Merge pull request #332 from trackmate-sc/conda-run

Rework the conda configuration and the way conda tools are run in TrackMate

Author: tinevez

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>TrackMate</artifactId>
-	<version>8.0.1-SNAPSHOT</version>
+	<version>8.1.0-SNAPSHOT</version>
 
 	<name>TrackMate</name>
 	<description>TrackMate plugin for Fiji.</description>

src/main/java/fiji/plugin/trackmate/util/cli/CLIUtils.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -75,6 +75,15 @@ public static final Process createProcess( final CLIConfigurator cli, final File
 	{
 		final List< String > cmd = CommandBuilder.build( cli );
 		final ProcessBuilder pb = new ProcessBuilder( cmd );
+		if ( cli instanceof CondaCLIConfigurator )
+		{
+			// Env variables.
+			final Map< String, String > env = new HashMap<>();
+			final String condaRootPrefix = getCondaRootPrefix();
+			env.put( "MAMBA_ROOT_PREFIX", condaRootPrefix );
+			env.put( "CONDA_ROOT_PREFIX", condaRootPrefix );
+			pb.environment().putAll( env );
+		}
 		pb.redirectOutput( ProcessBuilder.Redirect.appendTo( logFile ) );
 		pb.redirectError( ProcessBuilder.Redirect.appendTo( logFile ) );
 		return pb.start();
@@ -319,6 +328,11 @@ public static List< String > preparePythonCommand( final String envName, final S
 		return cmd;
 	}
 
+	public static void clearEnvMap()
+	{
+		envMap = null;
+	}
+
 	public static Map< String, String > getEnvMap() throws IOException
 	{
 		if ( envMap == null )

src/main/java/fiji/plugin/trackmate/util/cli/CondaCLIConfigurator.java

@@ -8,26 +8,23 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
  * #L%
  */
 package fiji.plugin.trackmate.util.cli;
 
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
-import ij.IJ;
-
 public abstract class CondaCLIConfigurator extends CLIConfigurator
 {
 
@@ -127,55 +124,41 @@ protected CondaCLIConfigurator()
 		setCommandTranslator( condaEnv, s -> {
 			final List< String > cmd = new ArrayList<>();
 			final String condaPath = CLIUtils.getCondaPath();
-			// Conda and executable stuff.
-			final String envname = ( String ) s;
-			if ( IJ.isWindows() )
+			final String os = System.getProperty( "os.name" ).toLowerCase();
+			if ( os.contains( "win" ) )
 			{
-				/*
-				 * In Windows: Launch a shell, change the conda environment,
-				 * runs the command in this environment.
-				 */
+				// In Windows: Launch a cmd.exe shell.
 				cmd.addAll( Arrays.asList( "cmd.exe", "/c" ) );
-				cmd.addAll( Arrays.asList( condaPath, "activate", envname ) );
-				cmd.add( "&" );
 			}
 			else
 			{
-				/*
-				 * On Mac: we cannot change the conda environment in the process
-				 * builder (I tried very hard). So we use the environment to
-				 * retrieve what is the path of the Python executable of this
-				 * env, and runs the tool as a module. It won't work if the tool
-				 * cannot be run as a module. No escape yet.
-				 *
-				 * Unsure whether this works in Linux.
-				 */
-				try
-				{
-					final String pythonPath = CLIUtils.getEnvMap().get( envname );
-					cmd.add( pythonPath );
-					cmd.add( "-m" );
-				}
-				catch ( final IOException e )
-				{
-					System.err.println( "Could not find the conda executable or change the conda environment.\n"
-							+ "Please configure the path to your conda executable in Edit > Options > Configure TrackMate Conda path..." );
-					e.printStackTrace();
-				}
-				catch ( final Exception e )
-				{
-					System.err.println( "Error running the conda executable:\n" );
-					e.printStackTrace();
-				}
+				// On Mac or Linux.
+			}
+			// Call conda run.
+			cmd.add( condaPath );
+			cmd.add( "run" );
+			cmd.add( "-n" );
+			// The executable stuff.
+			final String envname = ( String ) s;
+			cmd.add( envname );
+			// Only add these flags for conda/mamba, NOT for micromamba
+			if ( !isMicromamba( condaPath ) )
+			{
+				cmd.add( "--no-capture-output" );
 			}
-			// Split by spaces
+			// The rest of the command, split by spaces.
 			final String executableCommand = getCommand();
 			final String[] split = executableCommand.split( " " );
 			cmd.addAll( Arrays.asList( split ) );
 			return cmd;
 		} );
 	}
 
+	private static boolean isMicromamba( final String path )
+	{
+		return path != null && path.toLowerCase().contains( "micromamba" );
+	}
+
 	@Override
 	public CondaEnvironmentCommand getCommandArg()
 	{