napari-spatialdata 0.7.0__tar.gz → 0.7.2__tar.gz

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/.github/workflows/benchmarks.yml

@@ -170,7 +170,7 @@ jobs:
 
           fi
 
-      - uses: actions/upload-artifact@v5
+      - uses: actions/upload-artifact@v7
         if: always()
         with:
           name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}-${{ matrix.benchmark-name }}
@@ -182,13 +182,13 @@ jobs:
     if: always()
     steps:
       - name: Download artifact
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v8
         with:
           pattern: asv-benchmark-results*
           path: asv_result
           merge-multiple: true
       - name: Upload artifact
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v7
         with:
           name: asv-benchmark-results-${{ github.run_id }}-${{ github.run_number }}-${{ github.run_attempt }}
           path: asv_result

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/.github/workflows/benchmarks_report.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: "Download artifact"
-        uses: actions/github-script@v8
+        uses: actions/github-script@v9
         with:
           script: |
             let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
@@ -68,7 +68,7 @@ jobs:
 
       - name: "Comment on PR"
         if: env.PR_NUMBER != ''
-        uses: actions/github-script@v8
+        uses: actions/github-script@v9
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |
@@ -84,7 +84,7 @@ jobs:
 
       - name: "Remove run-benchmarks label"
         if: env.PR_NUMBER != ''
-        uses: actions/github-script@v8
+        uses: actions/github-script@v9
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           script: |

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/.github/workflows/release.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
       - name: Download built artifact to dist/
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/.github/workflows/test.yml

@@ -62,11 +62,11 @@ jobs:
           PLATFORM: ${{ matrix.platform }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
 
       - name: Archive figures generated during testing
         if: always()
-        uses: actions/upload-artifact@v5
+        uses: actions/upload-artifact@v7
         with:
           name: plotting-results-${{ matrix.python-version }}-${{ matrix.platform }}
           path: /Users/runner/work/napari-spatialdata/napari-spatialdata/tests/plots/generated/*

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v1.20.2
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.3.1
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.12
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/.readthedocs.yaml

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

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-spatialdata
-Version: 0.7.0
+Version: 0.7.2
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -44,7 +44,7 @@ Requires-Dist: scanpy
 Requires-Dist: scipy
 Requires-Dist: shapely
 Requires-Dist: scikit-learn
-Requires-Dist: spatialdata>=0.7.0dev1
+Requires-Dist: spatialdata>=0.7.2
 Requires-Dist: superqt
 Requires-Dist: typing_extensions>=4.8.0
 Requires-Dist: vispy
@@ -59,24 +59,24 @@ Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: pytest-mock; extra == "test"
 Requires-Dist: pytest-qt; extra == "test"
 Requires-Dist: pre-commit>=2.9.0; extra == "test"
-Provides-Extra: doc
-Requires-Dist: sphinx>=4.5; extra == "doc"
-Requires-Dist: sphinx-book-theme>=1.0.0; extra == "doc"
-Requires-Dist: myst-parser>=2.0.0; extra == "doc"
-Requires-Dist: sphinxcontrib-bibtex>=2.5.0; extra == "doc"
-Requires-Dist: sphinx-autodoc-typehints>=1.11.0; extra == "doc"
-Requires-Dist: sphinx-autobuild; extra == "doc"
-Requires-Dist: scanpydoc; extra == "doc"
-Requires-Dist: ipykernel; extra == "doc"
-Requires-Dist: ipython; extra == "doc"
-Requires-Dist: sphinx-copybutton; extra == "doc"
-Requires-Dist: sphinx-qt-documentation; extra == "doc"
-Requires-Dist: myst-nb>=1.0.0; extra == "doc"
-Requires-Dist: squidpy; extra == "doc"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.5; extra == "docs"
+Requires-Dist: sphinx-book-theme>=1.0.0; extra == "docs"
+Requires-Dist: myst-parser>=2.0.0; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex>=2.5.0; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=1.11.0; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: scanpydoc; extra == "docs"
+Requires-Dist: ipykernel; extra == "docs"
+Requires-Dist: ipython; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-qt-documentation; extra == "docs"
+Requires-Dist: myst-nb>=1.0.0; extra == "docs"
+Requires-Dist: squidpy; extra == "docs"
 Provides-Extra: readthedocs
 Requires-Dist: pydantic>2; extra == "readthedocs"
 Provides-Extra: pre
-Requires-Dist: spatialdata>=0.7.0dev0; extra == "pre"
+Requires-Dist: spatialdata>=0.7.3a1; extra == "pre"
 Provides-Extra: all
 Requires-Dist: napari[pyqt5]; extra == "all"
 Dynamic: license-file

napari_spatialdata-0.7.2/docs/notebooks/mibitof_analysis.ipynb

@@ -0,0 +1,250 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "# Analyse MIBI-TOF in Napari-SpatialData\n"
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "This tutorial shows how to load and analyse the MIBI-TOF dataset with the Napari-SpatialData plugin.\n"
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Import packages and data"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "There are two options to install napari-spatialdata:\n",
+    "\n",
+    "(1) Install [napari](https://napari.org/stable/tutorials/fundamentals/installation.html) \n",
+    "\n",
+    "(2a) Run `pip install napari-spatialdata`\n",
+    "\n",
+    "or, \n",
+    "\n",
+    "(2b) Clone this [repo](https://github.com/scverse/napari-spatialdata) and run `pip install -e .`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import matplotlib.pyplot as plt\n",
+    "from napari_spatialdata import Interactive\n",
+    "from spatialdata import SpatialData\n",
+    "import squidpy as sq\n",
+    "import scanpy as sc\n",
+    "\n",
+    "plt.rcParams['figure.figsize'] = (20, 20)"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Please download the MIBI-TOF data from https://spatialdata.scverse.org/en/stable/tutorials/notebooks/datasets/README.html and adjust the variable containing the location of the .zarr file.\n",
+    "\n",
+    "Information regarding data licensing and attribution for the dataset listed above is available at: https://github.com/scverse/spatialdata-notebooks/tree/main/datasets."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We will load the dataset from the filepath and create a {class}`spatialdata.SpatialData` object. We'll use this object with the class `Interactive` to visualise this dataset in Napari."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "FILE_PATH = \"tutorial_data/mibitof_data/data.zarr\"  # Path to the data file. Change if your data is stored in a different location.\n",
+    "sdata = SpatialData.read(FILE_PATH)"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "To make it easier to analyse our data, we will filter the SpatialData object by the coordinate system \"point8\"."
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "sdata = sdata.filter_by_coordinate_system(\"point8\")\n",
+    "adata = sdata.table"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "The `scikit-misc package` could be required for highly variable genes identification."
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Next, we will use the Scatter Widget offered by Napari SpatialData to visualize the UMAP coordinates.\n",
+    "\n",
+    "First, we instantiate the `Interactive` class with our {class}`spatialdata.SpatialData` object, and view it in Napari."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "interactive = Interactive(sdata)\n",
+    "interactive.run()"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plt.imshow(interactive.screenshot())\n",
+    "plt.axis('off')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "We select the coordinate system \"point8\" and load the elements \"point8_image\" and \"point8_labels\" into the viewer."
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "plt.imshow(interactive.screenshot())\n",
+    "plt.axis('off')"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "Select \"point8_labels\" in the list of layers. Then, we open the \"Scatter\" Widget by using the menu bar and going to Plugins > napari-spatialdata > Scatter. This loads the AnnData object associated with that layer into the \"Scatter\" Widget."
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "plt.imshow(interactive.screenshot())\n",
+    "plt.axis('off')"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Then, we can now pick specific x-axis, y-axis and color values to visualize in the scatterplot.\n",
+    "\n",
+    "In the example below, we're visualizing the UMAP (Uniform Manifold Approximation and Projection) coordinates of two different axes and coloring it by cell size."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "plt.imshow(interactive.screenshot())\n",
+    "plt.axis('off')"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "After plotting, it is possible to interactively select clusters and export it to AnnData.\n",
+    "\n",
+    "In the example below, we used the cursor to select a cluster on the left half of the scatterplot. We can export it into AnnData by clicking on the \"Annotate\" button."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "plt.imshow(interactive.screenshot())\n",
+    "plt.axis('off')"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "After exporting, we can now view the selected points with the View widget. Close the Scatter Widget and from the menu bar, go to Plugins > napari-spatialdata > View. You should be able to observe \"my_annotation\" under \"Observations:\". This is selected points we exported in the previous step."
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": "Double clicking on \"my_annotation\" loads it as a layer in the Napari viewer."
+  },
+  {
+   "attachments": {},
+   "cell_type": "code",
+   "metadata": {},
+   "source": [
+    "plt.imshow(interactive.screenshot())\n",
+    "plt.axis('off')"
+   ],
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

{napari_spatialdata-0.7.0 → napari_spatialdata-0.7.2}/docs/notebooks/nanostring_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": {},