Update Cellpose3Detector to use pixi for environment configuration

* Add a toml file for env configuration

Author: stefanhahmann

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose3.java

@@ -33,6 +33,7 @@
 import javax.annotation.Nullable;
 
 import org.apposed.appose.Service;
+import org.mastodon.mamut.util.ResourceUtils;
 
 /**
  * Cellpose3 is a specialized implementation of the {@link Cellpose} class, specifically
@@ -43,21 +44,11 @@ public class Cellpose3 extends Cellpose
 {
 	public static final String ENV_NAME = "cellpose3";
 
-	public static final String ENV_FILE_CONTENT = "name: " + ENV_NAME + "\n"
-			+ "channels:\n"
-			+ "  - nvidia\n"
-			+ "  - pytorch\n"
-			+ "  - conda-forge\n"
-			+ "channel_priority: strict\n"
-			+ "dependencies:\n"
-			+ "  - python=3.10\n"
-			+ "  - pip\n"
-			+ "  - pip:\n"
-			+ "    - cellpose==3.1.1.2\n"
-			+ "    - appose==" + APPOSE_PYTHON_VERSION + "\n"
-			+ "  - pytorch\n"
-			+ "  - pytorch-cuda\n"
-			+ "  - numpy\n";
+	public static final String ENV_FILE_CONTENT =
+			ResourceUtils.readResourceAsString( "org/mastodon/mamut/detection/cellpose/cellpose3.toml", Cellpose3.class )
+					.replace( "{ENV_NAME}", ENV_NAME )
+					.replace( "{APPOSE_VERSION}", APPOSE_PYTHON_VERSION );
+
 
 	private final ModelType modelType;
 

src/main/java/org/mastodon/mamut/detection/cellpose/Cellpose3Detector.java

@@ -179,7 +179,7 @@ protected String getPythonEnvName()
 	@Override
 	protected Builder< ? > getBuilder()
 	{
-		return Appose.mamba().scheme( "environment.yml" );
+		return Appose.pixi();
 	}
 
 	@Override

src/main/resources/org/mastodon/mamut/detection/cellpose/cellpose3.toml

@@ -0,0 +1,58 @@
+[workspace]
+name = "{ENV_NAME}"
+version = "0.0.1"
+description = "Cellpose3 segmentation environment."
+authors = ["Stefan Hahmann"]
+channels = ["conda-forge", "pytorch", "nvidia"]
+platforms = ["osx-arm64", "osx-64", "linux-64", "win-64"]
+
+[dependencies]
+numpy = ">=1.20,<2.1"
+pip = "*"
+
+[pypi-dependencies]
+appose = "=={APPOSE_VERSION}"
+
+# ---------------------------------------------------------------------------
+# macOS Apple Silicon
+# ---------------------------------------------------------------------------
+[target.osx-arm64.dependencies]
+python = "3.10.*"
+
+[target.osx-arm64.pypi-dependencies]
+cellpose = "==3.1.1.2"
+torch = "==2.10.0"
+torchvision = "==0.25.0"
+
+# ---------------------------------------------------------------------------
+# macOS Intel
+# ---------------------------------------------------------------------------
+[target.osx-64.dependencies]
+python = "3.10.*"
+
+[target.osx-64.pypi-dependencies]
+cellpose = "==3.1.1.2"
+torch = "==2.1.2"
+torchvision = "==0.16.2"
+
+# ---------------------------------------------------------------------------
+# Linux
+# ---------------------------------------------------------------------------
+[target.linux-64.dependencies]
+python = "3.11.*"
+pytorch = "*"
+pytorch-cuda = "*"
+
+[target.linux-64.pypi-dependencies]
+cellpose = "==3.1.1.2"
+
+# ---------------------------------------------------------------------------
+# Windows
+# ---------------------------------------------------------------------------
+[target.win-64.dependencies]
+python = "3.11.*"
+pytorch = "*"
+pytorch-cuda = "*"
+
+[target.win-64.pypi-dependencies]
+cellpose = "==3.1.1.2"