-test.yaml

@@ -25,14 +25,14 @@ jobs:
         os:
           - ubuntu-latest
           - macos-latest
-        python-version: ['3.12']
+        python-version: ['3.13']
         dependencies: [full]
         tests-type: [unit]
         test-runner: [pytest]
         venv-loc: [bin]
         include:
           - os: windows-latest
-            python-version: '3.12'
+            python-version: '3.13'
             dependencies: full
             tests-type: unit
             test-runner: pytest

.github/workflows/wheels.yaml

@@ -33,7 +33,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Build wheels for CPython
-        uses: pypa/cibuildwheel@v2.21.2
+        uses: pypa/cibuildwheel@v2.22.0
         with:
           output-dir: dist
 
@@ -82,7 +82,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
     - name: install check-manifest
       run: |
         python -m pip install --upgrade pip
@@ -124,7 +124,7 @@ jobs:
           merge-multiple: true
 
       - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.10.3
+        uses: pypa/gh-action-pypi-publish@v1.12.4
         with:
           user: __token__
           password: ${{ secrets.pypi_token }}

.pre-commit-config.yaml

@@ -30,13 +30,13 @@ repos:
 # TODO: replace this with ruff when it supports embedded python blocks
 # see https://github.com/astral-sh/ruff/issues/8237
 -   repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
     -   id: blacken-docs
         additional_dependencies: [black==24.3.0]
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.9
+  rev: v0.9.4
   hooks:
   - id: ruff-format
   - id: ruff
@@ -51,7 +51,7 @@ repos:
     -   id: rst-backticks
 
 - repo: https://github.com/MarcoGorelli/cython-lint
-  rev: v0.16.2
+  rev: v0.16.6
   hooks:
   - id: cython-lint
     args: [--no-pycodestyle]

README.md

@@ -7,7 +7,7 @@
 [![Devel Mailing List](https://img.shields.io/badge/Devel-List-lightgrey.svg)](https://mail.python.org/archives/list/yt-dev@python.org//)
 [![Data Hub](https://img.shields.io/badge/data-hub-orange.svg)](https://hub.yt/)
 [![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](http://numfocus.org)
-[![Sponsor our Project](https://img.shields.io/badge/donate-to%20yt-blueviolet)](https://numfocus.salsalabs.org/donate-to-yt/index.html)
+[![Sponsor our Project](https://img.shields.io/badge/donate-to%20yt-blueviolet)](https://numfocus.org/donate-to-yt)
 
 <!--- Tests and style --->
 [![Build and Test](https://github.com/yt-project/yt/actions/workflows/build-test.yaml/badge.svg)](https://github.com/yt-project/yt/actions/workflows/build-test.yaml)

conftest.py

@@ -156,8 +156,7 @@ def pytest_configure(config):
             # https://github.com/h5py/h5py/pull/2242
             config.addinivalue_line(
                 "filterwarnings",
-                "ignore:`product` is deprecated as of NumPy 1.25.0"
-                ":DeprecationWarning",
+                "ignore:`product` is deprecated as of NumPy 1.25.0:DeprecationWarning",
             )
 
     if PANDAS_VERSION is not None and PANDAS_VERSION >= Version("2.2.0"):
@@ -184,6 +183,16 @@ def pytest_configure(config):
                 ":DeprecationWarning",
             )
 
+    if find_spec("datatree"):
+        # the cf_radial dependency arm-pyart<=1.9.2 installs the now deprecated
+        # xarray-datatree package (which imports as datatree), which triggers
+        # a bunch of runtimewarnings when importing xarray.
+        # https://github.com/yt-project/yt/pull/5042#issuecomment-2457797694
+        config.addinivalue_line(
+            "filterwarnings",
+            "ignore:" r"Engine.*loading failed.*" ":RuntimeWarning",
+        )
+
 
 def pytest_collection_modifyitems(config, items):
     r"""

doc/source/conf.py

@@ -68,9 +68,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = "4.4"
+version = "4.5"
 # The full version, including alpha/beta/rc tags.
-release = "4.4-dev"
+release = "4.5-dev"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/cookbook/custom_colorbar_tickmarks.ipynb

@@ -71,7 +71,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we call `_setup_plots()` to ensure the plot is properly initialized. Without this, the custom tickmarks we are adding will be ignored."
+    "Next, we call `render()` to ensure the plot is properly rendered. Without this, the custom tickmarks we are adding will be ignored."
    ]
   },
   {
@@ -82,7 +82,7 @@
    },
    "outputs": [],
    "source": [
-    "slc._setup_plots()"
+    "slc.render()"
    ]
   },
   {

doc/source/cookbook/geographic_xforms_and_projections.ipynb

@@ -174,7 +174,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that this doesn't have a lot of contextual information. We can add annotations for the coastlines just as we would with matplotlib. Before the annotations are set, we need to call `p._setup_plots` to make the axes available for annotation. "
+    "Note that this doesn't have a lot of contextual information. We can add annotations for the coastlines just as we would with matplotlib. Before the annotations are set, we need to call `p.render` to make the axes available for annotation. "
    ]
   },
   {
@@ -184,7 +184,7 @@
    "outputs": [],
    "source": [
     "p = yt.SlicePlot(ds, \"altitude\", \"AIRDENS\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -212,7 +212,7 @@
    "source": [
     "p = yt.SlicePlot(ds, \"altitude\", \"AIRDENS\")\n",
     "p.set_mpl_projection(\"Robinson\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -233,7 +233,7 @@
    "source": [
     "p = yt.SlicePlot(ds, \"altitude\", \"AIRDENS\")\n",
     "p.set_mpl_projection((\"Robinson\", (37.5,)))\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -253,7 +253,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"Orthographic\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -289,7 +289,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection((\"Orthographic\", (90, 45)))\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -311,7 +311,7 @@
     "p.set_mpl_projection(\n",
     "    (\"Orthographic\", (), {\"central_latitude\": -45, \"central_longitude\": 275})\n",
     ")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -338,7 +338,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection((\"RotatedPole\", (177.5, 37.5)))\n",
-    "p._setup_plots()\n",
+    "p.redner()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -353,7 +353,7 @@
     "p.set_mpl_projection(\n",
     "    (\"RotatedPole\", (), {\"pole_latitude\": 37.5, \"pole_longitude\": 177.5})\n",
     ")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -366,7 +366,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"NorthPolarStereo\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -379,7 +379,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"AlbersEqualArea\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -392,7 +392,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"InterruptedGoodeHomolosine\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -405,7 +405,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"Robinson\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -418,7 +418,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"Gnomonic\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"
@@ -465,7 +465,7 @@
    "outputs": [],
    "source": [
     "p.set_mpl_projection(\"Robinson\")\n",
-    "p._setup_plots()\n",
+    "p.render()\n",
     "p.plots[\"AIRDENS\"].axes.set_global()\n",
     "p.plots[\"AIRDENS\"].axes.coastlines()\n",
     "p.show()"

doc/source/visualizing/callbacks.rst

@@ -257,7 +257,7 @@ Overplot Contours
    Add contours in ``field`` to the plot.  ``levels`` governs the number of
    contours generated, ``factor`` governs the number of points used in the
    interpolation, ``take_log`` governs how it is contoured and ``clim`` gives
-   the (upper, lower) limits for contouring.
+   the (lower, upper) limits for contouring.
 
 .. python-script::