Switch to mirroring water supply runtime

runtime/Dockerfile

@@ -1,43 +1,31 @@
-FROM continuumio/miniconda3:23.10.0-1
+FROM mambaorg/micromamba:bookworm-slim
 
-# install OS dependencies
 USER root
-ENV DEBIAN_FRONTEND=noninteractive LANG=C.UTF-8 LC_ALL=C.UTF-8
-RUN apt update --fix-missing && \
-    apt install -y --no-install-recommends \
-    software-properties-common pkg-config build-essential unzip git gcc g++ && \
-    apt autoremove -y && \
-    apt clean && \
-    rm -rf /var/lib/apt/lists/* && \
-    rm -rf /usr/local/src/*
-
-# create a limited user
-ARG NEW_USER=appuser
-RUN groupadd -g 999 $NEW_USER && \
-    useradd -ms /bin/bash -r -u 1000 -g $NEW_USER $NEW_USER
-
-# create the working directory with the entrypoint
-RUN mkdir /submission && \
-    chown -R $NEW_USER /submission
-RUN mkdir /data && \
-    chown -R $NEW_USER /data
-USER $NEW_USER
-
-# create conda environment
-COPY environment.yml /tmp/
-RUN conda env create -n condaenv -f /tmp/environment.yml && \
-    conda clean --all --yes
-
-# copy the tests into the container
-COPY ./tests /tests
-
-# install the entrypoint as root
-USER root
-COPY ./entrypoint.sh /entrypoint.sh
-COPY ./validate.py /validate.py
-RUN chmod +x /entrypoint.sh
-USER $NEW_USER
-
-# Execute the entrypoint.sh script inside the container when we do docker run
-WORKDIR /submission
-CMD ["/bin/bash", "/entrypoint.sh"]
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    LANG=C.UTF-8  \
+    LC_ALL=C.UTF-8 \
+    PYTHONUNBUFFERED=1 \
+    SHELL=/bin/bash
+
+COPY apt.txt apt.txt
+RUN apt-get update --fix-missing \
+    && apt-get install -y apt-utils 2> /dev/null \
+    && xargs -a apt.txt apt-get install -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /apt.txt
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yml
+RUN micromamba install --name base --yes --file /tmp/env.yml && \
+    micromamba clean --all --force-pkgs-dirs --yes
+
+RUN mkdir -p /code_execution/submission
+RUN chown -R ${MAMBA_USER}:${MAMBA_USER} /code_execution
+
+COPY entrypoint.sh /entrypoint.sh
+
+WORKDIR /code_execution
+USER ${MAMBA_USER}
+COPY runtime/tests /code_execution/tests
+
+CMD ["bash", "/entrypoint.sh"]

runtime/apt.txt

@@ -0,0 +1,5 @@
+curl
+libxml2
+tzdata
+wget
+zip

runtime/entrypoint.sh

@@ -1,52 +1,30 @@
 #!/bin/bash
-set -e
-
-exit_code=0
-
-run_user_code() {
-    if [ -f "main.sh" ]
-    then
-        echo "Running main.sh ..."
-        sh main.sh
-    else
-        echo "ERROR: Could not find main.sh in submission.zip"
-        exit_code=1
-    fi
-}
 
-split () {
-  echo "********************************************************************************"
-}
+set -euxo pipefail
 
+main () {
+    expected_filename=main.sh
 
-{
-    sleep 10
-    source activate condaenv
-    cd /submission
+    cd /code_execution
 
-    echo "Unpacking submission..."
-    unzip -o /submission/submission.zip -d ./
-    python /validate.py pre_create .
+    submission_files=$(zip -sf ./submission/submission.zip)
+    if ! grep -q ${expected_filename}<<<$submission_files; then
+        echo "Submission zip archive must include $expected_filename"
+    return 1
+    fi
 
-    run_user_code
-    python /validate.py post_query .
+    echo Unpacking submission
+    unzip ./submission/submission.zip -d ./src
 
-    echo "Exporting submission.csv result..."
+    echo Printing submission contents
+    find src
 
-    # Valid scripts must create a "submission.csv" file within the same directory as main
-    if [ -f "submission.csv" ]
-    then
-        echo "Script completed its run."
-    else
-        echo "ERROR: Script did not produce a submission.csv file in the main directory."
-        exit_code=1
-    fi
+    LOGURU_LEVEL=INFO sh main.sh
+}
+
+main |& tee "/code_execution/submission/log.txt"
+exit_code=${PIPESTATUS[0]}
 
-    echo "Running acceptance tests..."
-    # conda run -n condaenv --no-capture-output pytest --verbose --rootdir=. /tests/test_submission.py
-    echo "================ END ================"
-} |& tee "/submission/log.txt"
+cp /code_execution/submission/log.txt /tmp/log
 
-# copy for additional log uses
-cp /submission/log.txt /tmp/log
-exit $exit_code
+exit $exit_code

runtime/environment.yml

@@ -1,11 +1,23 @@
-name: condaenv
+name: spacecraftpose
 channels:
   - conda-forge
 dependencies:
-  - python=3.11.6
-  - numpy
-  - pandas
-  - pip
-  - pip:
-    - loguru
-    - tqdm
+  - keras=2.13
+  - lightgbm=4.1
+  - loguru=0.7
+  - geopandas=0.14
+  - numba=0.58
+  - numpy=1.26
+  - pandas=2.1
+  - pip=23.3
+  - pydantic=1.10
+  - pytest=7.4
+  - python=3.10
+  - pytorch=1.*=cpu*
+  - pytorch-lightning
+  - scikit-learn=1.3
+  - scipy=1.11
+  - statsmodels=0.14
+  - tensorflow=2.13.*=cpu*
+  - tqdm=4.66
+  - xgboost=1.7.*=cpu*

runtime/tests/test_packages.py

@@ -0,0 +1,19 @@
+import importlib
+
+import pytest
+
+packages = [
+    "keras",
+    "numpy",
+    "pandas",
+    "scipy",
+    "sklearn",
+    "tensorflow",
+    "torch",
+]
+
+
+@pytest.mark.parametrize("package_name", packages, ids=packages)
+def test_import(package_name):
+    """Test that certain dependencies are importable."""
+    importlib.import_module(package_name)

runtime/tests/test_submission.py

@@ -1,10 +1,13 @@
+import os
+
 from pathlib import Path
 
-from loguru import logger
 import pytest
 
-SUBMISSION_PATH = Path("/submission/submission.csv")
+SUBMISSION_PATH = Path("/code_execution/submission/submission.csv")
+CHECK_SUBMISSION = os.environ.get("CHECK_SUBMISSION", "false") == "true"
 
 
+@pytest.mark.skipif(not CHECK_SUBMISSION, reason="Not checking submission yet")
 def test_submission_exists():
     assert SUBMISSION_PATH.exists()