Allow environment editing in python options

Closes #9

Author: hinerm

src/main/java/org/scijava/plugins/scripting/python/OptionsPython.java

@@ -35,6 +35,7 @@
 import java.nio.file.Paths;
 import java.util.LinkedHashMap;
 import java.util.Map;
+import java.util.StringJoiner;
 
 import org.scijava.app.AppService;
 import org.scijava.command.CommandService;
@@ -48,6 +49,7 @@
 import org.scijava.ui.DialogPrompt;
 import org.scijava.ui.UIService;
 import org.scijava.widget.Button;
+import org.scijava.widget.TextWidget;
 
 /**
  * Options for configuring the Python environment.
@@ -72,6 +74,14 @@ public class OptionsPython extends OptionsPlugin {
 	@Parameter(label = "Python environment directory", persist = false)
 	private File pythonDir;
 
+	@Parameter(label = "Conda dependencies", style = TextWidget.AREA_STYLE,
+		persist = false)
+	private String condaDependencies;
+
+	@Parameter(label = "Pip dependencies", style = TextWidget.AREA_STYLE,
+		persist = false)
+	private String pipDependencies;
+
 	@Parameter(label = "Build Python environment", callback = "rebuildEnv")
 	private Button rebuildEnvironment;
 
@@ -83,6 +93,8 @@ public class OptionsPython extends OptionsPlugin {
 	private UIService uiService;
 
 	private boolean initialPythonMode = false;
+	private String initialCondaDependencies;
+	private String initialPipDependencies;
 
 	// -- OptionsPython methods --
 
@@ -142,10 +154,70 @@ public void load() {
 
 		// Store the initial value of pythonMode for later comparison
 		initialPythonMode = pythonMode;
+
+		// Populate condaDependencies and pipDependencies from environment.yml
+		condaDependencies = "";
+		pipDependencies = "";
+		java.util.Set<String> pipBlacklist = new java.util.HashSet<>();
+		pipBlacklist.add("appose-python");
+		pipBlacklist.add("pyimagej");
+		File envFile = getEnvironmentYamlFile();
+		if (envFile.exists()) {
+			try {
+				java.util.List<String> lines = java.nio.file.Files.readAllLines(envFile
+					.toPath());
+				boolean inDeps = false, inPip = false;
+				StringJoiner condaDeps = new StringJoiner("\n");
+				StringJoiner pipDeps = new StringJoiner("\n");
+				for (String line : lines) {
+					String trimmed = line.trim();
+					if (trimmed.startsWith("#") || trimmed.isEmpty()) {
+						// Ignore empty and comment lines
+						continue;
+					}
+					if (trimmed.startsWith("dependencies:")) {
+						inDeps = true;
+						continue;
+					}
+					if (inDeps && trimmed.startsWith("- pip")) {
+						inPip = true;
+						continue;
+					}
+					if (inDeps && trimmed.startsWith("- ") && !inPip) {
+						String dep = trimmed.substring(2).trim();
+						if (!dep.equals("pip")) condaDeps.add(dep);
+						continue;
+					}
+					if (inPip && trimmed.startsWith("- ")) {
+						String pipDep = trimmed.substring(2).trim();
+						boolean blacklisted = false;
+						for (String bad : pipBlacklist) {
+							if (pipDep.contains(bad)) {
+								blacklisted = true;
+								break;
+							}
+						}
+						if (!blacklisted) pipDeps.add(pipDep);
+						continue;
+					}
+					if (inDeps && !trimmed.startsWith("- ") && !trimmed.isEmpty())
+						inDeps = false;
+					if (inPip && (!trimmed.startsWith("- ") || trimmed.isEmpty())) inPip =
+						false;
+				}
+				condaDependencies = condaDeps.toString().trim();
+				pipDependencies = pipDeps.toString().trim();
+				initialCondaDependencies = condaDependencies;
+				initialPipDependencies = pipDependencies;
+			}
+			catch (Exception e) {
+				log.debug("Could not read environment.yml: " + e.getMessage());
+			}
+		}
 	}
 
 	public void rebuildEnv() {
-		File environmentYaml = getEnvironmentYamlFile();
+		File environmentYaml = writeEnvironmentYaml();
 		commandService.run(RebuildEnvironment.class, true, "environmentYaml",
 			environmentYaml, "targetDir", pythonDir);
 	}
@@ -163,7 +235,6 @@ private File getEnvironmentYamlFile() {
 			environmentYaml = stringToFile(appPath, pythonEnvFileProp);
 		}
 		return environmentYaml;
-
 	}
 
 	@Override
@@ -197,6 +268,9 @@ public void save() {
 		if (pythonMode && (pythonDir == null || !pythonDir.exists())) {
 			rebuildEnv();
 		}
+		else {
+			writeEnvironmentYaml();
+		}
 		// Warn the user if pythonMode was just enabled and wasn't before
 		if (!initialPythonMode && pythonMode && uiService != null) {
 			String msg =
@@ -208,6 +282,50 @@ public void save() {
 		}
 	}
 
+	private File writeEnvironmentYaml() {
+		File envFile = getEnvironmentYamlFile();
+
+		// skip writing if nothing has changed
+		if (initialCondaDependencies.equals(condaDependencies) &&
+			initialPipDependencies.equals(pipDependencies)) return envFile;
+
+		// Update initial dependencies to detect future changes
+		initialCondaDependencies = condaDependencies;
+		initialPipDependencies = pipDependencies;
+
+		// Write environment.yml from condaDependencies and pipDependencies
+		try {
+			String name = "fiji";
+			String[] channels = { "conda-forge" };
+			String pyimagej = "pyimagej>=1.7.0";
+			String apposePython =
+				"git+https://github.com/apposed/appose-python.git@efe6dadb2242ca45820fcbb7aeea2096f99f9cb2";
+			StringBuilder yml = new StringBuilder();
+			yml.append("name: ").append(name).append("\nchannels:\n");
+			for (String ch : channels)
+				yml.append("  - ").append(ch).append("\n");
+			yml.append("dependencies:\n");
+			for (String dep : condaDependencies.split("\n")) {
+				String trimmed = dep.trim();
+				if (!trimmed.isEmpty()) yml.append("  - ").append(trimmed).append("\n");
+			}
+			yml.append("  - pip\n");
+			yml.append("  - pip:\n");
+			for (String dep : pipDependencies.split("\n")) {
+				String trimmed = dep.trim();
+				if (!trimmed.isEmpty()) yml.append("    - ").append(trimmed).append(
+					"\n");
+			}
+			yml.append("    - ").append(pyimagej).append("\n");
+			yml.append("    - ").append(apposePython).append("\n");
+			java.nio.file.Files.write(envFile.toPath(), yml.toString().getBytes());
+		}
+		catch (Exception e) {
+			log.debug("Could not write environment.yml: " + e.getMessage());
+		}
+		return envFile;
+	}
+
 	// -- Utility methods --
 
 	/**