Fix docs links (#389)

* fix docs links

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* cleanup import

* attempt fix ci

* add lowerbound spatialdata

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: LucaMarconato

.readthedocs.yaml

@@ -12,7 +12,7 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - "doc"
+        - "docs"
         - "all"
         - "readthedocs"
         - "pre"

docs/notebooks/mibitof_analysis.ipynb

@@ -4,17 +4,13 @@
    "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "# Analyse Nanostring data in Napari-SpatialData \n"
-   ]
+   "source": "# Analyse Cosmx data in Napari-SpatialData\n"
   },
   {
    "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "This tutorial shows how to load and analyse Nanostring data with the Napari-SpatialData plugin.\n"
-   ]
+   "source": "This tutorial shows how to load and analyze Cosmx data with the Napari-SpatialData plugin.\n"
   },
   {
    "attachments": {},
@@ -60,43 +56,7 @@
    "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "Next, we will download the Nanostring dataset (cosmx_io) for analysis. \n",
-    "\n",
-    "If on Windows, download the dataset from https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip.\n",
-    "\n",
-    "In on Linux, uncomment the lines below to download the dataset. "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "--2023-05-03 21:11:58--  https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip\n",
-      "Resolving s3.embl.de (s3.embl.de)... 194.94.45.80\n",
-      "Connecting to s3.embl.de (s3.embl.de)|194.94.45.80|:443... connected.\n",
-      "HTTP request sent, awaiting response... 200 OK\n",
-      "Length: 2210531049 (2,1G) [application/zip]\n",
-      "Saving to: ‘tutorial_data/nanostring_data/cosmx_io.zip’\n",
-      "\n",
-      "cosmx_io.zip        100%[===================>]   2,06G  10,9MB/s    in 3m 21s  \n",
-      "\n",
-      "2023-05-03 21:15:19 (10,5 MB/s) - ‘tutorial_data/nanostring_data/cosmx_io.zip’ saved [2210531049/2210531049]\n",
-      "\n"
-     ]
-    }
-   ],
-   "source": [
-    "# !mkdir tutorial_data\n",
-    "# !mkdir tutorial_data/nanostring_data\n",
-    "# !wget -P tutorial_data/nanostring_data https://s3.embl.de/spatialdata/spatialdata-sandbox/cosmx_io.zip\n",
-    "# !unzip tutorial_data/nanostring_data/cosmx_io.zip -d tutorial_data/nanostring_data"
-   ]
+   "source": "Please download the CosMx raw data from https://brukerspatialbiology.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/nsclc-ffpe-dataset/, parse it using `spatialdata_io` and save it to the SpatialData Zarr format (you can for instance [use this script](https://github.com/giovp/spatialdata-sandbox/blob/main/cosmx_io/to_zarr.py)).\n"
   },
   {
    "attachments": {},