Add Makefile and CI

.github/workflows/ci.yml

@@ -0,0 +1,13 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build and test
+        run: make test

.gitignore

@@ -0,0 +1,2 @@
+build/
+lib/

Makefile

@@ -0,0 +1,64 @@
+IJ_VERSION := 1.54p
+IJ_JAR := lib/ij-$(IJ_VERSION).jar
+IJ_URL := https://repo1.maven.org/maven2/net/imagej/ij/$(IJ_VERSION)/ij-$(IJ_VERSION).jar
+
+BUILD_DIR := build/classes
+DIST_DIR := build/dist
+JAVA_SOURCES := $(wildcard *.java)
+TEST_SOURCES := $(wildcard tests/*.java)
+TEST_MARKER := $(BUILD_DIR)/.tests-compiled
+TEST_CLASSES := $(basename $(notdir $(TEST_SOURCES)))
+
+ifeq ($(OS),Windows_NT)
+  CP_SEP := ;
+else
+  CP_SEP := :
+endif
+
+CLASSPATH := $(IJ_JAR)
+CLASSPATH_WITH_CLASSES := $(CLASSPATH)$(CP_SEP)$(BUILD_DIR)
+
+.PHONY: all build clean test download-deps
+
+all: build
+
+$(IJ_JAR):
+	@mkdir -p $(dir $@)
+	@echo "Downloading ImageJ runtime to $(IJ_JAR)"
+	@curl -L -o $@ $(IJ_URL)
+
+$(BUILD_DIR)/.compiled: $(IJ_JAR) $(JAVA_SOURCES)
+	@mkdir -p $(BUILD_DIR)
+	@javac -cp "$(CLASSPATH)" -d $(BUILD_DIR) $(JAVA_SOURCES)
+	@touch $@
+
+$(DIST_DIR)/OpenComet_.jar: $(BUILD_DIR)/.compiled
+	@mkdir -p $(DIST_DIR)
+	@jar cf $@ -C $(BUILD_DIR) .
+
+build: $(DIST_DIR)/OpenComet_.jar
+
+ifeq ($(strip $(TEST_SOURCES)),)
+$(TEST_MARKER): $(BUILD_DIR)/.compiled
+	@touch $@
+else
+$(TEST_MARKER): $(TEST_SOURCES) $(BUILD_DIR)/.compiled
+	@javac -cp "$(CLASSPATH_WITH_CLASSES)" -d $(BUILD_DIR) $(TEST_SOURCES)
+	@touch $@
+endif
+
+test: $(BUILD_DIR)/.compiled $(TEST_MARKER)
+	@if [ -z "$(strip $(TEST_CLASSES))" ]; then \
+		echo "No tests to run."; \
+	else \
+		for cls in $(TEST_CLASSES); do \
+			echo "Running $$cls"; \
+			java -cp "$(CLASSPATH_WITH_CLASSES)" $$cls || exit $$?; \
+		done; \
+	fi
+
+clean:
+	@rm -rf build
+
+download-deps: $(IJ_JAR)
+	@true

README.md

@@ -8,10 +8,13 @@ The open-access publication on OpenComet is available at
 comet assay image analysis", Redox Biology, 2:457-465,
 2014.](http://www.sciencedirect.com/science/article/pii/S2213231714000032)
 
-The easiest way to build and package the plugin is to download and extract
-[Fiji](http://imagej.net/Fiji/Downloads) and
+For more information including downloads, documentation and tutorials, visit https://cometbio.org/.
 
-    javac -classpath "<path_to_fiji>/Fiji.app/jars/*" *.java
-    jar cf OpenComet_.jar *.class
+## Building locally
 
-For more information including downloads, documentation and tutorials, visit http://opencomet.org.
+The plugin jar file can be built using
+```sh
+make build
+```
+
+The compiled plugin will be written to `build/dist/OpenComet_.jar`

tests/TestRunner.java

@@ -0,0 +1,65 @@
+import ij.gui.Roi;
+
+/**
+ * Minimal sanity checks that can run headlessly in CI.
+ */
+public class TestRunner {
+    public static void main(String[] args) {
+        testMeasurementString();
+        System.out.println("All tests passed.");
+    }
+
+    private static void testMeasurementString() {
+        Comet comet = new Comet(new Roi(0, 0, 5, 5));
+        comet.id = 42;
+
+        comet.status = Comet.INVALID;
+        if (!comet.getMeasurementString(",").isEmpty()) {
+            throw new AssertionError("Invalid comet should not produce output");
+        }
+
+        comet.status = Comet.VALID;
+        comet.cometArea = 10.0;
+        comet.cometIntensity = 20.0;
+        comet.cometLength = 30.0;
+        comet.cometDNA = 40.0;
+        comet.headArea = 50.0;
+        comet.headIntensity = 60.0;
+        comet.headLength = 70.0;
+        comet.headDNA = 80.0;
+        comet.headDNAPercent = 90.0;
+        comet.tailArea = 12.0;
+        comet.tailIntensity = 22.0;
+        comet.tailLength = 32.0;
+        comet.tailDNA = 42.0;
+        comet.tailDNApercent = 52.0;
+        comet.tailMoment = 62.0;
+        comet.tailOliveMoment = 72.0;
+
+        String expected = String.join(",",
+                "42",
+                "normal",
+                "10.0",
+                "20.0",
+                "30.0",
+                "40.0",
+                "50.0",
+                "60.0",
+                "70.0",
+                "80.0",
+                "90.0",
+                "12.0",
+                "22.0",
+                "32.0",
+                "42.0",
+                "52.0",
+                "62.0",
+                "72.0");
+
+        String actual = comet.getMeasurementString(",");
+        if (!expected.equals(actual)) {
+            throw new AssertionError("Unexpected measurement string:\nexpected: "
+                    + expected + "\nactual: " + actual);
+        }
+    }
+}