chore: migrate to uv for reproducibility (#12)

Author: bathienle

.gitignore

@@ -6,4 +6,7 @@ local-outputs/
 
 # Archives
 *.tar
-*.zip
+*.zip
+
+# venv
+.venv

.python-version

@@ -0,0 +1 @@
+3.10

Dockerfile

@@ -1,10 +1,25 @@
 FROM python:3.10.14-slim-bullseye
 
+COPY --from=ghcr.io/astral-sh/uv:0.9.9 /uv /uvx /bin/
+
+ENV PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    UV_COMPILE_BYTECODE=1 \
+    UV_LINK_MODE=copy \
+    UV_PROJECT_ENVIRONMENT=/usr/local
+
 WORKDIR /app
-COPY build/requirements.txt /app/requirements.txt
-RUN pip install -r /app/requirements.txt
 
+RUN --mount=type=cache,target=/root/.cache/uv \
+    --mount=type=bind,source=uv.lock,target=uv.lock \
+    --mount=type=bind,source=pyproject.toml,target=pyproject.toml \
+    uv sync --locked --no-install-project
+
+COPY ./pyproject.toml ./uv.lock /app/
 COPY ./models/ /models
-COPY scripts/run.py /app/run.py
+COPY ./scripts/run.py /app/run.py
+
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --locked
 
 ENTRYPOINT ["python", "run.py"]

README.md

@@ -1,7 +1,5 @@
 # Stardist Nuclei Segmentation
 
-
-
 ## How to run it manually ?
 
 ### Get the docker image
@@ -11,11 +9,11 @@
 Either from an existing task bundle
 
 ```bash
-$> unzip com.cytomine.nuclei.segmentation.stardist-0.1.0.zip
-Archive:  ./com.cytomine.nuclei-segmentation.stardist-0.1.0.zip
-  inflating: com.cytomine.nuclei.segmentation.stardist-0.1.0.tar
+$> unzip com.cytomine.nuclei.segmentation.stardist-0.2.0.zip
+Archive:  ./com.cytomine.nuclei-segmentation.stardist-0.2.0.zip
+  inflating: com.cytomine.nuclei.segmentation.stardist-0.2.0.tar
   inflating: descriptor.yml
-$> docker image load --input com.cytomine.nuclei.segmentation.stardist-0.1.0.tar
+$> docker image load --input com.cytomine.nuclei.segmentation.stardist-0.2.0.tar
 0949773899cf: Loading layer [==================================================>]   84.2MB/84.2MB
 95c8f57bd29d: Loading layer [==================================================>]  3.405MB/3.405MB
 95ce64f868d0: Loading layer [==================================================>]  30.56MB/30.56MB
@@ -26,22 +24,22 @@ 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:0.1.0
+Loaded image: com/cytomine/nuclei-segmentation/stardist:0.2.0
 
 ```
 
 ### Build the docker image yourself
 
 ```
-docker build -t com/cytomine/nuclei-segmentation/stardist:0.1.0 .
+docker build -t com/cytomine/nuclei-segmentation/stardist:0.2.0 .
 ```
 
 ## 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:0.1.0
+docker run -v ./examples/inputs:/inputs -v ./local-outputs:/outputs --rm -it com/cytomine/nuclei-segmentation/stardist:0.2.0
 ```
 
 You can then explore the results in the `./local-outputs` directory.
@@ -51,10 +49,10 @@ 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-0.1.0.tar com/cytomine/nuclei-segmentation/stardist:0.1.0 
+docker save -o com.cytomine.nuclei.segmentation.stardist-0.2.0.tar com/cytomine/nuclei-segmentation/stardist:0.2.0 
 ```
 3. Build the bundle
 ```bash
-zip com.cytomine.nuclei.segmentation.stardist-0.1.0.zip descriptor.yml com.cytomine.nuclei.segmentation.stardist-0.1.0.tar
+zip com.cytomine.nuclei.segmentation.stardist-0.2.0.zip descriptor.yml com.cytomine.nuclei.segmentation.stardist-0.2.0.tar
 ```
 4. Upload the bundle on Cytomine

build/requirements.txt

@@ -1,6 +1,6 @@
 name: StarDist Nuclei Segmentation
 name_short: stardist
-version: 0.1.1
+version: 0.2.0
 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-0.1.1.tar
+    file: /com.cytomine.nuclei.segmentation.stardist-0.2.0.tar
 
 inputs:
   image:

descriptor.yml

@@ -0,0 +1,15 @@
+[project]
+name = "task-stardist"
+version = "0.2.0"
+description = "Integration of Stardist algorithm as a Cytomine task"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+  "csbdeep==0.8.0",
+  "geojson==3.1.0",
+  "imageio==2.34.1",
+  "numpy==1.26.4",
+  "pyyaml==6.0.1",
+  "stardist==0.9.1",
+  "tensorflow-cpu==2.16.1",
+]