Upgrade Python version and minor fixes (#75)

* Upgrade supported Python versions (drop 3.10, include 3.12, 3.13)

* Host of small fixes to let tests pass on a new clone and MacOS

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ on:
       - published
 
 env:
-  MINIMUM_PYTHON_VERSION: '3.10'
+  MINIMUM_PYTHON_VERSION: '3.11'
 
 jobs:
   precommit:
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

grand_challenge_forge/generation_utils.py

@@ -136,7 +136,7 @@ def copy_and_render(
         # Create directories in the output path
         current_output_dir.mkdir(parents=True, exist_ok=True)
 
-        for file in files:
+        for file in sorted(files):
             source_file = root / file
             output_file = current_output_dir / file
 

grand_challenge_forge/partials/docker-bash-scripts/do_test_run.sh.j2

@@ -24,6 +24,7 @@ cleanup() {
     # Ensure permissions are set correctly on the output
     # This allows the host user (e.g. you) to access and handle these files
     docker run --rm \
+      --platform=linux/amd64 \
       --quiet \
       --volume "$OUTPUT_DIR":/output \
       --entrypoint /bin/sh \

tests/resources/partials/disallowed_symlink_include/1_initial.j2

@@ -0,0 +1 @@
+{% include 'sym_template.j2' %}

tests/test_evaluate_helpers.py

@@ -56,10 +56,10 @@ def forever_process(*_):
         time.sleep(1)
 
 
-def stop_children(process, interval):
+def stop_children(process_pid, interval):
     stopped = False
     while not stopped:
-        process = psutil.Process(process.pid)
+        process = psutil.Process(process_pid)
         children = process.children(recursive=True)
         if children:
             for child in children:
@@ -110,7 +110,9 @@ def test_prediction_processing_catching_killing_of_child_processes():
     def add_child_terminator(*args, **kwargs):
         process = _start_pool_worker(*args, **kwargs)
         nonlocal child_stopper
-        child_stopper = Process(target=partial(stop_children, process, 0.5))
+        child_stopper = Process(
+            target=partial(stop_children, process.pid, 0.5)
+        )
         child_stopper.start()  # Hasta la vista, baby
         return process
 
@@ -121,5 +123,5 @@ def add_child_terminator(*args, **kwargs):
                     fn=forever_process, predictions=predictions
                 )
     finally:
-        if child_stopper:
+        if child_stopper and child_stopper.is_alive():
             child_stopper.terminate()