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Add an options dialog to choose Python environment
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‎pom.xml

Lines changed: 12 additions & 1 deletion
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@@ -10,7 +10,7 @@
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</parent>
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<artifactId>scripting-python</artifactId>
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<version>0.3.1-SNAPSHOT</version>
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<version>0.4.0-SNAPSHOT</version>
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<name>SciJava Scripting: Python</name>
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<description>Python scripting language plugin to be used via scyjava.</description>
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<!-- NB: Deploy releases to the SciJava Maven repository. -->
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<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
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<appose.version>0.3.0</appose.version>
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</properties>
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<dependencies>
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<!-- SciJava dependencies -->
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>app-launcher</artifactId>
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</dependency>
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<dependency>
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<groupId>org.scijava</groupId>
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<artifactId>scijava-common</artifactId>
@@ -105,6 +111,11 @@
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<groupId>com.fifesoft</groupId>
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<artifactId>rsyntaxtextarea</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apposed</groupId>
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<artifactId>appose</artifactId>
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<version>${appose.version}</version>
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</dependency>
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<!-- Test dependencies -->
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<dependency>

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

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/*-
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* #%L
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* Python scripting language plugin to be used via scyjava.
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* %%
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* Copyright (C) 2021 - 2025 SciJava developers.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.plugins.scripting.python;
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import org.scijava.app.AppService;
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import org.scijava.command.CommandService;
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import org.scijava.launcher.Config;
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import org.scijava.log.LogService;
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import org.scijava.menu.MenuConstants;
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import org.scijava.options.OptionsPlugin;
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import org.scijava.plugin.Menu;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import org.scijava.widget.Button;
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import java.io.File;
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import java.io.IOException;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.LinkedHashMap;
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import java.util.Map;
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/**
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* Options for configuring the Python environment.
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*
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* @author Curtis Rueden
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*/
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@Plugin(type = OptionsPlugin.class, menu = {
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@Menu(label = MenuConstants.EDIT_LABEL,
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weight = MenuConstants.EDIT_WEIGHT,
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mnemonic = MenuConstants.EDIT_MNEMONIC),
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@Menu(label = "Options", mnemonic = 'o'),
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@Menu(label = "Python...", weight = 10),
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})
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public class OptionsPython extends OptionsPlugin {
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@Parameter
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private AppService appService;
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@Parameter
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private CommandService commandService;
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@Parameter
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private LogService log;
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@Parameter(label = "Python environment directory", persist = false)
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private File pythonDir;
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@Parameter(label = "Rebuild Python environment", callback = "rebuildEnv")
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private Button rebuildEnvironment;
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@Parameter(label = "Launch in Python mode", callback = "updatePythonConfig", persist = false)
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private boolean pythonMode;
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// -- OptionsPython methods --
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public File getPythonDir() {
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return pythonDir;
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}
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public boolean isPythonMode() {
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return pythonMode;
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}
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public void setPythonDir(final File pythonDir) {
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this.pythonDir = pythonDir;
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}
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public void setPythonMode(final boolean pythonMode) {
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this.pythonMode = pythonMode;
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}
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// -- Callback methods --
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@Override
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public void load() {
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// Read python-dir and launch-mode from app config file.
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String configFileProp = System.getProperty("scijava.app.config-file");
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File configFile = configFileProp == null ? null : new File(configFileProp);
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if (configFile != null && configFile.canRead()) {
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try {
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final Map<String, String> config = Config.load(configFile);
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final String cfgPythonDir = config.get("python-dir");
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if (cfgPythonDir != null) {
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final Path appPath = appService.getApp().getBaseDirectory().toPath();
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pythonDir = stringToFile(appPath, cfgPythonDir);
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}
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final String cfgLaunchMode = config.get("launch-mode");
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if (cfgLaunchMode != null) pythonMode = cfgLaunchMode.equals("PYTHON");
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}
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catch (IOException e) {
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// Proceed gracefully if config file is not accessible.
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log.debug(e);
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}
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}
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if (pythonDir == null) {
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// For the default Python directory, try to match the platform string used for Java installations.
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final String javaPlatform = System.getProperty("scijava.app.java-platform");
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final String platform = javaPlatform != null ? javaPlatform :
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System.getProperty("os.name") + "-" + System.getProperty("os.arch");
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final Path pythonPath = appService.getApp().getBaseDirectory().toPath().resolve("python").resolve(platform);
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pythonDir = pythonPath.toFile();
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}
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}
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public void rebuildEnv() {
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// Use scijava.app.python-env-file system property if present.
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final Path appPath = appService.getApp().getBaseDirectory().toPath();
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File environmentYaml = appPath.resolve("config").resolve("environment.yml").toFile();
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final String pythonEnvFileProp = System.getProperty("scijava.app.python-env-file");
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if (pythonEnvFileProp != null) {
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environmentYaml = OptionsPython.stringToFile(appPath, pythonEnvFileProp);
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}
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commandService.run(RebuildEnvironment.class, true,
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"environmentYaml", environmentYaml,
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"targetDir", pythonDir
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);
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}
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@Override
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public void save() {
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// Write python-dir and launch-mode values to app config file.
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final String configFileProp = System.getProperty("scijava.app.config-file");
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if (configFileProp == null) return; // No config file to update.
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final File configFile = new File(configFileProp);
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Map<String, String> config = null;
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if (configFile.isFile()) {
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try {
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config = Config.load(configFile);
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}
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catch (IOException exc) {
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// Proceed gracefully if config file is not accessible.
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log.debug(exc);
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}
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}
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if (config == null) config = new LinkedHashMap<>();
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final Path appPath = appService.getApp().getBaseDirectory().toPath();
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config.put("python-dir", fileToString(appPath, pythonDir));
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config.put("launch-mode", pythonMode ? "PYTHON" : "JVM");
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try {
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Config.save(configFile, config);
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}
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catch (IOException exc) {
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// Proceed gracefully if config file cannot be written.
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log.debug(exc);
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}
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}
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// -- Utility methods --
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/**
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* Converts a path string to a file, treating relative path expressions as
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* relative to the given base directory, not the current working directory.
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*/
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static File stringToFile(Path baseDir, String value) {
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final Path path = Paths.get(value);
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final Path absPath = path.isAbsolute() ? path : baseDir.resolve(path);
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return absPath.toFile();
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}
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/**
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* Converts a file to a path string, which in the case of a file beneath the
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* given base directory, will be a path expression relative to that base.
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*/
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static String fileToString(Path baseDir, File file) {
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Path filePath = file.toPath();
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Path relPath = filePath.startsWith(baseDir) ?
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baseDir.relativize(filePath) : filePath.toAbsolutePath();
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return relPath.toString();
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}
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}

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

Lines changed: 111 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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/*-
2+
* #%L
3+
* Python scripting language plugin to be used via scyjava.
4+
* %%
5+
* Copyright (C) 2021 - 2025 SciJava developers.
6+
* %%
7+
* Redistribution and use in source and binary forms, with or without
8+
* modification, are permitted provided that the following conditions are met:
9+
*
10+
* 1. Redistributions of source code must retain the above copyright notice,
11+
* this list of conditions and the following disclaimer.
12+
* 2. Redistributions in binary form must reproduce the above copyright notice,
13+
* this list of conditions and the following disclaimer in the documentation
14+
* and/or other materials provided with the distribution.
15+
*
16+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
17+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
18+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
19+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
20+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
21+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
22+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
23+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
24+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
25+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
26+
* POSSIBILITY OF SUCH DAMAGE.
27+
* #L%
28+
*/
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package org.scijava.plugins.scripting.python;
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import org.apposed.appose.Appose;
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import org.apposed.appose.Builder;
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import org.scijava.app.AppService;
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import org.scijava.command.Command;
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import org.scijava.launcher.Splash;
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import org.scijava.log.Logger;
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import org.scijava.plugin.Parameter;
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import org.scijava.plugin.Plugin;
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import java.io.File;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.Comparator;
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import java.util.stream.Stream;
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/**
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* SciJava command wrapper to build a Python environment.
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*
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* @author Curtis Rueden
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*/
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@Plugin(type = Command.class, label = "Rebuild Python environment")
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public class RebuildEnvironment implements Command {
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@Parameter
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private AppService appService;
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@Parameter
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private Logger log;
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@Parameter(label = "environment definition file")
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private File environmentYaml;
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@Parameter(label = "Target directory")
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private File targetDir;
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// -- OptionsPython methods --
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@Override
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public void run() {
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final File backupDir = new File(targetDir.getPath() + ".old");
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if (backupDir.exists()) {
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// Delete the previous backup environment recursively.
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try (Stream<Path> x = Files.walk(backupDir.toPath())) {
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x.sorted(Comparator.reverseOrder()).forEach(p -> {
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try {
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Files.delete(p);
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}
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catch (IOException exc) {
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log.error(exc);
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}
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});
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}
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catch (IOException exc) {
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log.error(exc);
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}
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}
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// Rename the old environment to a backup directory.
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if (targetDir.exists()) targetDir.renameTo(backupDir);
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// Build the new environment.
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try {
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Builder builder = Appose
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.file(environmentYaml, "environment.yml")
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.subscribeOutput(this::report)
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.subscribeError(this::report)
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.subscribeProgress((msg, cur, max) -> Splash.update(msg, (double) cur / max));
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System.err.println("Building Python environment"); // HACK: stderr stream triggers console window show.
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Splash.show();
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builder.build(targetDir);
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}
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catch (IOException exc) {
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log.error("Failed to build Python environment", exc);
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}
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}
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private void report(String s) {
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if (s.isEmpty()) System.err.print(".");
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else System.err.print(s);
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}
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}

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