Add test

.github/workflows/ci.yml

@@ -1,12 +1,4 @@
-# Continuous integration testing for ChRIS Plugin.
-# https://github.com/FNNDSC/python-chrisapp-template/wiki/Continuous-Integration
-#
-# - on push and PR: run pytest
-# - on push to main: build and push container images as ":latest"
-# - on push to semver tag: build and push container image with tag and
-#                          upload plugin description to https://chrisstore.co
-
-name: build
+name: ci
 
 on:
   push:
@@ -76,6 +68,55 @@ jobs:
           load: true
           cache-from: type=gha
 
+      - name: Download example data
+        run: ./download_example_data.sh example_data_dir/
+      - name: Run examples
+        id: run_examples
+        run: |
+          mkdir /tmp/outgoing
+          docker run --rm -u "$(id -u):$(id -g)" \
+            -v "${{ github.workspace }}/example_data_dir/data:/incoming:ro" \
+            -v "/tmp/outgoing:/outgoing:rw" \
+            ${{ steps.info.outputs.local_tag }} \
+            emerald --mask-suffix '_mask.nii' --outputs '0.0:_brain.nii,0.2:_overlay02.nii' /incoming /outgoing
+      - name: Assert example outputs are found
+        run: |
+          expected_outputs=(
+            /tmp/outgoing/stack-1_brain.nii
+            /tmp/outgoing/stack-1_mask.nii
+            /tmp/outgoing/stack-1_overlay02.nii
+            /tmp/outgoing/stack-2_brain.nii
+            /tmp/outgoing/stack-2_mask.nii
+            /tmp/outgoing/stack-2_overlay02.nii
+            /tmp/outgoing/stack-3_brain.nii
+            /tmp/outgoing/stack-3_mask.nii
+            /tmp/outgoing/stack-3_overlay02.nii
+            /tmp/outgoing/stack-4_brain.nii
+            /tmp/outgoing/stack-4_mask.nii
+            /tmp/outgoing/stack-4_overlay02.nii
+            /tmp/outgoing/stack-5_brain.nii
+            /tmp/outgoing/stack-5_mask.nii
+            /tmp/outgoing/stack-5_overlay02.nii
+            /tmp/outgoing/stack-6_brain.nii
+            /tmp/outgoing/stack-6_mask.nii
+            /tmp/outgoing/stack-6_overlay02.nii
+            /tmp/outgoing/stack-7_brain.nii
+            /tmp/outgoing/stack-7_mask.nii
+            /tmp/outgoing/stack-7_overlay02.nii
+            /tmp/outgoing/stack-8_brain.nii
+            /tmp/outgoing/stack-8_mask.nii
+            /tmp/outgoing/stack-8_overlay02.nii
+          )
+
+          for expected_output in "${expected_outputs[@]}"; do
+            if ! [ -f "$expected_output" ]; then
+              echo "expected $expected_output to be a file, but it does not."
+              parent_dir="$(dirname "$expected_output")"
+              set -ex
+              ls -lh "$parent_dir"
+              exit 1
+            fi
+          done
       - name: Login to DockerHub
         if: (github.event_name == 'push' || github.event_name == 'release') && contains(steps.info.outputs.tags_csv, 'docker.io')
         uses: docker/login-action@v3

.gitignore

@@ -3,3 +3,5 @@ __pycache__
 
 .idea
 .mambaenv
+
+/example_data_dir

README.md

@@ -1,5 +1,9 @@
 # Automatic Brain Masking
 
+[![GitHub tag](https://img.shields.io/github/v/tag/FNNDSC/pl-emerald?filter=v*.*.*&label=version)](https://github.com/FNNDSC/pl-emerald/pkgs/container/pl-emerald)
+[![MIT License](https://img.shields.io/github/license/fnndsc/pl-emerald)](https://github.com/FNNDSC/pl-emerald/blob/master/LICENSE)
+[![ci](https://github.com/FNNDSC/pl-emerald/actions/workflows/ci.yml/badge.svg)](https://github.com/FNNDSC/pl-emerald/actions/workflows/ci.yml)
+
 ## Description
 
 Deep learning based project made to automatically mask fetal brains.

download_example_data.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+COMMIT='7c8ac54213cecd4fbb15f700b14d73f7086cf11d'
+REPO='https://github.com/kevin-keraudren/example-motion-correction'
+URL="$REPO/archive/$COMMIT.tar.gz"
+DIR_INSIDE_TARBALL="$(basename "$REPO")-$COMMIT"
+
+tarball="$(mktemp --suffix '.tar.gz')"
+output_dir="$1"
+
+if [ -z "$output_dir" ]; then
+  echo "usage: $0 example_data_dir/"
+  exit 1
+fi
+
+if [ -e "$output_dir" ]; then
+  echo "error: $output_dir exists"
+  exit 1
+fi
+
+set -ex
+wget -O "$tarball" "$URL"
+tar xvf "$tarball" --directory=/tmp
+mv -v "/tmp/$DIR_INSIDE_TARBALL" "$output_dir"
+rm -v "$tarball"
+
+find "$output_dir" -name '*.nii.gz' -type f | parallel gzip -d