Add common docker runtime arguments (#327)

.github/workflows/ci.yml

@@ -5,6 +5,10 @@ on: [push, pull_request]
 env:
   PYTHON_VERSION: '3.9'
 
+concurrency:
+  group: ${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
 jobs:
 
   precommit:

HISTORY.rst

@@ -2,6 +2,11 @@
 History
 =======
 
+0.3.1 (2022-01-24)
+------------------
+
+* Added parameters to docker run commands to better reflect how containers are executed
+
 0.3.0 (2021-10-08)
 ------------------
 

evalutils/__version__.py

@@ -1,3 +1,3 @@
-VERSION = (0, 3, 0)
+VERSION = (0, 3, 1)
 
 __version__ = ".".join(map(str, VERSION))

evalutils/evalutils.py

@@ -685,8 +685,8 @@ def score_aggregates(self):
 
         totals = self._case_results.sum()
 
-        for s in totals.index:
-            aggregate_results[s]["sum"] = totals[s]
+        for s in ["true_positives", "false_positives", "false_negatives"]:
+            aggregate_results[s]["sum"] = int(totals[s])
 
         tp = aggregate_results["true_positives"]["sum"]
         fp = aggregate_results["false_positives"]["sum"]

evalutils/templates/algorithm/{{ cookiecutter.package_name }}/Dockerfile

@@ -29,8 +29,3 @@ RUN python -m pip install --user -rrequirements.txt
 COPY --chown=algorithm:algorithm process.py /opt/algorithm/
 
 ENTRYPOINT python -m process $0 $@
-
-## ALGORITHM LABELS ##
-
-# These labels are required
-LABEL nl.diagnijmegen.rse.algorithm.name={{ cookiecutter.algorithm_name }}

evalutils/templates/algorithm/{{ cookiecutter.package_name }}/test.sh

@@ -5,10 +5,19 @@ SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
 ./build.sh
 
 VOLUME_SUFFIX=$(dd if=/dev/urandom bs=32 count=1 | md5sum | cut --delimiter=' ' --fields=1)
+MEM_LIMIT="4g"  # Maximum is currently 30g, configurable in your algorithm image settings on grand challenge
 
 docker volume create {{ cookiecutter.package_name|lower }}-output-$VOLUME_SUFFIX
 
+# Do not change any of the parameters to docker run, these are fixed
 docker run --rm \
+        --memory="${MEM_LIMIT}" \
+        --memory-swap="${MEM_LIMIT}" \
+        --network="none" \
+        --cap-drop="ALL" \
+        --security-opt="no-new-privileges" \
+        --shm-size="128m" \
+        --pids-limit="256" \
         -v $SCRIPTPATH/test/:/input/ \
         -v {{ cookiecutter.package_name|lower }}-output-$VOLUME_SUFFIX:/output/ \
         {{ cookiecutter.package_name|lower }}

evalutils/templates/evaluation/{{ cookiecutter.package_name }}/test.sh

@@ -8,8 +8,15 @@ VOLUME_SUFFIX=$(dd if=/dev/urandom bs=32 count=1 | md5sum | cut --delimiter=' '
 
 docker volume create {{ cookiecutter.package_name|lower }}-output-$VOLUME_SUFFIX
 
+# Do not change any of the parameters to docker run, these are fixed
 docker run --rm \
-        --memory=4g \
+        --memory="4g" \
+        --memory-swap="4g" \
+        --network="none" \
+        --cap-drop="ALL" \
+        --security-opt="no-new-privileges" \
+        --shm-size="128m" \
+        --pids-limit="256" \
         -v $SCRIPTPATH/test/:/input/ \
         -v {{ cookiecutter.package_name|lower }}-output-$VOLUME_SUFFIX:/output/ \
         {{ cookiecutter.package_name|lower }}

pytest.ini

@@ -6,4 +6,5 @@ markers =
     slow
 filterwarnings =
     error
-    ignore:.*The default dtype for empty Series will be 'object' instead of 'float64' in a future version.*:DeprecationWarning:pandas
+    ignore:.*The default dtype for empty Series will be 'object' instead of 'float64' in a future version.*
+    ignore:.*Use pandas.concat instead\.:FutureWarning