update python and pip package versions

Author: adrianthu

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9-slim
+FROM python:3.12-slim
 ARG task_type
 
 ENV TASK_TYPE=$task_type
@@ -18,7 +18,7 @@ ENV PATH="/home/algorithm/.local/bin:${PATH}"
 RUN python -m pip install --user -U pip
 
 COPY --chown=algorithm:algorithm requirements.txt /opt/algorithm/
-RUN python -m pip install --user -rrequirements.txt
+RUN python -m pip install --user -r requirements.txt
 
 COPY --chown=algorithm:algorithm .env /opt/algorithm/
 COPY --chown=algorithm:algorithm process.py /opt/algorithm/

README.md

@@ -80,7 +80,7 @@ With this template, you can submit your algorithm (with minimal effort) to the t
 
 ### Dependencies
 
-For building the algorithm for submission, the user should have access to Docker [https://docs.docker.com/] on their system. (Note: Submissions to the test phase are allowed only with docker containers). This algorithm template was tested using Ubuntu 20.04.6 and Docker 23.0.4.
+For building the algorithm for submission, the user should have access to Docker [https://docs.docker.com/] on their system. (Note: Submissions to the test phase are allowed only with docker containers). This algorithm template was tested using Ubuntu 24.04 and Docker 28.1.1.
 
 Please make sure to list the requirements for your algorithm in the `requirements.txt` file as this will be picked up when building the docker container. 
 

requirements.txt

@@ -1,8 +1,7 @@
-
 evalutils==0.3.1
 SimpleITK
-scikit-learn==0.24.2
-# torch # Uncomment if you want to use PyTorch
+scikit-learn
+#torch # Uncomment if you want to use PyTorch
 numpy
-scipy==1.6.3
-python-dotenv==1.0.0
+scipy
+python-dotenv

test.sh

@@ -24,12 +24,12 @@ docker run --rm \
 
 docker run --rm \
         -v synthrad_algorithm-output-$VOLUME_SUFFIX:/output/ \
-        python:3.9-slim cat /output/results.json | python -m json.tool
+        python:3.12-slim cat /output/results.json | python3 -m json.tool
 
 docker run --rm \
         -v $SCRIPTPATH/test:/input \
         -v synthrad_algorithm-output-$VOLUME_SUFFIX:/output/ \
-        python:3.9-slim python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
+        python:3.12-slim python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
 
 if [ $? -eq 0 ]; then
     echo "Tests successfully passed..."

test_gpu.sh

@@ -25,12 +25,12 @@ docker run --rm \
 
 docker run --rm \
         -v synthrad_algorithm-output-$VOLUME_SUFFIX:/output/ \
-        python:3.9-slim cat /output/results.json | python -m json.tool
+        python:3.12-slim cat /output/results.json | python3 -m json.tool
 
 docker run --rm \
         -v $SCRIPTPATH/test:/input \
         -v synthrad_algorithm-output-$VOLUME_SUFFIX:/output/ \
-        python:3.9-slim python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
+        python:3.12-slim python -c "import json, sys; f1 = json.load(open('/output/results.json')); f2 = json.load(open('/input/expected_output.json')); sys.exit(f1 != f2);"
 
 if [ $? -eq 0 ]; then
     echo "Tests successfully passed..."