Skip to content

A folder for containing the older versions of squidpy #152

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 3 commits into
base: main
Choose a base branch
from
Open

A folder for containing the older versions of squidpy #152

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9684edb
init
selmanozleyen Oct 1, 2025
bdd8bfe
update notebooks
selmanozleyen Oct 1, 2025
98d97da
remove empty cells
selmanozleyen Oct 1, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 9 additions & 0 deletions deprecated_features/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
Deprecated Features
=========

This section contains various deprecated features in :mod:`squidpy`. We keep notebook here that we don't expect to be run by our current suggested workflow.

.. toctree::
:maxdepth: 1

tutorial_napari
0 tutorials/tutorial_napari.ipynb → deprecated_features/tutorial_napari.ipynb
View file
Open in desktop
File renamed without changes.
17 changes: 0 additions & 17 deletions examples/image/compute_crops.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -207,23 +207,6 @@
"adata_crop = crop_corner.subset(adata)\n",
"adata_crop"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"Visualize the result in Napari:\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"crop_corner.interactive(adata_crop)"
]
}
],
"metadata": {
Expand Down
5 changes: 2 additions & 3 deletions examples/image/compute_custom_features.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -230,9 +230,8 @@
"metadata": {},
"source": [
"Use `squidpy.pl.extract` to plot the histogram features on the tissue\n",
"image or have a look at [our interactive visualization\n",
"tutorial](../../tutorials/tutorial_napari.ipynb) to learn how to use our\n",
"interactive `napari` plugin.\n"
"image or have a look at [napari-spatialdata](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). Here, we show all calculated segmentation\n",
"features.\n"
]
},
{
Expand Down
4 changes: 1 addition & 3 deletions examples/image/compute_segmentation_features.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -322,9 +322,7 @@
"metadata": {},
"source": [
"Use `squidpy.pl.extract` to plot the texture features on the tissue\n",
"image or have a look at [our interactive visualization\n",
"tutorial](../../tutorials/tutorial_napari.ipynb) to learn how to use our\n",
"interactive `napari` plugin. Here, we show all calculated segmentation\n",
"image or have a look at [napari-spatialdata](https://spatialdata.scverse.org/projects/napari/en/stable/notebooks/spatialdata.html). Here, we show all calculated segmentation\n",
"features.\n"
]
},
Expand Down
10 changes: 10 additions & 0 deletions examples/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,3 +65,13 @@ This section contains various examples from the :mod:`squidpy.pl` module.
:glob:

plotting/plot_*


Older versions
---------------
This section contains examples from older versions of Squidpy. Kept here for reference.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
This section contains examples from older versions of Squidpy. Kept here for reference.
This section contains tutorials and examples that have since been deprecated from Squidpy. They are listed here for reference.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
This section contains examples from older versions of Squidpy. Kept here for reference.
This section contains tutorials and examples that have since been deprecated from Squidpy. They are listed here for reference.


.. toctree::
:maxdepth: 1

older_versions/compute_crops.ipynb
2 changes: 0 additions & 2 deletions tutorials/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,15 +28,13 @@ Advanced Tutorials
This section contains tutorials showcasing advanced :mod:`squidpy` functionalities, such as:

- loading spatial data.
- interactive visualization.
- working with z-stacks.

.. toctree::
:maxdepth: 1

tutorial_read_spatial
tutorial_image_container
tutorial_napari
tutorial_image_container_zstacks


Expand Down