Adapt to possibly using micromamba.

Author: tinevez

src/main/java/fiji/plugin/trackmate/cellpose/CellposeDetector.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>.
@@ -34,6 +34,7 @@
 import java.nio.file.Paths;
 import java.time.Duration;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -540,6 +541,13 @@ public String call() throws Exception
 				{
 					final ProcessBuilder pbOmni = new ProcessBuilder( cmd );
 					pbOmni.redirectErrorStream( true );
+					// Env variables.
+					final Map< String, String > env = new HashMap<>();
+					final String condaRootPrefix = CLIUtils.getCondaRootPrefix();
+					env.put( "MAMBA_ROOT_PREFIX", condaRootPrefix );
+					env.put( "CONDA_ROOT_PREFIX", condaRootPrefix );
+					pbOmni.environment().putAll( env );
+
 					process = pbOmni.start();
 
 					final BufferedReader reader = new BufferedReader( new InputStreamReader( process.getInputStream() ) );
@@ -575,6 +583,7 @@ public String call() throws Exception
 						final ProcessBuilder updatedPbOmni = new ProcessBuilder( cmd2 );
 						updatedPbOmni.redirectOutput( ProcessBuilder.Redirect.INHERIT );
 						updatedPbOmni.redirectError( ProcessBuilder.Redirect.INHERIT );
+						updatedPbOmni.environment().putAll( env );
 
 						process = updatedPbOmni.start();
 						process.waitFor();
@@ -589,6 +598,12 @@ else if ( pythonErrorOutput.contains( "pretrained model has incorrect path" ) )
 					final ProcessBuilder pb = new ProcessBuilder( cmd );
 					pb.redirectOutput( ProcessBuilder.Redirect.INHERIT );
 					pb.redirectError( ProcessBuilder.Redirect.INHERIT );
+					// Env variables.
+					final Map< String, String > env = new HashMap<>();
+					final String condaRootPrefix = CLIUtils.getCondaRootPrefix();
+					env.put( "MAMBA_ROOT_PREFIX", condaRootPrefix );
+					env.put( "CONDA_ROOT_PREFIX", condaRootPrefix );
+					pb.environment().putAll( env );
 
 					process = pb.start();
 					process.waitFor();

src/main/java/fiji/plugin/trackmate/cellpose/sam/CellposeSAMDetector.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>.
@@ -32,6 +32,7 @@
 import java.nio.file.Paths;
 import java.time.Duration;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -510,6 +511,12 @@ public String call() throws Exception
 				final ProcessBuilder pb = new ProcessBuilder( cmd );
 				pb.redirectOutput( ProcessBuilder.Redirect.INHERIT );
 				pb.redirectError( ProcessBuilder.Redirect.INHERIT );
+				// Env variables.
+				final Map< String, String > env = new HashMap<>();
+				final String condaRootPrefix = CLIUtils.getCondaRootPrefix();
+				env.put( "MAMBA_ROOT_PREFIX", condaRootPrefix );
+				env.put( "CONDA_ROOT_PREFIX", condaRootPrefix );
+				pb.environment().putAll( env );
 
 				process = pb.start();
 				process.waitFor();