Finish porting all tests to GitHub Actions

This new port now tries to *not* rely too much on GitHub Actions
conventions (which are not that many, anyway), and also splits the big
test.sh script we used with Travis into smaller scripts in a new .ci
directory that can be invoked separately, therefore allowing us to model
each individual test as a different step on the GitHub Actions workflow.

Signed-off-by: Rodrigo Tobar <[email protected]>

.ci/check_hdf5_docs.sh

@@ -0,0 +1,18 @@
+# Generate the HDF5 output documentation and check it's up to date
+# otherwise tell the user how to update it
+hdf5_file="$1"
+rst_file="$2"
+hdf5_file_basename=`basename "${hdf5_file}"`
+full_rst_file="doc/hdf5_properties/${rst_file}"
+
+scripts/properties_as_list.sh "${TEST_OUTPUTS_DIR}/${TEST_SIM_NAME}/${hdf5_file}" > props.rst
+_diff="`diff -Naur "${full_rst_file}" props.rst`"
+if [ -n "${_diff}" ]; then
+	echo "\nThe file ${full_rst_file} is out of date. This probably means that you added a new\n" \
+	"dataset to shark's output, but forgot to update the corresponding documentation.\n" \
+	"The full difference follows:\n\n${_diff}\n\n" \
+	"Please run the script/properties_as_lish.sh script against a ${hdf5_file_basename} file\n" \
+	"to re-generate its documentation, then commit your changes. For example:\n\n" \
+	"scripts/properties_as_list.sh my-output/model/199/0/${hdf5_file_basename} > ${full_rst_file}" >&2
+	exit 1
+fi

.ci/compare_galaxies.sh

@@ -0,0 +1,9 @@
+reference_model_name=$1
+shift
+this_model_name=$1
+shift
+
+python scripts/compare_galaxies.py -m \
+  "${TEST_OUTPUTS_DIR}/${TEST_SIM_NAME}/${reference_model_name}/199/0/galaxies.hdf5" \
+  "${TEST_OUTPUTS_DIR}/${TEST_SIM_NAME}/${this_model_name}/199/0/galaxies.hdf5" \
+  $@

.ci/run_shark.sh

@@ -0,0 +1,10 @@
+model_name=$1
+shift
+
+${CI_BUILD_DIR}/shark ci-test.cfg \
+    -o execution.output_bh_histories=true -o execution.snapshots_bh_histories=199 \
+    -o simulation.redshift_file=${TEST_INPUTS_DIR}/redshifts.txt \
+    -o simulation.tree_files_prefix=${TEST_INPUTS_DIR}/tree_199 \
+    -o simulation.sim_name=${TEST_SIM_NAME} \
+    -o execution.name_model=$model_name \
+    $@

.github/workflows/build-and-test.yaml

@@ -10,31 +10,87 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
+    env:
+      CI_BUILD_DIR: build
+      TEST_INPUTS_DIR: inputs
+      TEST_OUTPUTS_DIR: outputs
+      TEST_SIM_NAME: mini-SURFS
 
     steps:
       - uses: actions/checkout@v3
         with:
           submodules: true
 
-      - name: Install dependencies
+      - name: Install system dependencies (Linux)
         if: ${{ matrix.os == 'ubuntu-latest' }}
         run: |
-          sudo apt install libhdf5-dev hdf5-tools libboost-filesystem-dev libboost-program-options-dev libboost-log-dev cxxtest libgsl-dev
+          sudo apt install ninja-build libhdf5-dev hdf5-tools libboost-filesystem-dev libboost-program-options-dev libboost-log-dev cxxtest libgsl-dev
 
-      - name: Install dependencies
+      - name: Install system dependencies (MacOS)
         if: ${{ matrix.os == 'macos-latest' }}
         run: |
-          brew install hdf5 boost cxxtest gsl
+          brew install ninja hdf5 boost cxxtest gsl
+
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Python dependencies
+        run: pip install matplotlib h5py scipy
 
       - name: Configure
         # Leaving Werror out for now because there *are* errors
         # and I don't know what the proper fix is.
-        run: cmake -B build/ -DSHARK_TEST=ON -DCMAKE_CXX_FLAGS="-Wall" #-Werror
+        run: cmake -B ${CI_BUILD_DIR} -G Ninja -DSHARK_TEST=ON -DCMAKE_CXX_FLAGS="-Wall" #-Werror
 
       - name: Build
-        run: cmake --build build/
+        run: cmake --build ${CI_BUILD_DIR}
 
       - name: Run unit tests
         run: |
-          cd build
+          cd ${CI_BUILD_DIR}
           ctest --output-on-failure
+
+      - name: Prepare test dataset
+        run: |
+          mkdir -p ${TEST_INPUTS_DIR}
+          curl -L -o ${TEST_INPUTS_DIR}/redshifts.txt 'https://docs.google.com/uc?export=download&id=1xvNmJB_KmoBHuQz-QzdPnY0HFs7smkUB'
+          curl -L -o ${TEST_INPUTS_DIR}/tree_199.0.hdf5 'https://docs.google.com/uc?export=download&id=1JDK8ak13bEhzg9H9xt0uE8Fh_2LD3KpZ'
+          sed "
+            s|output_directory.*|output_directory = ${TEST_OUTPUTS_DIR}|
+            s|redshift_file.*|redshift_file = ${TEST_INPUTS_DIR}/redshifts.txt|
+            s|tree_files_prefix.*|tree_files_prefix = ${TEST_INPUTS_DIR}/tree_199|
+            s|sim_name.*|sim_name = ${TEST_SIM_NAME}|
+          " sample.cfg > ci-test.cfg
+
+      - name: Run shark with fixed seed
+        run: .ci/run_shark.sh my_model -o execution.seed=123456
+
+      - name: Check output properties' documentation
+        run: |
+          .ci/check_hdf5_docs.sh my_model/199/0/galaxies.hdf5 galaxies.rst
+          .ci/check_hdf5_docs.sh my_model/156/0/star_formation_histories.hdf5 star_formation_histories.rst
+          .ci/check_hdf5_docs.sh my_model/199/0/black_hole_histories.hdf5 black_hole_histories.rst
+
+      - name: Check fixed seed is reproducible
+        run: |
+          .ci/run_shark.sh my_model_same_seed -o execution.seed=123456
+          .ci/compare_galaxies.sh my_model my_model_same_seed
+
+      - name: Check fixed seed is reproducible when multithreaded
+        run: |
+          # "-t 0" lets shark use the maximum number of OpenMP threads,
+          # which OpenMP implementations usually constrain to the available hardware
+          .ci/run_shark.sh my_model_same_seed_parallel -o execution.seed=123456 -t 0
+          .ci/compare_galaxies.sh my_model my_model_same_seed_parallel
+
+      - name: Check random seed gives different results
+        run: |
+          .ci/run_shark.sh my_model_random_seed
+          .ci/compare_galaxies.sh my_model my_model_random_seed --expect-unequal
+
+      - name: Generate all plots
+        run: |
+          echo "backend: Agg" >> matplotlibrc
+          python standard_plots/all.py -c ci-test.cfg