Handle micromamba special cases.

Author: tinevez

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

@@ -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();

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

@@ -141,8 +141,11 @@ protected CondaCLIConfigurator()
 			// The executable stuff.
 			final String envname = ( String ) s;
 			cmd.add( envname );
-			// Important: don't buffer output
-			cmd.add( "--no-capture-output" );
+			// Only add these flags for conda/mamba, NOT for micromamba
+			if ( !isMicromamba( condaPath ) )
+			{
+				cmd.add( "--no-capture-output" );
+			}
 			// The rest of the command, split by spaces.
 			final String executableCommand = getCommand();
 			final String[] split = executableCommand.split( " " );
@@ -151,6 +154,11 @@ protected CondaCLIConfigurator()
 		} );
 	}
 
+	private static boolean isMicromamba( final String path )
+	{
+		return path != null && path.toLowerCase().contains( "micromamba" );
+	}
+
 	@Override
 	public CondaEnvironmentCommand getCommandArg()
 	{