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Commit 00a1960

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hadimhadim
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Remove the possibility to install the kernel from Fiji.
1 parent f1a45c6 commit 00a1960

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‎README.md‎

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@@ -18,7 +18,7 @@ The kernel has been originally created to work with ImageJ. See [here](https://i
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A documentation is available as a series of notebooks [here](./notebooks/Welcome.ipynb).
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## Installation - Standalone
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## Installation
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- Install [Anaconda](https://www.continuum.io/downloads)
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- Install `scijava-jupyter-kernel` with :
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jupyter lab
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```
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*Note : It is suggested to install the kernel in an isolated Conda environment (not in the root environment).*
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## Installation - With Fiji integration
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- [Download](https://imagej.net/Fiji/Downloads) the last Fiji release.
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- Add the *Scijava Jupyter Kernel* update site in Fiji:
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- Click [Help ▶ Update...](https://imagej.net/Update_Sites).
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- Click `Manage update sites`.
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- Select the *Scijava Jupyter Kernel* checkbox (see also [List of update sites](https://imagej.net/List_of_update_sites)).
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- Click `Apply changes` and restart Fiji.
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- Launch `Analyze > Jupyter Kernel > Install Scijava Kernel`.
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- Set the path to your Python binary.
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- Choose a log level.
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- Check the kernel has been installed with : `jupyter kernelspec list`.
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- Launch `jupyter notebook` or `jupyter lab` and **select the kernel you want in the kernel list**.
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![Scijava Jupyter Kernel Installation](teaser.gif)
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*Note : It is strongly suggested to install the kernel in an isolated Conda environment (not in the root environment).*
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## Development
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‎src/main/java/org/scijava/jupyter/commands/InstallScijavaKernel.java‎

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‎src/main/java/org/scijava/jupyter/service/DefaultJupyterService.java‎

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import org.apache.commons.cli.ParseException;
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import org.scijava.Context;
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import org.scijava.command.CommandService;
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import org.scijava.jupyter.commands.InstallScijavaKernel;
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import org.scijava.jupyter.kernel.ScijavaKernel;
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import org.scijava.jupyter.kernel.configuration.ScijavaKernelConfigurationFile;
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import org.scijava.jupyter.kernel.evaluator.ScijavaEvaluator;
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@Parameter
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private transient CommandService command;
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/* Install kernel */
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@Override
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public void installKernel(String... args) {
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Map<String, Object> parameters = parseArgumentsInstall(args);
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// TODO : Ensure parameters contains the appropriate keys.
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installKernel((String) parameters.get("logLevel"),
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(String) parameters.get("pythonBinaryPath"),
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(String) parameters.get("classpath"),
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(String) parameters.get("javaBinaryPath"));
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}
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@Override
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public void installKernel(String logLevel, String pythonBinaryPath) {
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installKernel(logLevel, Paths.get(pythonBinaryPath));
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}
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@Override
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public void installKernel(String logLevel, Path pythonBinaryPath) {
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installKernel(logLevel, pythonBinaryPath.toFile());
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}
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@Override
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public void installKernel(String logLevel, File pythonBinaryPath) {
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installKernel(logLevel, pythonBinaryPath, null, null);
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}
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@Override
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public void installKernel(String logLevel, String pythonBinaryPath, String classpath, String javaBinaryPath) {
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installKernel(logLevel, new File(pythonBinaryPath), classpath, javaBinaryPath);
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}
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@Override
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public void installKernel(String logLevel, File pythonBinaryPath, String classpath, String javaBinaryPath) {
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Map<String, Object> parameters = new HashMap<>();
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parameters.put("logLevel", logLevel);
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parameters.put("pythonBinaryPath", pythonBinaryPath);
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parameters.put("classpath", classpath);
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parameters.put("javaBinaryPath", new File(javaBinaryPath));
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command.run(InstallScijavaKernel.class, true, parameters);
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}
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/* Run kernel */
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@Override
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public void runKernel(String... args) {
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return null;
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}
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private Map<String, Object> parseArgumentsInstall(final String... args) {
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if (args.length > 0) {
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try {
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Options options = new Options();
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options.addOption("pythonBinaryPath", true, "Python Binary Path");
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options.addOption("verbose", true, "Verbose Mode");
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options.addOption("classpath", true, "Additional JAVA classpath ?");
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options.addOption("javaBinaryPath", true, "Java Binary Path");
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CommandLineParser parser = new DefaultParser();
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CommandLine cmd = parser.parse(options, args);
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Map<String, Object> parameters = new HashMap<>();
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parameters.put("pythonBinaryPath", cmd.getOptionValue("pythonBinaryPath"));
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parameters.put("logLevel", cmd.getOptionValue("verbose"));
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if (cmd.getOptionValue("classpath") != null) {
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parameters.put("classpath", cmd.getOptionValue("classpath"));
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} else {
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parameters.put("classpath", null);
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}
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if (cmd.getOptionValue("javaBinaryPath") != null) {
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parameters.put("javaBinaryPath", cmd.getOptionValue("javaBinaryPath"));
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} else {
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parameters.put("javaBinaryPath", null);
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}
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return parameters;
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} catch (ParseException ex) {
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log.error("Error parsing arguments : " + ex.toString());
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}
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} else {
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log.error("No parameters passed to the Scijava kernel.");
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}
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return null;
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}
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}

‎src/main/java/org/scijava/jupyter/service/JupyterService.java‎

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*/
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public interface JupyterService extends SciJavaService {
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/* Install kernel */
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void installKernel(String... args);
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void installKernel(String logLevel, String pythonBinaryPath);
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void installKernel(String logLevel, Path pythonBinaryPath);
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void installKernel(String logLevel, File pythonBinaryPath);
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void installKernel(String logLevel, String pythonBinaryPath, String classpath, String javaBinaryPath);
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void installKernel(String logLevel, File pythonBinaryPath, String classpath, String javaBinaryPath);
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/* Run kernel */
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void runKernel(String... args);
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‎teaser.gif‎

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