Merge branch 'main' into features/dependency-graph

docs/docs/configuration.md

@@ -5,7 +5,7 @@
 The `nf-test.config` file is a configuration file used to customize settings and behavior for `nf-test`. This file must be located in the root of your project, and it is automatically loaded when you run `nf-test test`. Below are the parameters that can be adapted:
 
 | Parameter    | Description                                                                                                                                                        | Default Value             |
-| ------------ |--------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------|
+|--------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------| ------------------------- |
 | `testsDir`   | Location for storing all nf-test cases (test scripts). If you want all test files to be in the same directory as the script itself, you can set the testDir to `.` | `"tests"`                 |
 | `workDir`    | Directory for storing temporary files and working directories for each test. This directory should be added to `.gitignore`.                                       | `".nf-test"`              |
 | `configFile` | Location of an optional `nextflow.config` file specifically used for executing tests. [Learn more](#testsnextflowconfig).                                          | `"tests/nextflow.config"` |
@@ -14,7 +14,8 @@ The `nf-test.config` file is a configuration file used to customize settings and
 | `withTrace`  | Enable or disable tracing options during testing. Disable tracing if your containers don't include the `procps` tool.                                              | `true`                    |
 | `autoSort`   | Enable or disable sorted channels by default when running tests.                                                                                                   | `true`                    |
 | `options`    | Custom Nextflow command-line options to be applied when running tests. For example `"-dump-channels -stub-run"`                                                    |                           |
- | `ignore`    | List of filenames or patterns that should be ignored when building the dependency graph. For example: `ignore ['folder/**/*.nf', 'modules/module.nf']`             | ``                        |
+| `ignore`     | List of filenames or patterns that should be ignored when building the dependency graph. For example: `ignore ['folder/**/*.nf', 'modules/module.nf']`             | ``                        |
+| `requires`   | Can be used to specify the minimum required version of nf-test. Requires nf-test > 0.9.0                                                                           | ``                        |
 
 Here's an example of what an `nf-test.config` file could look like:
 
@@ -31,6 +32,17 @@ config {
 }
 ```
 
+The `requires` keyword can be used to specify the minimum required version of nf-test.
+For instance, to ensure the use of at least nf-test version 0.9.0, define it as follows:
+
+```groovy
+config {
+    requires (
+        "nf-test": "0.9.0"
+    )
+}
+```
+
 ## `tests/nextflow.config`
 
 This optional `nextflow.config` file is used to execute tests. This is a good place to set default `params` for all your tests. Example number of threads:

src/main/java/com/askimed/nf/test/config/Config.java

@@ -3,7 +3,11 @@
 import java.io.File;
 import java.util.List;
 import java.util.Vector;
+import java.util.Map;
 
+import com.askimed.nf.test.App;
+import com.askimed.nf.test.nextflow.NextflowCommand;
+import com.askimed.nf.test.util.Version;
 import org.codehaus.groovy.control.CompilerConfiguration;
 import org.codehaus.groovy.control.customizers.ImportCustomizer;
 
@@ -20,6 +24,8 @@ public class Config {
 
 	public static final String DEFAULT_HOME = ".nf-test";
 
+	public static final String KEY_NF_TEST_VERSION = "nf-test";
+
 	private String workDir = ".nf-test";
 
 	private String testsDir = "tests";
@@ -43,6 +49,8 @@ public class Config {
 	private String stageMode = FileStaging.MODE_COPY;
 
 	private List<String> ignore = new Vector<String>();
+
+	private Map<String, Object> requires = null;
 
 	public void testsDir(String testsDir) {
 		this.testsDir = testsDir;
@@ -60,6 +68,18 @@ public String getWorkDir() {
 		return workDir;
 	}
 
+	public void requires(Map<String, Object> requires) {
+		setRequires(requires);
+	}
+
+	public void setRequires(Map<String, Object> requires) {
+		this.requires = requires;
+	}
+
+	public Map<String, Object> getRequires() {
+		return requires;
+	}
+
 	public void profile(String profile) {
 		this.profile = profile;
 	}
@@ -212,6 +232,17 @@ public static Config parse(File script) throws Exception {
 		Object object = shell.evaluate(script);
 		Config config = (Config) object;
 
+		// no requirements
+		if (config.getRequires() == null ){
+			return config;
+		}
+
+		// check nf-test version
+		String appVersion = config.getRequires().getOrDefault(KEY_NF_TEST_VERSION, App.VERSION).toString();
+		if (Version.compare(appVersion, App.VERSION) >= 1) {
+			throw new Exception("nf-test " + appVersion + " or above is required to run this project");
+		}
+
 		return config;
 	}
 

src/main/java/com/askimed/nf/test/util/Version.java

@@ -0,0 +1,41 @@
+package com.askimed.nf.test.util;
+
+public class Version {
+
+    public static int compare(String version1, String version2) {
+
+        String parts1[] = version1.split("-", 2);
+        String parts2[] = version2.split("-", 2);
+
+        String tiles1[] = parts1[0].split("\\.");
+        String tiles2[] = parts2[0].split("\\.");
+
+        for (int i = 0; i < tiles1.length; i++) {
+            int number1 = Integer.parseInt(tiles1[i].trim());
+            int number2 = Integer.parseInt(tiles2[i].trim());
+
+            if (number1 != number2) {
+
+                return number1 > number2 ? 1 : -1;
+
+            }
+
+        }
+
+        if (parts1.length > 1) {
+            if (parts2.length > 1) {
+                return parts1[1].compareTo(parts2[1]);
+            } else {
+                return -1;
+            }
+        } else {
+            if (parts2.length > 1) {
+                return 1;
+            }
+        }
+
+        return 0;
+
+    }
+
+}

src/test/java/com/askimed/nf/test/lang/ProcessTest.java

@@ -290,6 +290,23 @@ public void testProfilesOverwriteInConfig() throws Exception {
 
 	}
 
+	@Test
+	public void testRequires() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/process/profiles/hello.a.nf.test", "--config",
+				"test-data/process/requires/nf-test-0.1.0.config" });
+		assertEquals(0, exitCode);
+
+		app = new App();
+		exitCode = app.run(new String[] { "test", "test-data/process/profiles/hello.a.nf.test", "--config",
+				"test-data/process/requires/nf-test-100.0.0.config" });
+		assertEquals(2, exitCode);
+
+
+	}
+
+
 	@Test
 	public void testUniquenessSnapshots() throws Exception {
 		App app = new App();

test-data/process/requires/nf-test-0.1.0.config

@@ -0,0 +1,6 @@
+config {
+    requires (
+        "nf-test": "0.1.0"
+    )
+    configFile ""
+}

test-data/process/requires/nf-test-100.0.0.config

@@ -0,0 +1,6 @@
+config {
+    requires (
+        "nf-test": "100.0.0"
+    )
+    configFile ""
+}