Update demos and examples

.github/workflows/deploy.yml

@@ -81,3 +81,34 @@ jobs:
           password: ${{ secrets.PYPI_API_TOKEN }}
           skip-existing: true
           verbose: true
+
+  update_citation:
+      name: update CITATION
+      needs: [upload_all]
+      runs-on: ubuntu-latest
+      if: github.event_name == 'release' && success()
+      steps:
+        - name: Checkout
+          uses: actions/checkout@v4
+
+        - name: Download Zenodo CFF
+          run: |
+            curl -L https://zenodo.org/records/14199059/export/cff -o CITATION.cff
+            sed -i '/^abstract:/,/^authors:/d' CITATION.cff
+            sed -i '1iauthors:' CITATION.cff
+
+        - name: Update CITATION.cff
+          run: |
+            python -m pip install --upgrade pip
+            pip install cffconvert
+            cffconvert --output-format=cff-citation-file --output-path=CITATION.cff setup.py
+
+        - name: Commit CITATION.cff
+          env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          run: |
+            git config --global user.name "github-actions[bot]"
+            git config --global user.email "github-actions[bot]@users.noreply.github.com"
+            git add CITATION.cff
+            git diff-index --quiet HEAD || git commit -m "Update citation" --allow-empty
+            git push

.pre-commit-config.yaml

@@ -13,7 +13,6 @@ repos:
     -   id: check-yaml
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
-    -   id: check-added-large-files
     -   id: check-case-conflict
     -   id: check-merge-conflict
     -   id: check-symlinks

CITATION.cff

@@ -0,0 +1,21 @@
+authors:
+- affiliation: Institut Pasteur, Paris
+  family-names: Stephane Rigaud
+- affiliation: Data Science Center ScaDS.AI, Uni Leipzig
+  family-names: Robert Haase
+- affiliation: DFG cluster of excellence, Physics of Life, TU Dresden
+  family-names: Johannes Soltwedel
+- family-names: grahamross123
+- affiliation: Institut Pasteur
+  family-names: Marvin Albert
+- affiliation: Walter and Eliza Hall Institute of Medical Research
+  family-names: Pradeep Rajasekhar
+cff-version: 1.2.0
+date-released: '2024-11-21'
+doi: 10.5281/zenodo.14199059
+license:
+- cc-by-4.0
+repository-code: https://github.com/clEsperanto/pyclesperanto/tree/0.16.0
+title: 'clEsperanto/pyclesperanto: 0.16.0'
+type: software
+version: 0.16.0

README.md

@@ -1,7 +1,7 @@
 # py-clesperanto
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/pyclesperanto.svg)](https://anaconda.org/conda-forge/pyclesperanto)
 [![PyPI](https://img.shields.io/pypi/v/pyclesperanto.svg?color=green)](https://pypi.org/project/pyclesperanto)
-[![License](https://img.shields.io/pypi/l/pyclesperanto.svg?color=green)](https://github.com/clEsperanto/pyclesperanto/raw/main/LICENSE)
+[![License](https://img.shields.io/pypi/l/pyclesperanto.svg?color=green)](https://github.com/clEsperanto/pyclesperanto/blob/main/LICENSE)
 [![Development Status](https://img.shields.io/pypi/status/pyclesperanto.svg)](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha)
 [![Build](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build.yml/badge.svg)](https://github.com/clEsperanto/pyclesperanto/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/clesperanto/pyclesperanto/branch/main/graph/badge.svg)](https://codecov.io/gh/clesperanto/pyclesperanto)
@@ -37,10 +37,12 @@ mamba activate cle
 mamba install -c conda-forge pyclesperanto
 ```
 
-__MacOS__ users may need to install the following package: `mamba install -c conda-forge ocl_icd_wrapper_apple`
-__Linux__ users may need to install the following package: `mamba install -c conda-forge ocl-icd-system`
+> [!WARNING]
+> __MacOS__ users may need to install the following package: `mamba install -c conda-forge ocl_icd_wrapper_apple`
+> __Linux__ users may need to install the following package: `mamba install -c conda-forge ocl-icd-system`
 
-**NOTE:** It is also possible to install pyclesperanto with `pip`
+> [!NOTE]
+> pyclesperanto package is also available on `PyPI` and can be install with the command `pip install pyclesperanto`
 
 ## Troubleshooting: Graphics cards drivers
 
@@ -69,7 +71,7 @@ from skimage.io import imread, imsave
 device = cle.select_device()
 print("Used GPU: ", device)
 
-image = imread("https://samples.fiji.sc/blobs.png")
+image = imread("https://samples.fiji.sc/blobs.png?raw=true")
 
 # push image to device memory
 input_image = cle.push(image)
@@ -91,73 +93,68 @@ output_image = cle.pull(labeled)
 imsave("result.tif", output_image)
 ```
 
-## __Examples & Demos gallery__
+## __Examples & Demos__
 
 <table border="0">
-
 <tr><td>
-<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/labeled_blobs.png" width="300"/>
+<img src="https://github.com/clEsperanto/pyclesperanto/blob/main/demos/images/select_device.png?raw=true" width="300"/>
 </td><td>
 
-[Segment + analyze blobs](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/count_blobs.ipynb)
+* [Select and Manage devices](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/api/select_devices.ipynb)
+* [Host-Device memory management](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/api/push_pull_create.ipynb)
+* [Process an image](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/api/process_image.ipynb)
 
 </td></tr>
 
 <tr><td>
-<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/cell_segmentation.png" width="300"/>
+<img src="https://github.com/clEsperanto/pyclesperanto/blob/main/demos/images/crop_and_paste_images.png?raw=true" width="300"/>
 </td><td>
 
-[Cell segmentation + Voronoi labeling](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/cell_segmentation.ipynb)
+* [Crop, Flip, Paste arrays](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/crop_flip_paste.ipynb)
+* [Math operations](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/arithmetic_operators.ipynb)
+* [Matrix operations](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/matrices_operations.ipynb)
+* [Vector and Matrix operations](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/vector_and_matrices_operations.ipynb)
+* [Inspecting 3D image](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/basics/inspecting_3d_images.ipynb)
 
 </td></tr>
 
+
 <tr><td>
-<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/image_filtering.png" width="300"/>
+<img src="https://github.com/clEsperanto/pyclesperanto/blob/main/demos/images/segmentation_3d.png?raw=true" width="300"/>
 </td><td>
 
-[3D image filtering](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/image_filtering.ipynb)
+* [Segment and analyse blosb](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/analyse_blobs.ipynb)
+* [Segment cell based on membrane](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/membrane_segmentation_2d.ipynb)
+* [Cell segmentation in 3D](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/Segmentation_3D.ipynb)
+* [Voronoi_Otsu_labeling](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/voronoi_otsu_labeling.ipynb)
 
 </td></tr>
 
 
 <tr><td>
-<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/find_local_maxima.png" width="300"/>
+<img src="https://github.com/clEsperanto/pyclesperanto/blob/main/demos/images/affine_transforms.png?raw=true" width="300"/>
 </td><td>
 
-[Find local maxima](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/find_local_maxima.ipynb)
+* [Edge detection](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/edge_detection_and_enhancement.ipynb)
+* [Parametric maps](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/parametric_maps.ipynb)
+* [Rotation, scaling, translation, and affine transform](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/affine_transforms.ipynb)
+<!-- * [Morphomathic operations](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/morphomath_operation.ipynb)   -->
 
 </td></tr>
 
-<tr><td>
-<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/tribolium3d_segmentation.png" width="300"/>
-</td><td>
-
-[3D Tribolium nuclei segmentation](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/process_tribolium.ipynb)
-
-</td></tr>
 
 <tr><td>
-<img src="https://github.com/clEsperanto/pyclesperanto/raw/main/demos/images/explore_API.png" width="300"/>
+<img src="https://github.com/clEsperanto/pyclesperanto/blob/main/demos/images/multi-device-tiling.png?raw=true" width="300"/>
 </td><td>
 
-[Explore application programming interface (API)](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/explore_API.ipynb)
+* [Multi-device tile processing](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/example/multi-gpu_tile_processing_with_dask.ipynb)
+* [Bia-Bob](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/interoperability/multi-biabob-example.ipynb)
 
 </td></tr>
 
-<!--
-<tr><td>
-
-<img src="https://raw.githubusercontent.com/clEsperanto/pyclesperanto/main/demos/images/multi-gpu.png" width="300"/>
-
-</td><td>
-
-[Multi-GPU developer_docs](https://github.com/clEsperanto/pyclesperanto/tree/main/demos/multi_gpu_demo.ipynb)
-
-</td></tr>
--->
 </table>
 
-More usage and example can be found as notebooks in the [demos](./user_docs) folder
+More usage and example can be found as notebooks in the [demos](https://github.com/clEsperanto/pyclesperanto/tree/main/demos) folder. As well as in the [documentation](https://clesperanto.github.io/pyclesperanto/).
 
 # __Contributing and Feedback__