chore: bump python from 3.10 to 3.11 (#26)

Author: bathienle

.python-version

@@ -1 +1 @@
-3.10
+3.11

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.10.14-slim-bullseye
+FROM python:3.11.14-slim-bookworm
 
 COPY --from=ghcr.io/astral-sh/uv:0.9.9 /uv /uvx /bin/
 

README.md

@@ -11,11 +11,11 @@ This repository relies on the library https://github.com/stardist/stardist and p
 Either from an existing task bundle
 
 ```bash
-$> unzip com.cytomine.nuclei.segmentation.stardist-0.2.1.zip
-Archive:  ./com.cytomine.nuclei-segmentation.stardist-0.2.1.zip
-  inflating: com.cytomine.nuclei.segmentation.stardist-0.2.1.tar
+$> unzip com.cytomine.nuclei.segmentation.stardist-0.3.0.zip
+Archive:  ./com.cytomine.nuclei-segmentation.stardist-0.3.0.zip
+  inflating: com.cytomine.nuclei.segmentation.stardist-0.3.0.tar
   inflating: descriptor.yml
-$> docker image load --input com.cytomine.nuclei.segmentation.stardist-0.2.1.tar
+$> docker image load --input com.cytomine.nuclei.segmentation.stardist-0.3.0.tar
 0949773899cf: Loading layer [==================================================>]   84.2MB/84.2MB
 95c8f57bd29d: Loading layer [==================================================>]  3.405MB/3.405MB
 95ce64f868d0: Loading layer [==================================================>]  30.56MB/30.56MB
@@ -26,22 +26,21 @@ c70e485b159b: Loading layer [==================================================>
 84cc4f8d1ed4: Loading layer [==================================================>]  2.087GB/2.087GB
 e05ca7daf251: Loading layer [==================================================>]   5.78MB/5.78MB
 987f4b5a221e: Loading layer [==================================================>]  6.656kB/6.656kB
-Loaded image: com/cytomine/nuclei-segmentation/stardist:0.2.1
-
+Loaded image: com/cytomine/nuclei-segmentation/stardist:0.3.0
 ```
 
 ### Build the docker image yourself
 
 ```
-docker build -t com/cytomine/nuclei-segmentation/stardist:0.2.1 .
+docker build -t com/cytomine/nuclei-segmentation/stardist:0.3.0 .
 ```
 
 ## Run on data
 
 From this repository, run :
 
 ```bash
-docker run -v ./examples/inputs:/inputs -v ./local-outputs:/outputs --rm -it com/cytomine/nuclei-segmentation/stardist:0.2.1
+docker run -v ./examples/inputs:/inputs -v ./local-outputs:/outputs --rm -it com/cytomine/nuclei-segmentation/stardist:0.3.0
 ```
 
 You can then explore the results in the `./local-outputs` directory.
@@ -51,10 +50,10 @@ You can then explore the results in the `./local-outputs` directory.
 1. Build the docker image as described above
 2. save it as `tar` archive
 ```bash
-docker save -o com.cytomine.nuclei.segmentation.stardist-0.2.1.tar com/cytomine/nuclei-segmentation/stardist:0.2.1
+docker save -o com.cytomine.nuclei.segmentation.stardist-0.3.0.tar com/cytomine/nuclei-segmentation/stardist:0.3.0
 ```
 3. Build the bundle
 ```bash
-zip com.cytomine.nuclei.segmentation.stardist-0.2.1.zip descriptor.yml com.cytomine.nuclei.segmentation.stardist-0.2.1.tar
+zip com.cytomine.nuclei.segmentation.stardist-0.3.0.zip descriptor.yml com.cytomine.nuclei.segmentation.stardist-0.3.0.tar
 ```
 4. Upload the bundle on Cytomine

descriptor.yml

@@ -1,6 +1,6 @@
 name: StarDist Nuclei Segmentation
 name_short: stardist
-version: 0.2.1
+version: 0.3.0
 namespace: com.cytomine.nuclei.segmentation.stardist
 $schema: https://raw.githubusercontent.com/cytomine/cytomine/refs/heads/main/app-engine/src/main/resources/schemas/tasks/task.v0.json
 
@@ -20,7 +20,7 @@ configuration:
   input_folder: /inputs
   output_folder: /outputs
   image:
-    file: /com.cytomine.nuclei.segmentation.stardist-0.2.1.tar
+    file: /com.cytomine.nuclei.segmentation.stardist-0.3.0.tar
 
 inputs:
   image:

pyproject.toml

@@ -1,9 +1,9 @@
 [project]
 name = "task-stardist"
-version = "0.2.1"
+version = "0.3.0"
 description = "Integration of Stardist algorithm as a Cytomine task"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
   "csbdeep==0.8.0",
   "geojson==3.1.0",