Preview for PR #25 b1382f7

Author: timtreis

pr-25/_sources/notebooks/tutorials/cropping.ipynb

@@ -30,10 +30,10 @@
    "id": "72859ca0",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2026-08-27T02:12:57.715456Z",
-     "iopub.status.busy": "2026-08-27T02:12:57.715330Z",
-     "iopub.status.idle": "2026-08-27T02:13:03.901349Z",
-     "shell.execute_reply": "2026-08-27T02:13:03.900588Z"
+     "iopub.execute_input": "2026-08-27T13:43:05.296671Z",
+     "iopub.status.busy": "2026-08-27T13:43:05.296566Z",
+     "iopub.status.idle": "2026-08-27T13:43:25.040624Z",
+     "shell.execute_reply": "2026-08-27T13:43:25.039413Z"
     }
    },
    "outputs": [
@@ -98,10 +98,10 @@
    "id": "01b51d6d",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2026-08-27T02:13:03.903707Z",
-     "iopub.status.busy": "2026-08-27T02:13:03.903293Z",
-     "iopub.status.idle": "2026-08-27T02:13:04.332143Z",
-     "shell.execute_reply": "2026-08-27T02:13:04.331389Z"
+     "iopub.execute_input": "2026-08-27T13:43:25.044345Z",
+     "iopub.status.busy": "2026-08-27T13:43:25.043812Z",
+     "iopub.status.idle": "2026-08-27T13:43:26.396450Z",
+     "shell.execute_reply": "2026-08-27T13:43:26.395429Z"
     }
    },
    "outputs": [
@@ -145,10 +145,10 @@
    "id": "824a4ca3",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2026-08-27T02:13:04.337201Z",
-     "iopub.status.busy": "2026-08-27T02:13:04.337032Z",
-     "iopub.status.idle": "2026-08-27T02:13:04.692560Z",
-     "shell.execute_reply": "2026-08-27T02:13:04.691992Z"
+     "iopub.execute_input": "2026-08-27T13:43:26.402902Z",
+     "iopub.status.busy": "2026-08-27T13:43:26.402680Z",
+     "iopub.status.idle": "2026-08-27T13:43:26.920605Z",
+     "shell.execute_reply": "2026-08-27T13:43:26.919825Z"
     }
    },
    "outputs": [
@@ -196,10 +196,10 @@
    "id": "14117b6e",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2026-08-27T02:13:04.696509Z",
-     "iopub.status.busy": "2026-08-27T02:13:04.696103Z",
-     "iopub.status.idle": "2026-08-27T02:13:05.525941Z",
-     "shell.execute_reply": "2026-08-27T02:13:05.525324Z"
+     "iopub.execute_input": "2026-08-27T13:43:26.924986Z",
+     "iopub.status.busy": "2026-08-27T13:43:26.924538Z",
+     "iopub.status.idle": "2026-08-27T13:43:27.809979Z",
+     "shell.execute_reply": "2026-08-27T13:43:27.809070Z"
     }
    },
    "outputs": [
@@ -255,10 +255,10 @@
    "id": "7062d268",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2026-08-27T02:13:05.529958Z",
-     "iopub.status.busy": "2026-08-27T02:13:05.529828Z",
-     "iopub.status.idle": "2026-08-27T02:13:06.129053Z",
-     "shell.execute_reply": "2026-08-27T02:13:06.128367Z"
+     "iopub.execute_input": "2026-08-27T13:43:27.814144Z",
+     "iopub.status.busy": "2026-08-27T13:43:27.813951Z",
+     "iopub.status.idle": "2026-08-27T13:43:28.680311Z",
+     "shell.execute_reply": "2026-08-27T13:43:28.679358Z"
     }
    },
    "outputs": [
@@ -324,10 +324,10 @@
    "id": "b77f94ff",
    "metadata": {
     "execution": {
-     "iopub.execute_input": "2026-08-27T02:13:06.131043Z",
-     "iopub.status.busy": "2026-08-27T02:13:06.130897Z",
-     "iopub.status.idle": "2026-08-27T02:13:06.200239Z",
-     "shell.execute_reply": "2026-08-27T02:13:06.199208Z"
+     "iopub.execute_input": "2026-08-27T13:43:28.683410Z",
+     "iopub.status.busy": "2026-08-27T13:43:28.683212Z",
+     "iopub.status.idle": "2026-08-27T13:43:28.897909Z",
+     "shell.execute_reply": "2026-08-27T13:43:28.896545Z"
     }
    },
    "outputs": [
@@ -340,7 +340,7 @@
       "IPython version      : 9.13.0\n",
       "\n",
       "spatialdata     : 0.7.3\n",
-      "spatialdata_plot: 0.4.2.dev11+g1d833abbf.d20260826\n",
+      "spatialdata_plot: 0.4.2\n",
       "matplotlib      : 3.10.9\n",
       "numpy           : 2.4.4\n",
       "\n",

pr-25/contributing.html

@@ -571,7 +571,7 @@ <h2>Code-style<a class="headerlink" href="#code-style" title="Link to this headi
 <section id="writing-tests">
 <span id="id1"></span><h2>Writing tests<a class="headerlink" href="#writing-tests" title="Link to this heading">#</a></h2>
 <p>This package uses <a class="reference external" href="https://docs.pytest.org/">pytest</a> for automated testing.
-Please write <a class="reference external" href="https://scanpy.scverse.org/en/stable/dev/testing.html" title="(in Scanpy v1.12.3)"><span>Tests</span></a> for every function added to the package.</p>
+Please write <a class="reference external" href="https://scanpy.scverse.org/en/stable/dev/testing.html" title="(in Scanpy v1.12.4)"><span>Tests</span></a> for every function added to the package.</p>
 <p>Most IDEs integrate with pytest and provide a GUI to run tests.
 If you set up your virtual environments as described in <a class="reference internal" href="#installing-dev-dependencies">installing dev dependencies</a>,
 test cases should be automatically discovered by your IDE.</p>
@@ -648,7 +648,7 @@ <h2>Writing documentation<a class="headerlink" href="#writing-documentation" tit
 <li><p><a class="reference external" href="https://github.com/tox-dev/sphinx-autodoc-typehints">sphinx-autodoc-typehints</a>, to automatically reference annotated input and output types</p></li>
 <li><p>Citations (like <span class="bibtex-citation" id="id2">[<a class="reference internal" href="references.html#id2" title="Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Philipp Angerer, Volker Bergen, Pierre Boyeau, Maren Büttner, Gokcen Eraslan, David Fischer, Max Frank, Justin Hong, Michal Klein, Marius Lange, Romain Lopez, Mohammad Lotfollahi, Malte D. Luecken, Fidel Ramirez, Jeffrey Regier, Sergei Rybakov, Anna C. Schaar, Valeh Valiollah Pour Amiri, Philipp Weiler, Galen Xing, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle, and Fabian J. Theis and. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature Biotechnology, apr 2023. URL: https://doi.org/10.1038%2Fs41587-023-01733-8, doi:10.1038/s41587-023-01733-8.">VBH+23</a>]</span>) can be included with <a class="reference external" href="https://sphinxcontrib-bibtex.readthedocs.io/">sphinxcontrib-bibtex</a></p></li>
 </ul>
-<p>See scanpy’s <a class="reference external" href="https://scanpy.scverse.org/en/stable/dev/documentation.html" title="(in Scanpy v1.12.3)"><span>Documentation</span></a> for more information on how to write your own.</p>
+<p>See scanpy’s <a class="reference external" href="https://scanpy.scverse.org/en/stable/dev/documentation.html" title="(in Scanpy v1.12.4)"><span>Documentation</span></a> for more information on how to write your own.</p>
 <section id="tutorials-with-myst-nb-and-jupyter-notebooks">
 <h3>Tutorials with myst-nb and jupyter notebooks<a class="headerlink" href="#tutorials-with-myst-nb-and-jupyter-notebooks" title="Link to this heading">#</a></h3>
 <p>The documentation is set-up to render jupyter notebooks stored in the <code class="docutils literal notranslate"><span class="pre">docs/notebooks</span></code> directory using <a class="reference external" href="https://myst-nb.readthedocs.io/">myst-nb</a>.

pr-25/notebooks/tutorials/cropping.html

@@ -623,7 +623,7 @@ <h2>For reproducibility<a class="headerlink" href="#for-reproducibility" title="
 IPython version      : 9.13.0
 
 spatialdata     : 0.7.3
-spatialdata_plot: 0.4.2.dev11+g1d833abbf.d20260826
+spatialdata_plot: 0.4.2
 matplotlib      : 3.10.9
 numpy           : 2.4.4
 

pr-25/plotting.html

@@ -1007,7 +1007,7 @@ <h2> Contents </h2>
 <li><p><strong>pad_extent</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> | <a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></span> (default: <code class="docutils literal notranslate"><span class="pre">0</span></code>)) – Padding added around the computed spatial extent on all sides. Ignored when <code class="docutils literal notranslate"><span class="pre">crop_coord</span></code> is set.</p></li>
 <li><p><strong>crop_coord</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a>[<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.14)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>] | <a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.14)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">None</span></code></a></span> (default: <code class="docutils literal notranslate"><span class="pre">None</span></code>)) – Restrict the plot to a bounding box <code class="docutils literal notranslate"><span class="pre">(xmin,</span> <span class="pre">xmax,</span> <span class="pre">ymin,</span> <span class="pre">ymax)</span></code> in the rendered coordinate
 system’s units (same order as <code class="xref py py-meth docutils literal notranslate"><span class="pre">matplotlib.axes.Axes.axis()</span></code> and as <code class="docutils literal notranslate"><span class="pre">crop_coord</span></code> in
-<a class="reference external" href="https://scanpy.scverse.org/en/stable/api/generated/scanpy.pl.spatial.html#scanpy.pl.spatial" title="(in Scanpy v1.12.3)"><code class="xref py py-func docutils literal notranslate"><span class="pre">scanpy.pl.spatial()</span></code></a> / <code class="xref py py-func docutils literal notranslate"><span class="pre">squidpy.pl.spatial_scatter()</span></code>). Points and shapes are
+<a class="reference external" href="https://scanpy.scverse.org/en/stable/api/generated/scanpy.pl.spatial.html#scanpy.pl.spatial" title="(in Scanpy v1.12.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">scanpy.pl.spatial()</span></code></a> / <code class="xref py py-func docutils literal notranslate"><span class="pre">squidpy.pl.spatial_scatter()</span></code>). Points and shapes are
 subsetted before drawing for speed; large images (both the matplotlib and <code class="docutils literal notranslate"><span class="pre">datashader</span></code>
 backends) and labels are rasterized to the window only, so the full array is never
 materialized (fast at Visium HD scale) and the zoom keeps full figure resolution. For points